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null}',tool_version:"2.1.4",type:"tool",uuid:"019fe847-4fb9-441f-9450-505f855434e7",when:null,workflow_outputs:[{label:"Quantified-Peptides",output_name:"out_file1",uuid:"41b20ef9-acef-4b1d-9a93-1df0c1447a03"}]}},tags:["name:clinicalMP"],uuid:"e21d954c-bb46-46f3-8081-0095b6b0de1f",version:1},readme:`# Clinical Metaproteomics 4: Quantitation Quantitative proteomics is crucial for many important purposes. It allows researchers to measure and compare the levels of proteins or peptides in biological samples. This provides valuable insights into biomarker discovery, comparative analysis, and differential expression studies. Quantitative proteomics also helps in understanding the functional roles of proteins, the composition of protein complexes, and the effects of drugs on protein expression in pharmacological studies. Additionally, it serves as a quality control measure by validating initial protein identifications and providing data normalization for increased accuracy. The quantitative data are essential for hypothesis testing, and systems biology, and have clinical relevance in areas such as disease diagnosis, prognosis, and therapeutic decision-making. In summary, the quantitation workflow in proteomics is essential for understanding the complexities of protein expression and regulation, and it facilitates a wide range of biological and clinical applications. @@ -3045,7 +3045,7 @@ This workflow works only with an experimental setup containing exactly 2 conditi First release. `,trsID:"#workflow/github.com/iwc-workflows/rnaseq-de/main",tests:[{doc:"Test outline for RNAseq_DE_filtering_plotting",job:{"Gene Annotaton":{class:"File",location:"https://zenodo.org/records/14056162/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf",filetype:"gtf"},"Counts from changed condition":{class:"Collection",collection_type:"list",elements:[{class:"File",identifier:"SRR5085169 Counts Table",location:"https://zenodo.org/records/14056162/files/SRR5085169.tabular"},{class:"File",identifier:"SRR5085170 Counts Table",location:"https://zenodo.org/records/14056162/files/SRR5085170.tabular"}]},"Counts from reference condition":{class:"Collection",collection_type:"list",elements:[{class:"File",identifier:"SRR5085167 Counts Table",location:"https://zenodo.org/records/14056162/files/SRR5085167.tabular"},{class:"File",identifier:"SRR5085168 Counts Table",location:"https://zenodo.org/records/14056162/files/SRR5085168.tabular"}]},"Count files have header":!0,"Adjusted p-value threshold":.1,"log2 fold change threshold":.5},outputs:{"Annotated DESeq2 results table":{has_text_matching:{expression:"YKL081W 264.71[0-9]* -0.54[0-9]* 0.15[0-9]* -3.46[0-9]* 0.00[0-9]* 0.09[0-9]* chrXI 282890 284455 + protein_coding TEF4"}},"Heatmap of Z-scores":{has_size:{value:19510,delta:1e3}},"DESeq2 Normalized Counts":{has_text_matching:{expression:"YKL081W 313.76[0-9]* 322.37[0-9]* 223.48[0-9]* 199.24[0-9]*"}},"DESeq2 Plots":{has_size:{value:1193021,delta:6e4}},"Volcano Plot of DE genes":{has_size:{value:301346,delta:15e3}},"Heatmap of log transformed normalized counts":{has_size:{value:19501,delta:1e3}}}}]}],path:"./workflows/transcriptomics/rnaseq-de"},{version:1.2,workflows:[{name:"main",subclass:"Galaxy",publish:!0,primaryDescriptorPath:"/rnaseq-pe.ga",testParameterFiles:["/rnaseq-pe-tests.yml"],authors:[{name:"Lucille Delisle",orcid:"0000-0002-1964-4960"},{name:"Pavankumar Videm",orcid:"0000-0002-5192-126X"}],definition:{a_galaxy_workflow:"true",annotation:`This workflow takes as input a list of paired-end fastqs. 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`toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4`\n\n### Test dataset\n- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631\n\n## [0.9] 2024-09-23\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`\n\n## [0.8] 2024-07-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0`\n\n## [0.7] 2024-06-25\n\n### Automatic update (triggered manually)\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0`\n\n## [0.6] 2024-02-05\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0`\n\n## [0.5] 2023-09-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4`\n\n### Manual update\n- Use STAR to compute normalized strand-specific coverage\n- Add an option to use StringTie to compute FPKM\n- Make cufflinks step optional\n\n## [0.4.1] 2023-09-14\n- add author in dockstore file\n\n## [0.4] 2023-01-16\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1`\n\n## [0.3] 2022-12-17\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1`\n\n## [0.2] 2022-11-02\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1`\n\n## [0.1] 2022-10-21\n\nFirst release.\n",trsID:"#workflow/github.com/iwc-workflows/rnaseq-pe/main",tests:[{doc:"Test outline for RNAseq_PE",job:{"GTF file of annotation":{class:"File",location:"https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf",filetype:"gtf"},"Collection paired FASTQ files":{class:"Collection",collection_type:"list:paired",elements:[{class:"Collection",type:"paired",identifier:"SRR5085167",elements:[{class:"File",identifier:"forward",location:"https://zenodo.org/records/13987631/files/SRR5085167_forward.fastqsanger.gz"},{class:"File",identifier:"reverse",location:"https://zenodo.org/records/13987631/files/SRR5085167_reverse.fastqsanger.gz"}]}]},"Forward adapter":"AGATCGGAAGAG","Reverse adapter":"GATCGTCGGACT","Generate additional QC reports":!0,"Reference genome":"sacCer3","Use 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`toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3`\n- `toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0`\n\n## [1.0] 2024-09-23\n\n### Changes in workflows\n- Add an optional subworkflow with more QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes.\n- Add featureCounts as an alternative way to generate count files\n- Use fastp instead of cutadapt which uses pair overlap and allows to have optional adapter sequences\n\n### Tool update\n- `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4`\n\n### Test dataset\n- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631\n\n## [0.9] 2024-09-23\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`\n\n## [0.8] 2024-07-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0`\n\n## [0.7] 2024-06-25\n\n### Automatic update (triggered manually)\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0`\n\n## [0.6] 2024-02-05\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0`\n\n## [0.5] 2023-09-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4`\n\n### Manual update\n- Use STAR to 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0,c=o?te(()=>Z(()=>import("./Con-SsMM.js"),__vite__mapDeps([21,22]),import.meta.url).then(f=>f.default||f)):te(()=>Z(()=>import("./Ce316I13.js"),__vite__mapDeps([23,24]),import.meta.url).then(f=>f.default||f));return(f,d)=>(et(),At(ye(c),kf(Wc({statusCode:ye(r),statusMessage:ye(s),description:ye(i),stack:ye(l)})),null,16))}},Pa={__name:"nuxt-root",setup(e){const t=()=>null,n=ue(),r=n.deferHydration();if(n.isHydrating){const l=n.hooks.hookOnce("app:error",r);Qe().beforeEach(l)}const o=!1;hn(mo,du()),n.hooks.callHookWith(l=>l.map(a=>a()),"vue:setup");const s=yo();Cc((l,a,u)=>{if(n.hooks.callHook("vue:error",l,a,u).catch(c=>console.error("[nuxt] Error in `vue:error` hook",c)),ag(l)&&(l.fatal||l.unhandled))return n.runWithContext(()=>on(l)),!1});const i=!1;return(l,a)=>(et(),At(hc,{onResolve:ye(r)},{default:jn(()=>[ye(s)?(et(),At(ye(aw),{key:0,error:ye(s)},null,8,["error"])):ye(i)?(et(),At(ye(t),{key:1,context:ye(i)},null,8,["context"])):ye(o)?(et(),At(pd(ye(o)),{key:2})):(et(),At(ye(lw),{key:3}))]),_:1},8,["onResolve"]))}};let Ra;{let e;Ra=async function(){var i,l;if(e)return e;const r=!!((i=window.__NUXT__)!=null&&i.serverRendered||((l=document.getElementById("__NUXT_DATA__"))==null?void 0:l.dataset.ssr)==="true")?Dh(Pa):Fh(Pa),o=Wp({vueApp:r});async function s(a){await o.callHook("app:error",a),o.payload.error=o.payload.error||bo(a)}r.config.errorHandler=s;try{await Kp(o,cv)}catch(a){s(a)}try{await o.hooks.callHook("app:created",r),await o.hooks.callHook("app:beforeMount",r),r.mount(om),await o.hooks.callHook("app:mounted",r),await En()}catch(a){s(a)}return r.config.errorHandler===s&&(r.config.errorHandler=void 0),r},e=Ra().catch(t=>{throw console.error("Error while mounting app:",t),t})}export{uw as $,vw as A,gw as B,Me as C,ue as D,lr as E,je as F,Da as G,Af as H,ye as I,nt as J,fo as K,ua as L,Pw as M,Le as N,hn as O,Ed as P,pt as Q,Ec as R,En as S,hd as T,oo as U,Ew as V,at as W,Id as X,bw as Y,jt as Z,gf as _,Ot as a,kw as a0,kf as a1,Wc as a2,pf as a3,mo as a4,du as a5,kr as a6,Qe as a7,ww as a8,wy as a9,hi as aa,hc as ab,og as ac,Cw as ad,fr as ae,yw as af,Jr as ag,Z as ah,td as ai,By as aj,xw as ak,Jt as al,bo as am,hp as an,Cl as ao,go as ap,po as aq,se as ar,mn as as,Ie as at,Kr as au,fw as av,fe as b,Uc as c,Wr as d,Wy as e,hw as f,tm as g,ct as h,rc as i,_e as j,Sw as k,Q0 as l,Tw as m,rh as n,et as o,dw as p,At as q,mw as r,so as s,cw as t,Xg as u,_w as v,jn as w,pd as x,He as y,pw as z}; diff --git a/_nuxt/DNQZCvJm.js b/_nuxt/CcLh0WX_.js similarity index 85% rename from _nuxt/DNQZCvJm.js rename to _nuxt/CcLh0WX_.js index fd88e9182..b98acc88a 100644 --- a/_nuxt/DNQZCvJm.js +++ b/_nuxt/CcLh0WX_.js @@ -1 +1 @@ -import{h as i,ae as c,j as p,o as s,c as n,I as u,r as t}from"./BBXq2Q9n.js";const f=["id"],l=["href"],k=i({__name:"ProseH2",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 0:o.anchorLinks)==null?void 0:e.h2)});return(e,m)=>(s(),n("h2",{id:e.id},[e.id&&u(d)?(s(),n("a",{key:0,href:`#${e.id}`},[t(e.$slots,"default")],8,l)):t(e.$slots,"default",{key:1})],8,f))}});export{k as default}; +import{h as i,ae as c,j as p,o as s,c as n,I as u,r as t}from"./C_W1Z1b6.js";const f=["id"],l=["href"],k=i({__name:"ProseH2",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 0:o.anchorLinks)==null?void 0:e.h2)});return(e,m)=>(s(),n("h2",{id:e.id},[e.id&&u(d)?(s(),n("a",{key:0,href:`#${e.id}`},[t(e.$slots,"default")],8,l)):t(e.$slots,"default",{key:1})],8,f))}});export{k as default}; diff --git a/_nuxt/D0xhEAmm.js b/_nuxt/Ce316I13.js similarity index 97% rename from _nuxt/D0xhEAmm.js rename to _nuxt/Ce316I13.js index 058417441..bebd440a7 100644 --- a/_nuxt/D0xhEAmm.js +++ b/_nuxt/Ce316I13.js @@ -1 +1 @@ -import{_ as a,u as o,o as s,c as i,a as e,t as r,p as u,f as l}from"./BBXq2Q9n.js";const c=t=>(u("data-v-6fdef64d"),t=t(),l(),t),d={class:"font-sans antialiased bg-white dark:bg-black text-black dark:text-white grid min-h-screen place-content-center overflow-hidden"},p=c(()=>e("div",{class:"fixed -bottom-1/2 left-0 right-0 h-1/2 spotlight"},null,-1)),h={class:"max-w-520px text-center"},f=["textContent"],g=["textContent"],b={__name:"error-500",props:{appName:{type:String,default:"Nuxt"},version:{type:String,default:""},statusCode:{type:Number,default:500},statusMessage:{type:String,default:"Server error"},description:{type:String,default:"This page is temporarily unavailable."}},setup(t){const n=t;return o({title:`${n.statusCode} - ${n.statusMessage} | ${n.appName}`,script:[],style:[{children:'*,:before,:after{box-sizing:border-box;border-width:0;border-style:solid;border-color:var(--un-default-border-color, 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Q=C({name:"ContentQuery",props:{path:{type:String,required:!1,default:void 0},only:{type:Array,required:!1,default:void 0},without:{type:Array,required:!1,default:void 0},where:{type:Object,required:!1,default:void 0},sort:{type:Object,required:!1,default:void 0},limit:{type:Number,required:!1,default:void 0},skip:{type:Number,required:!1,default:void 0},locale:{type:String,required:!1,default:void 0},find:{type:String,required:!1,default:void 0}},async setup(a){const{path:t,only:r,without:o,where:u,sort:f,limit:l,skip:d,locale:s,find:h}=S(a),y=b(()=>{var e;return(e=t.value)==null?void 0:e.includes("/_")}),p=!N().public.content.experimental.advanceQuery;_(()=>a,()=>n(),{deep:!0});const i=e=>p?e!=null&&e.surround?e.surround:e!=null&&e._id||Array.isArray(e)?e:e==null?void 0:e.result:e.result,{data:v,refresh:n}=await g(`content-query-${O(a)}`,()=>{let e;return t.value?e=m(t.value):e=m(),r.value&&(e=e.only(r.value)),o.value&&(e=e.without(o.value)),u.value&&(e=e.where(u.value)),f.value&&(e=e.sort(f.value)),l.value&&(e=e.limit(l.value)),d.value&&(e=e.skip(d.value)),s.value&&(e=e.where({_locale:s.value})),h.value==="one"?e.findOne().then(i):h.value==="surround"?t.value?p?e.findSurround(t.value):e.withSurround(t.value).findOne().then(i):(console.warn("[Content] Surround queries requires `path` prop to be set."),console.warn("[Content] Query without `path` will return regular `find()` results."),e.find().then(i)):e.find().then(i)});return{isPartial:y,data:v,refresh:n}},render(a){var c;const t=k(),{data:r,refresh:o,isPartial:u,path:f,only:l,without:d,where:s,sort:h,limit:y,skip:p,locale:i,find:v}=a,n={path:f,only:l,without:d,where:s,sort:h,limit:y,skip:p,locale:i,find:v};if(n.find==="one"){if(!r&&(t!=null&&t["not-found"]))return t["not-found"]({props:n,...this.$attrs});if(t!=null&&t.empty&&(r==null?void 0:r._type)==="markdown"&&!((c=r==null?void 0:r.body)!=null&&c.children.length))return t.empty({props:n,...this.$attrs})}else if((!r||!r.length)&&t!=null&&t["not-found"])return t["not-found"]({props:n,...this.$attrs});return t!=null&&t.default?t.default({data:r,refresh:o,isPartial:u,props:n,...this.$attrs}):((w,q)=>A("pre",null,JSON.stringify({message:"You should use slots with !",slot:w,data:q},null,2)))("default",{data:r,props:n,isPartial:u})}}),J=Q;export{J as default}; +import{a as g,q as m}from"./kmgnN-AX.js";import{h as C,ai as S,j as b,ae as N,J as _,af as k,N as A}from"./C_W1Z1b6.js";import{h as O}from"./IShi1APO.js";import"./BptBDlga.js";const Q=C({name:"ContentQuery",props:{path:{type:String,required:!1,default:void 0},only:{type:Array,required:!1,default:void 0},without:{type:Array,required:!1,default:void 0},where:{type:Object,required:!1,default:void 0},sort:{type:Object,required:!1,default:void 0},limit:{type:Number,required:!1,default:void 0},skip:{type:Number,required:!1,default:void 0},locale:{type:String,required:!1,default:void 0},find:{type:String,required:!1,default:void 0}},async setup(a){const{path:t,only:r,without:o,where:u,sort:f,limit:l,skip:d,locale:s,find:h}=S(a),y=b(()=>{var e;return(e=t.value)==null?void 0:e.includes("/_")}),p=!N().public.content.experimental.advanceQuery;_(()=>a,()=>n(),{deep:!0});const i=e=>p?e!=null&&e.surround?e.surround:e!=null&&e._id||Array.isArray(e)?e:e==null?void 0:e.result:e.result,{data:v,refresh:n}=await g(`content-query-${O(a)}`,()=>{let e;return t.value?e=m(t.value):e=m(),r.value&&(e=e.only(r.value)),o.value&&(e=e.without(o.value)),u.value&&(e=e.where(u.value)),f.value&&(e=e.sort(f.value)),l.value&&(e=e.limit(l.value)),d.value&&(e=e.skip(d.value)),s.value&&(e=e.where({_locale:s.value})),h.value==="one"?e.findOne().then(i):h.value==="surround"?t.value?p?e.findSurround(t.value):e.withSurround(t.value).findOne().then(i):(console.warn("[Content] Surround queries requires `path` prop to be set."),console.warn("[Content] Query 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n.storage.setItem("integrity",r.integrity)}return await t.callHook("content:storage",n.storage),n}async function Ke(t){const r=await Ie();if(!U().getPreviewToken()&&Object.keys(t||{}).length===0)return r.storage.getItem("navigation");const n=await r.query(t).where({_partial:!1,navigation:{$ne:!1}}).find(),l=(await r.query().where({_path:/\/_dir$/i,_partial:!0}).find()).reduce((c,o)=>{var g;((g=o.title)==null?void 0:g.toLowerCase())==="dir"&&(o.title=void 0);const h=o._path.split("/").slice(0,-1).join("/")||"/";return c[h]={...o,...o.body},c},{});return he(n,l)}export{we as contentStorage,ve as createDB,Ke as generateNavigation,Ie as useContentDatabase}; diff --git a/_nuxt/h78BtKnP.js b/_nuxt/D1KLjdfo.js similarity index 85% rename from _nuxt/h78BtKnP.js rename to _nuxt/D1KLjdfo.js index b881c35e1..4652ed664 100644 --- a/_nuxt/h78BtKnP.js +++ b/_nuxt/D1KLjdfo.js @@ -1 +1 @@ -import{h as i,ae as c,j as p,o as s,c as n,I as u,r as t}from"./BBXq2Q9n.js";const f=["id"],l=["href"],k=i({__name:"ProseH4",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 0:o.anchorLinks)==null?void 0:e.h4)});return(e,m)=>(s(),n("h4",{id:e.id},[e.id&&u(d)?(s(),n("a",{key:0,href:`#${e.id}`},[t(e.$slots,"default")],8,l)):t(e.$slots,"default",{key:1})],8,f))}});export{k as default}; +import{h as i,ae as c,j as p,o as s,c as n,I as u,r as t}from"./C_W1Z1b6.js";const f=["id"],l=["href"],k=i({__name:"ProseH4",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 0:o.anchorLinks)==null?void 0:e.h4)});return(e,m)=>(s(),n("h4",{id:e.id},[e.id&&u(d)?(s(),n("a",{key:0,href:`#${e.id}`},[t(e.$slots,"default")],8,l)):t(e.$slots,"default",{key:1})],8,f))}});export{k as default}; diff --git a/_nuxt/DKHZHoS3.js b/_nuxt/DKHZHoS3.js new file mode 100644 index 000000000..7601df7bd --- /dev/null +++ b/_nuxt/DKHZHoS3.js @@ -0,0 +1 @@ +import{_ as m}from"./CXrToBy2.js";import"./C_W1Z1b6.js";export{m as default}; diff --git a/_nuxt/BAdipwh_.js b/_nuxt/DMtvn-XC.js similarity index 81% rename from _nuxt/BAdipwh_.js rename to _nuxt/DMtvn-XC.js index 9b6aa2dc6..2cbbd4318 100644 --- a/_nuxt/BAdipwh_.js +++ b/_nuxt/DMtvn-XC.js @@ -1 +1 @@ -import{h as a,o as n,q as o,w as s,r as f,e as u}from"./BBXq2Q9n.js";const _=a({__name:"ProseA",props:{href:{type:String,default:""},target:{type:String,default:void 0,required:!1}},setup(e){return(t,c)=>{const r=u;return n(),o(r,{href:e.href,target:e.target},{default:s(()=>[f(t.$slots,"default")]),_:3},8,["href","target"])}}});export{_ as default}; +import{h as a,o as n,q as o,w as s,r as f,e as u}from"./C_W1Z1b6.js";const _=a({__name:"ProseA",props:{href:{type:String,default:""},target:{type:String,default:void 0,required:!1}},setup(e){return(t,c)=>{const r=u;return n(),o(r,{href:e.href,target:e.target},{default:s(()=>[f(t.$slots,"default")]),_:3},8,["href","target"])}}});export{_ as default}; diff --git a/_nuxt/uXqnihjt.js b/_nuxt/D_ZQlA37.js similarity index 82% rename from _nuxt/uXqnihjt.js rename to _nuxt/D_ZQlA37.js index 08dbf1317..badbbee3f 100644 --- a/_nuxt/uXqnihjt.js +++ b/_nuxt/D_ZQlA37.js @@ -1 +1 @@ -import{_ as l}from"./mYNxw29K.js";import{h as n,o as s,q as i,w as r,a as o,s as g,U as u,r as f}from"./BBXq2Q9n.js";const h=n({__name:"ProsePre",props:{code:{type:String,default:""},language:{type:String,default:null},filename:{type:String,default:null},highlights:{type:Array,default:()=>[]},meta:{type:String,default:null},class:{type:String,default:null},style:{type:[String,Object],default:null}},setup(e){return(a,m)=>{const t=l;return s(),i(t,{code:e.code,language:e.language,filename:e.filename,highlights:e.highlights,meta:e.meta},{default:r(()=>[o("pre",{class:g(a.$props.class),style:u(e.style)},[f(a.$slots,"default")],6)]),_:3},8,["code","language","filename","highlights","meta"])}}});export{h as default}; +import{_ as l}from"./CXrToBy2.js";import{h as n,o as s,q as i,w as r,a as o,s as g,U as u,r as f}from"./C_W1Z1b6.js";const h=n({__name:"ProsePre",props:{code:{type:String,default:""},language:{type:String,default:null},filename:{type:String,default:null},highlights:{type:Array,default:()=>[]},meta:{type:String,default:null},class:{type:String,default:null},style:{type:[String,Object],default:null}},setup(e){return(a,m)=>{const t=l;return s(),i(t,{code:e.code,language:e.language,filename:e.filename,highlights:e.highlights,meta:e.meta},{default:r(()=>[o("pre",{class:g(a.$props.class),style:u(e.style)},[f(a.$slots,"default")],6)]),_:3},8,["code","language","filename","highlights","meta"])}}});export{h as default}; diff --git a/_nuxt/BWJjGEbI.js b/_nuxt/DkT_dU4V.js similarity index 58% rename from _nuxt/BWJjGEbI.js rename to _nuxt/DkT_dU4V.js index 1e398df65..d4ab64254 100644 --- a/_nuxt/BWJjGEbI.js +++ b/_nuxt/DkT_dU4V.js @@ -1 +1 @@ -import r from"./RKrZtgGl.js";import{h as o,af as f,j as u,E as c}from"./BBXq2Q9n.js";const i=o({name:"Markdown",extends:r,setup(t){const{parent:e}=c(),{between:n,default:a}=f(),s=u(()=>typeof t.unwrap=="string"?t.unwrap.split(" "):["*"]);return{fallbackSlot:a,tags:s,between:n,parent:e}}});export{i as default}; +import r from"./CUiib2xX.js";import{h as o,af as f,j as u,E as c}from"./C_W1Z1b6.js";const i=o({name:"Markdown",extends:r,setup(t){const{parent:e}=c(),{between:n,default:a}=f(),s=u(()=>typeof t.unwrap=="string"?t.unwrap.split(" "):["*"]);return{fallbackSlot:a,tags:s,between:n,parent:e}}});export{i as default}; diff --git a/_nuxt/UJYGigWK.js b/_nuxt/DlA5w2bT.js similarity index 85% rename from _nuxt/UJYGigWK.js rename to _nuxt/DlA5w2bT.js index 170c79084..f7cd351f0 100644 --- a/_nuxt/UJYGigWK.js +++ b/_nuxt/DlA5w2bT.js @@ -1 +1 @@ -import{h as i,ae as c,j as p,o as s,c as n,I as u,r as t}from"./BBXq2Q9n.js";const f=["id"],l=["href"],k=i({__name:"ProseH3",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 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__vite__fileDeps=["./vBq6Pg46.js","./BBXq2Q9n.js","./C6eOiQmV.js","./IShi1APO.js","./CeDAxlFd.js","./C-v3KzvZ.js"],__vite__mapDeps=i=>i.map(i=>__vite__fileDeps[i]); -import{q as f,w as m,e as v,s as g,j as d,u as l,a as h}from"./C6eOiQmV.js";import{ae as _,ah as y,h as C,ai as w,j as N,aj as P,af as $,N as r,e as j}from"./BBXq2Q9n.js";import{h as p}from"./IShi1APO.js";import{u as T}from"./CeDAxlFd.js";const D=async e=>{const{content:t}=_().public;typeof(e==null?void 0:e.params)!="function"&&(e=f(e));const a=e.params(),s=t.experimental.stripQueryParameters?m(`/navigation/${`${p(a)}.${t.integrity}`}/${v(a)}.json`):m(`/navigation/${p(a)}.${t.integrity}.json`);if(g())return(await y(()=>import("./vBq6Pg46.js"),__vite__mapDeps([0,1,2,3,4,5]),import.meta.url).then(o=>o.generateNavigation))(a);const n=await $fetch(s,{method:"GET",responseType:"json",params:t.experimental.stripQueryParameters?void 0:{_params:d(a),previewToken:T().getPreviewToken()}});if(typeof n=="string"&&n.startsWith(""))throw new Error("Not found");return n},E=C({name:"ContentNavigation",props:{query:{type:Object,required:!1,default:void 0}},async setup(e){const{query:t}=w(e),a=N(()=>{var n;return typeof((n=t.value)==null?void 0:n.params)=="function"?t.value.params():t.value});if(!a.value&&P("dd-navigation").value){const{navigation:n}=l();return{navigation:n}}const{data:s}=await h(`content-navigation-${p(a.value)}`,()=>D(a.value));return{navigation:s}},render(e){const t=$(),{navigation:a}=e,s=o=>r(j,{to:o._path},()=>o.title),n=(o,u)=>r("ul",u?{"data-level":u}:null,o.map(i=>i.children?r("li",null,[s(i),n(i.children,u+1)]):r("li",null,s(i)))),c=o=>n(o,0);return t!=null&&t.default?t.default({navigation:a,...this.$attrs}):c(a)}}),Q=E;export{Q as default}; +const __vite__fileDeps=["./D0vEgMCk.js","./C_W1Z1b6.js","./kmgnN-AX.js","./IShi1APO.js","./BptBDlga.js","./C-v3KzvZ.js"],__vite__mapDeps=i=>i.map(i=>__vite__fileDeps[i]); +import{q as f,w as m,e as v,s as g,j as d,u as l,a as h}from"./kmgnN-AX.js";import{ae as _,ah as y,h as C,ai as w,j as N,aj as P,af as $,N as r,e as j}from"./C_W1Z1b6.js";import{h as p}from"./IShi1APO.js";import{u as T}from"./BptBDlga.js";const D=async e=>{const{content:t}=_().public;typeof(e==null?void 0:e.params)!="function"&&(e=f(e));const a=e.params(),s=t.experimental.stripQueryParameters?m(`/navigation/${`${p(a)}.${t.integrity}`}/${v(a)}.json`):m(`/navigation/${p(a)}.${t.integrity}.json`);if(g())return(await y(()=>import("./D0vEgMCk.js"),__vite__mapDeps([0,1,2,3,4,5]),import.meta.url).then(o=>o.generateNavigation))(a);const n=await $fetch(s,{method:"GET",responseType:"json",params:t.experimental.stripQueryParameters?void 0:{_params:d(a),previewToken:T().getPreviewToken()}});if(typeof n=="string"&&n.startsWith(""))throw new Error("Not found");return n},E=C({name:"ContentNavigation",props:{query:{type:Object,required:!1,default:void 0}},async setup(e){const{query:t}=w(e),a=N(()=>{var n;return typeof((n=t.value)==null?void 0:n.params)=="function"?t.value.params():t.value});if(!a.value&&P("dd-navigation").value){const{navigation:n}=l();return{navigation:n}}const{data:s}=await h(`content-navigation-${p(a.value)}`,()=>D(a.value));return{navigation:s}},render(e){const t=$(),{navigation:a}=e,s=o=>r(j,{to:o._path},()=>o.title),n=(o,u)=>r("ul",u?{"data-level":u}:null,o.map(i=>i.children?r("li",null,[s(i),n(i.children,u+1)]):r("li",null,s(i)))),c=o=>n(o,0);return t!=null&&t.default?t.default({navigation:a,...this.$attrs}):c(a)}}),Q=E;export{Q as default}; diff --git a/_nuxt/BRDYwmvR.js b/_nuxt/DqP9tfh0.js similarity index 64% rename from _nuxt/BRDYwmvR.js rename to _nuxt/DqP9tfh0.js index 8264242ad..5df46666e 100644 --- a/_nuxt/BRDYwmvR.js +++ b/_nuxt/DqP9tfh0.js @@ -1 +1 @@ -import{_ as o,o as r,c as s,r as t}from"./BBXq2Q9n.js";const c={};function n(e,l){return r(),s("ol",null,[t(e.$slots,"default")])}const _=o(c,[["render",n]]);export{_ as default}; +import{_ as o,o as r,c as s,r as t}from"./C_W1Z1b6.js";const c={};function n(e,l){return r(),s("ol",null,[t(e.$slots,"default")])}const _=o(c,[["render",n]]);export{_ as default}; diff --git a/_nuxt/BIpoqWcO.js b/_nuxt/Dv1ucq_T.js similarity index 63% rename from _nuxt/BIpoqWcO.js rename to _nuxt/Dv1ucq_T.js index 514cbb33a..27cabbcd9 100644 --- a/_nuxt/BIpoqWcO.js +++ b/_nuxt/Dv1ucq_T.js @@ -1 +1 @@ -import{_ as r,o,c as s,r as t}from"./BBXq2Q9n.js";const c={};function n(e,a){return o(),s("p",null,[t(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; +import{_ as r,o,c as s,r as t}from"./C_W1Z1b6.js";const c={};function n(e,a){return o(),s("p",null,[t(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; diff --git a/_nuxt/DWRjzgqe.js b/_nuxt/LH2wtjbZ.js similarity index 64% rename from _nuxt/DWRjzgqe.js rename to _nuxt/LH2wtjbZ.js index 23d78800e..1a5d7497d 100644 --- a/_nuxt/DWRjzgqe.js +++ b/_nuxt/LH2wtjbZ.js @@ -1 +1 @@ -import{_ as o,o as r,c as n,r as 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t,r as s}from"./C_W1Z1b6.js";const c={};function n(e,a){return o(),t("td",null,[s(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; diff --git a/_payload.json b/_payload.json index 1a591f5e9..c6505856e 100644 --- a/_payload.json +++ b/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750397812] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917299724] \ No newline at end of file diff --git a/api/_content/cache.1731750378213.json b/api/_content/cache.1731750378213.json deleted file mode 100644 index 9d50fcdd3..000000000 --- a/api/_content/cache.1731750378213.json +++ /dev/null @@ -1 +0,0 @@ -{"generatedAt":1731750397789,"generateTime":30,"contents":[],"navigation":[]} \ No newline at end of file diff --git a/api/_content/cache.1731917280066.json b/api/_content/cache.1731917280066.json new file mode 100644 index 000000000..802cf6aec --- /dev/null +++ b/api/_content/cache.1731917280066.json @@ -0,0 +1 @@ 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IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
  • Clinical Metaproteomics Quantitation
  • MetaProSIP OpenMS 2.8
  • Segmentation and counting of cell nuclei in fluorescence microscopy images
  • bacterial_genome_annotation
  • amr_gene_detection
  • Gene-based Pathogen Identification
  • Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
  • Allele-based Pathogen Identification
  • Nanopore Preprocessing
  • Taxonomy Profiling and Visualization with Krona
  • Parallel Accession Download
  • sra_manifest_to_concatenated_fastqs_parallel
  • Differential gene expression for single-cell data using pseudo-bulk counts with edgeR
  • scRNA-seq_preprocessing_10X_cellPlex
  • scRNA-seq_preprocessing_10X_v3_Bundle
  • Velocyto-on10X-from-bundled
  • Velocyto-on10X-filtered-barcodes
  • baredSC_1d_logNorm
  • baredSC_2d_logNorm
  • COVID-19: variation analysis of ARTIC ONT data
  • SARS-CoV-2 Illumina Amplicon pipeline - iVar based
  • COVID-19: variation analysis on WGS SE data
  • COVID-19: variation analysis reporting
  • COVID-19: variation analysis on ARTIC PE data
  • COVID-19: consensus construction
  • COVID-19: variation analysis on WGS PE data
  • dcTMD calculations with GROMACS
  • Fragment-based virtual screening using rDock for docking and SuCOS for pose scoring
  • MMGBSA calculations with GROMACS
  • Create GRO and TOP complex files
  • Quality and Contamination Control For Genome Assembly
  • Assembly polishing with long reads
  • Bacterial Genome Assembly using Shovill
  • Genome assembly with Flye
  • Average Bigwig between replicates
  • Get Confident Peaks From ChIP_SR replicates
  • Get Confident Peaks From ChIP_PE replicates
  • Get Confident Peaks From ATAC or CUTandRUN replicates
  • ChIPseq_SR
  • ATACseq
  • CUTandRUN
  • ChIPseq_PE
  • Hi-C_fastqToCool_hicup_cooler
  • cHi-C_fastqToCool_hicup_cooler
  • Hi-C_juicermediumtabixToCool_cooler
  • Hi-C_fastqToPairs_hicup
  • RNAseq_SR
  • Goseq GO-KEGG Enrichment Analysis
  • BREW3R
  • RNAseq_DE_filtering_plotting
  • RNA-seq for Paired-end fastqs
  • Pox Virus Illumina Amplicon Workflow from half-genomes
  • kmer-profiling-hifi-VGP1
  • Assembly-decontamination-VGP9
  • Purge-duplicate-contigs-VGP6
  • Purging-duplicates-one-haplotype-VGP6b
  • Scaffolding-BioNano-VGP7
  • kmer-profiling-hifi-trio-VGP2
  • Generate Nx and Size plots for multiple assemblies
  • Assembly-Hifi-HiC-phasing-VGP4
  • Assembly-Hifi-Trio-phasing-VGP5
  • Scaffolding with Hi-C data VGP8
  • Mitogenome-Assembly-VGP0
  • Assembly-Hifi-only-VGP3
  • Paired end variant calling in haploid system
  • Generic variation analysis on WGS PE data
  • Generic variation analysis reporting
  • dada2 amplicon analysis pipeline - for paired end data
  • QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)
  • QIIME2 IIb: Denoising (sequence quality control) and feature table creation (paired-end)
  • QIIME2 Ia: multiplexed data (single-end)
  • QIIME2 Ib: multiplexed data (paired-end)
  • QIIME2 Ic: Demultiplexed data (single-end)
  • QIIME2 Id: Demultiplexed data (paired-end)
  • QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis
  • QIIME2 VI: Diversity metrics and estimations
  • Mass spectrometry: GCMS with metaMS
  • Mass spectrometry: LC-MS preprocessing with XCMS
  • Repeat masking with RepeatModeler and RepeatMasker

Clinical Metaproteomics Quantitation

Clinical Metaproteomics 4: Quantitation

name:clinicalMP
Details

MetaProSIP OpenMS 2.8

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Details

Segmentation and counting of cell nuclei in fluorescence microscopy images

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html

Details

bacterial_genome_annotation

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

GenomicsfastaABRomicsbacterial-genomicsAnnotationgenome-annotation
Details

amr_gene_detection

Antimicrobial resistance gene detection from assembled bacterial genomes

fastaGenomicsABRomicsantibiotic-resistanceantimicrobial-resistance-genesantimicrobial resistancebacterial-genomicsAMRAMR-detection
Details

Gene-based Pathogen Identification

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

name:Collectionname:PathoGFAIRname:IWCname:microGalaxy
Details

Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation

Pathogens of all samples report generation and visualization

name:Collectionname:microGalaxyname:PathoGFAIRname:IWC
Details

Allele-based Pathogen Identification

Microbiome - Variant calling and Consensus Building

name:Collectionname:microGalaxyname:PathoGFAIRname:IWC
Details

Nanopore Preprocessing

Microbiome - QC and Contamination Filtering

name:Collectionname:microGalaxyname:PathoGFAIRname:Nanoporename:IWC
Details

Taxonomy Profiling and Visualization with Krona

Microbiome - Taxonomy Profiling

name:Collectionname:microGalaxyname:PathoGFAIRname:IWC
Details

Parallel Accession Download

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

Details

sra_manifest_to_concatenated_fastqs_parallel

This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.

Details

Differential gene expression for single-cell data using pseudo-bulk counts with edgeR

This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.

Details

scRNA-seq_preprocessing_10X_cellPlex

This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

#single-cell
Details

scRNA-seq_preprocessing_10X_v3_Bundle

This workflow processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

#single-cell
Details

Velocyto-on10X-from-bundled

Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.

name:single-cell
Details

Velocyto-on10X-filtered-barcodes

Run velocyto to get loom with counts of spliced and unspliced

name:single-cell
Details

baredSC_1d_logNorm

Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.

Details

baredSC_2d_logNorm

Run baredSC in 2 dimensions in logNorm for 1 to N gaussians and combine models.

Details

COVID-19: variation analysis of ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the [ARTIC pipeline](https://artic.readthedocs.io/en/latest/). It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much higher error rate than Illumina-sequenced reads and are therefor plagued more by false-positive variant calls, this workflow does make no attempt to handle amplicons affected by potential primer-binding site mutations.

COVID-19ARTICONTcovid19.galaxyproject.org
Details

SARS-CoV-2 Illumina Amplicon pipeline - iVar based

Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade

COVID-19ARTICiwc
Details

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq

COVID-19covid19.galaxyproject.org
Details

COVID-19: variation analysis reporting

This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.

COVID-19covid19.galaxyproject.org
Details

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and tries to exclude reads derived from such tainted amplicons when calculating allele-frequencies of other variants.

COVID-19ARTICcovid19.galaxyproject.org
Details

COVID-19: consensus construction

Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.

COVID-19covid19.galaxyproject.org
Details

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq

COVID-19covid19.galaxyproject.orgiwcemergen_validated
Details

dcTMD calculations with GROMACS

Perform dcTMD free energy simulations and calculations

Details

Fragment-based virtual screening using rDock for docking and SuCOS for pose scoring

Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring

Details

MMGBSA calculations with GROMACS

MMGBSA simulation and calculation

Details

Create GRO and TOP complex files

Details

Quality and Contamination Control For Genome Assembly

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

Genomicsfastqbacterial-genomicstaxonomy-assignmentpaired-endqualityABRomicstrimming
Details

Assembly polishing with long reads

Racon polish with long reads, x4

Details

Bacterial Genome Assembly using Shovill

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

fastqGenomicsbacterial-genomicspaired-endassemblyqualityABRomics
Details

Genome assembly with Flye

Assemble long reads with Flye, then view assembly statistics and assembly graph

Details

Average Bigwig between replicates

We assume the identifiers of the input list are like: sample_name_replicateID. @@ -63,5 +63,5 @@ https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gcms/tutorial.html

metabolomicsMSworkflow4metabolomicsGC-MSGTNmetaMS
Details

Mass spectrometry: LC-MS preprocessing with XCMS

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012). -https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

metabolomicsMSLC-MSworkflow4metabolomicsxcmsGTN
Details

Repeat masking with RepeatModeler and RepeatMasker

Details
- \ No newline at end of file +https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

metabolomicsMSLC-MSworkflow4metabolomicsxcmsGTN
Details

Repeat masking with RepeatModeler and RepeatMasker

Details
+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/_payload.json index 8cbab7c4e..88f6c9133 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398578] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300678] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/index.html index ca07c2417..9fab065bb 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-HiC-phasing-VGP4%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/_payload.json index f4a26b7a6..8f43e0e6b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398580] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300693] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/index.html index 59c92ac70..32078762d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-Trio-phasing-VGP5%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/_payload.json index 36eb657cd..2dc607695 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398602] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300708] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/index.html index 708dae7e6..1e0161d05 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-Hifi-only-VGP3%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/_payload.json index d2a79d42b..aa7c0ffaa 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398557] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300638] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/index.html index 786ba83a5..41b96ef1c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FAssembly-decontamination-VGP9%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/_payload.json index b31e43fbf..a4c36762f 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398591] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300698] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/index.html index 9043ec0e8..78edbe933 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FMitogenome-assembly-VGP0%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/_payload.json index feee574b8..63193981e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398576] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300666] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/index.html index ff22bae5a..1468ffb36 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPlot-Nx-Size%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/_payload.json index 2824fc2be..04f6dbf0e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398559] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300648] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/index.html index 3d0aa26fd..6508e8821 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicate-contigs-VGP6%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/_payload.json index 1f3ee83e8..b1f02811c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398561] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300652] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/index.html index 54bfb368a..419fb0eba 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FPurge-duplicates-one-haplotype-VGP6b%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/_payload.json index 4ae37c040..5dfd895ec 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398563] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300655] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/index.html index ccf1df026..f8cc6b198 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-Bionano-VGP7%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/_payload.json index 39670408e..de6efd684 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398588] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300696] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/index.html index 12e1b87a6..147310a73 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2FScaffolding-HiC-VGP8%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/_payload.json index 5934c7158..25c39b007 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398253] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300348] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/index.html index 2abeb48a2..a2ad62023 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fallele-based-pathogen-identification%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/_payload.json index 86cba060c..0cd97e20b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398248] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300344] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/index.html index f62ebbe38..a61f9c19c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Famr_gene_detection%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/_payload.json index 84935b9ca..67504ed1a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398447] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300543] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/index.html index 352310ec4..5484e4195 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fassembly-with-flye%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/_payload.json index 58d1fe9a7..ac4db622c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398475] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300557] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/index.html index 935a52f6a..26f5cb8cc 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fatacseq%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/_payload.json index 06758292e..9ac06f09e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398449] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300545] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/index.html index 75adfb451..132082a2b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Faverage-bigwig-between-replicates%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/_payload.json index 7cb9cc225..b94dbaee1 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398443] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300540] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/index.html index 7a7153c6f..8ec77661f 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial-genome-assembly%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/_payload.json index 49a3dd667..9ffde88b4 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398247] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300341] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/index.html index e97a7264a..d412e4411 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbacterial_genome_annotation%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/_payload.json index 5d2f9cba3..5a6e2c56a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398356] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300453] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/index.html index b81a93371..f3ee94453 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-1d-logNorm/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/_payload.json index f13d2980d..bb3b233b7 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398358] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300456] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/index.html index 93ff56b6c..23e651b47 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbaredsc%2FbaredSC-2d-logNorm/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/_payload.json index 16e6f75cc..de2e4b25a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398528] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300627] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/index.html index 0761fc2f2..3596e3e4c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fbrew3r%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/_payload.json index 57e998be1..2b4f2fa3e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398480] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300571] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/index.html index e8815abc7..96de736e5 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-pe%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/_payload.json index 447b6d340..c95a6310a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398473] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300554] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/index.html index dc60c067d..8321eda97 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fchipseq-sr%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/_payload.json index c21685bdb..0cfe1ccbb 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398242] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300335] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/index.html index 0db91fae3..a0af3e041 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fclinicalmp-quantitation%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/_payload.json index 2e859e760..a913219bd 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398460] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300552] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/index.html index 0c7c2b31c..a6f452fb6 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-atac-cutandrun/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/_payload.json index 0f4f900e1..77d4f0efb 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398457] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300550] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/index.html index 4c96a8b5b..8a8477d29 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-pe/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/_payload.json index adc40b4ac..3a082fc0e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398455] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300548] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/index.html index 4f9a43b8f..6d5c150be 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fconsensus-peaks%2Fconsensus-peaks-chip-sr/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/_payload.json index cf3cd0cf6..b19940a23 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398477] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300569] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/index.html index cd443ab00..e84442d88 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fcutandrun%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/_payload.json index 2934ba06f..707edf24d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398631] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300725] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/index.html index 2da350bbf..2ac8e0e3a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fdada2%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/_payload.json index 2638b32d3..6213c2162 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398263] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300358] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/index.html index da105ee17..a15fa8503 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-cellplex/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/_payload.json index 4889ac9c1..e77a8c279 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398264] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300359] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/index.html index ab27311ca..a6d0fa4ea 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffastq-to-matrix-10x%2Fscrna-seq-fastq-to-matrix-10x-v3/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/_payload.json index 77d9845ea..d2e131a6d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398245] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300339] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/index.html index 406e45ca3..9cfac0442 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffluorescence-nuclei-segmentation-and-counting%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/_payload.json index 5d0c2e547..622a71ef9 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398393] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300483] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/index.html index d6ddbbec5..51655da05 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ffragment-based-docking-scoring%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/_payload.json index 03737db15..75ad2db9d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398670] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300784] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/index.html index cd02e6c13..0014dd861 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgcms-metams%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/_payload.json index 5887e228e..a8e86ba73 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398250] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300345] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/index.html index 427fd5910..f909fbcb9 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgene-based-pathogen-identification%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/_payload.json index 9f6320900..68cfee580 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398626] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300721] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/index.html index 781b70445..213762017 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgeneric-variant-calling-wgs-pe%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/_payload.json index 84c870b98..93bc34639 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398503] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300610] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/index.html index c56b6a00b..a8151e3ad 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgoseq%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/_payload.json index e77bdfc61..3ea9ac051 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398390] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300481] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/index.html index 47fb501af..a0e5d8d5a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-dctmd%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/_payload.json index 0dfab2fb8..85df9e89c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398395] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300486] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/index.html index fc56f5e1b..08d2b078b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fgromacs-mmgbsa%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/_payload.json index 3c462f3f0..912ffe292 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398620] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300718] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/index.html index e773f25c0..69f96246e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhaploid-variant-calling-wgs-pe%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/_payload.json index b03371c5b..203c9713b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398484] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300576] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/index.html index ab46e399c..8b236fb2d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fchic-fastq-to-cool-hicup-cooler/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/_payload.json index 5b9969434..b59a8ca4e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398482] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300574] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/index.html index 5dfb2e8c5..aa547b798 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-cool-hicup-cooler/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/_payload.json index 325ba164b..10c3fbed3 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398494] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300592] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/index.html index 5565355bf..7ba097de1 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-fastq-to-pairs-hicup/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/_payload.json index 499f9361a..92e241d54 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398487] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300589] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/index.html index 050d8c1ef..0ab59f781 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fhic-hicup-cooler%2Fhic-juicermediumtabix-to-cool-cooler/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/_payload.json index 3f2b4daf8..b7b1c3fab 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398547] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300636] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/index.html index c992e838a..400a39cc0 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-VGP1%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/_payload.json index 9fd91898d..e70a67d63 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398574] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300664] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/index.html index effe9c3d5..c70aaab48 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fkmer-profiling-hifi-trio-VGP2%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/_payload.json index 8629cb427..20bc85b2c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398672] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300787] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/index.html index d9080b799..076484d7f 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Flcms-preprocessing%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/_payload.json index d85fc62cf..3890049d0 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398254] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300349] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/index.html index 15d1f247e..2a99ee159 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fnanopore-pre-processing%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/_payload.json index 1d62ff44c..64b97f091 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398244] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300337] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/index.html index 03ec796e7..f7a7fe66b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fopenms-metaprosip%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/_payload.json index 44d7efb72..69b63b8c1 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398257] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300352] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/index.html index 0ab7cc38a..829bcae6a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fparallel-accession-download%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/_payload.json index 4fb2a5aa2..5bd4fdd3e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398251] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300347] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/index.html index 354b20bca..5b10a6a6e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpathogen-detection-pathogfair-samples-aggregation-and-visualisation%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/_payload.json index 19fddac89..a1d5c395f 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398404] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300522] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/index.html index e5b20543e..0bee2e76f 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpolish-with-long-reads%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/_payload.json index 97c6bc665..ba6178be7 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398544] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300633] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/index.html index b119cbabf..11fdb76f4 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpox-virus-amplicon%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/_payload.json index 39730faeb..3620a25f6 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398398] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300489] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/index.html index d765dc4e2..bb32796df 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fprotein-ligand-complex-parameterization%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/_payload.json index ed9218ac2..358aa478d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398261] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300356] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/index.html index 5c837a70f..6cf015b35 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fpseudobulk-worflow-decoupler-edger%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/_payload.json index 3f73a343c..a68a3be16 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398643] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300746] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/index.html index 2c6846fc8..210855bca 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIa-import-multiplexed-se/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/_payload.json index b02e506b6..45af44d35 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398645] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300748] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/index.html index 05eed8697..9db912aa2 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIb-import-multiplexed-pe/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/_payload.json index 1f08e6062..1271f232e 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398650] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300750] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/index.html index 25e15c41b..be6a95acc 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FIc-import-demultiplexed-se/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/_payload.json index b3848009d..9a7ea118a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398652] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300752] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/index.html index f24c91170..77a568dd4 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-I-import%2FId-import-demultiplexed-pe/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/_payload.json index 9d0e3b969..0828f71af 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398638] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300727] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/index.html index e32c11063..b296cc7f0 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIa-denoising-se/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/_payload.json index ff789988e..07f128030 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398640] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300735] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/index.html index e65dddce1..8ea0c36a0 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-II-denoising%2FIIb-denoising-pe/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/_payload.json index 6d1a7ccd0..022d542be 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398666] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300755] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/index.html index 1a7ce2357..98e60e4b3 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/_payload.json index 4ddb1cd89..83ec68eba 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398668] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300770] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/index.html index f57e261ef..b5820ea6c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fqiime2-III-VI-downsteam%2FQIIME2-VI-diversity-metrics-and-estimations/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/_payload.json index bcce625a3..d5fe2c431 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398402] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300492] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/index.html index 01ca0beb9..2477dcd36 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fquality-and-contamination-control%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/_payload.json index a59033a29..1ddb9fa5c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398682] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300791] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/index.html index 93dbe03b0..d08ef4e71 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frepeatmasking%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/_payload.json index 663cf235b..3a1868bd1 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398531] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300629] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/index.html index 15d3b2a20..869a79767 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-de%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/_payload.json index 300f6d4a4..c8275011a 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398541] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300631] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/index.html index 7f32a8523..cf6818f18 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-pe%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/_payload.json index 95a6c5459..351360f14 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398497] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300608] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/index.html index fd53a0e9e..764695b73 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Frnaseq-sr%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/_payload.json index 097d370d3..c184a4bf1 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398385] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300470] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/index.html index 5124de97a..8f7d099db 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-consensus-from-variation%2FCOVID-19-CONSENSUS-CONSTRUCTION/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/_payload.json index eee2c999f..0deeb9c76 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398360] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300458] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/index.html index bf5f1c35f..104ba5b88 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-ont-artic-variant-calling%2FCOVID-19-ARTIC-ONT/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/_payload.json index 828c6b380..9407dde90 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398363] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300461] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/index.html index ef3ece6d6..2dd31fd16 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-ivar-analysis%2FSARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/_payload.json index d36fb1f49..6a98a6541 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398383] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300468] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/index.html index 682779429..5bd0142a0 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-artic-variant-calling%2FCOVID-19-PE-ARTIC-ILLUMINA/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/_payload.json index 319fcedd5..140c10d31 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398388] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300478] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/index.html index 3ab745079..68b0e1dcb 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-pe-illumina-wgs-variant-calling%2FCOVID-19-PE-WGS-ILLUMINA/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/_payload.json index 5627dbbfb..0d1fa210c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398365] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300463] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/index.html index 1d6ad4341..2388c80dc 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-se-illumina-wgs-variant-calling%2FCOVID-19-SE-WGS-ILLUMINA/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/_payload.json index 455d4ab51..80d09ba0c 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398381] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300466] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/index.html index 7994627d5..329d8d379 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsars-cov-2-variation-reporting%2FCOVID-19-VARIATION-REPORTING/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/_payload.json index 14bfd0f2b..248edde0d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398259] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300354] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/index.html index 045314ec6..c35b6a46b 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fsra-manifest-to-concatenated-fastqs%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
Contribute GitHub
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- \ No newline at end of file + + + + +
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/_payload.json index 331fe690e..49788cdd5 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398255] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300351] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/index.html index 452341aa8..7c0b15e84 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Ftaxonomy-profiling-and-visualization-with-krona%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/_payload.json index fda5453e0..7310037a5 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398629] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300723] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/index.html index d5fbf439c..ebcffc198 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvariation-reporting%2Fmain/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/_payload.json index 2a86b2edf..958610996 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398353] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300442] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/index.html index a536c6734..4de407226 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-filtered-barcodes/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/_payload.json b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/_payload.json index fed2b63c1..ac215263d 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/_payload.json +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731750398279] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1731917300365] \ No newline at end of file diff --git a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/index.html b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/index.html index 61efa7f0b..a8393f246 100644 --- a/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/index.html +++ b/workflow/%23workflow%2Fgithub.com%2Fiwc-workflows%2Fvelocyto%2FVelocyto-on10X-from-bundled/index.html @@ -33,17 +33,17 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - + + + - - - - -
IWC Logo Galaxy IWC - Workflow Library
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+ \ No newline at end of file diff --git a/workflow_manifest.json b/workflow_manifest.json index aa89a7887..c59f84412 100644 --- a/workflow_manifest.json +++ b/workflow_manifest.json @@ -56592,7 +56592,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.0", + "release": "1.1", "name": "RNA-seq for Paired-end fastqs", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -56936,7 +56936,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3", "errors": null, "id": 12, "input_connections": { @@ -56987,15 +56987,15 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "dbfc505896e9", + "changeset_revision": "a626e8c0e1ba", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": \"30\", \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": \"15\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": false, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_sequence2\": {\"__class__\": \"ConnectedValue\"}, \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.23.4+galaxy2", + "tool_version": "0.24.0+galaxy3", "type": "tool", "uuid": "80d855a6-7a77-46e9-9124-9dd3d9d72cc1", "when": null, @@ -57727,7 +57727,7 @@ } }, "tags": [], - "uuid": "451bba09-1c21-4978-b693-4e64402c5787" + "uuid": "7abe9e86-1aea-4cc5-bbc3-8a98e09f0bc6" }, "tool_id": null, "type": "subworkflow", @@ -58314,7 +58314,7 @@ } }, "tags": [], - "uuid": "f5bde9df-1387-4d76-a90c-1043c93e8de5" + "uuid": "d2af388a-2469-44c1-ad24-ef9511546b8e" }, "tool_id": null, "type": "subworkflow", @@ -58330,7 +58330,7 @@ }, "21": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0", "errors": null, "id": 21, "input_connections": { @@ -58385,15 +58385,15 @@ "output_name": "output_summary" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0", "tool_shed_repository": { - "changeset_revision": "f9d49f5cb597", + "changeset_revision": "1b851f87fbe0", "name": "featurecounts", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"alignment\": {\"__class__\": \"ConnectedValue\"}, \"anno\": {\"anno_select\": \"history\", \"__current_case__\": 2, \"reference_gene_sets\": {\"__class__\": \"ConnectedValue\"}, \"gff_feature_type\": \"exon\", \"gff_feature_attribute\": \"gene_id\", \"summarization_level\": false}, \"extended_parameters\": {\"multifeatures\": {\"multifeat\": \"\", \"__current_case__\": 0}, \"exon_exon_junction_read_counting_enabled\": {\"count_exon_exon_junction_reads\": \"\", \"__current_case__\": 1}, \"long_reads\": false, \"by_read_group\": false, \"largest_overlap\": false, \"min_overlap\": \"1\", \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"read_extension_5p\": \"0\", \"read_extension_3p\": \"0\", \"read_reduction\": \"\", \"R\": false}, \"format\": \"tabdel_short\", \"include_feature_length_file\": false, \"pe_parameters\": {\"paired_end_status\": \"PE_fragments\", \"__current_case__\": 2, \"check_distance_enabled\": {\"checkFragLength\": \"false\", \"__current_case__\": 1}, \"only_both_ends\": false, \"exclude_chimerics\": true}, \"read_filtering_parameters\": {\"mapping_quality\": \"0\", \"splitonly\": \"\", \"primary\": false, \"ignore_dup\": false}, \"strand_specificity\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.3+galaxy2", + "tool_version": "2.0.6+galaxy0", "type": "tool", "uuid": "5a03b546-eb3f-4e99-b845-24c8f54ed183", "when": "$(inputs.when)", @@ -58522,10 +58522,6 @@ "description": "runtime parameter for tool Cufflinks", "name": "advanced_settings" }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "input" - }, { "description": "runtime parameter for tool Cufflinks", "name": "reference_annotation" @@ -58597,7 +58593,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"RuntimeValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"RuntimeValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"RuntimeValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1.4", "type": "tool", "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", @@ -59083,7 +59079,7 @@ } }, "tags": [], - "uuid": "1d5779a5-fb3a-453a-9fec-8acd491ce5ab" + "uuid": "de2ecd60-7f89-4062-8db5-60406bc79148" }, "tool_id": null, "type": "subworkflow", @@ -59882,7 +59878,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "b5e9c0d2-62f4-41b2-a1c7-5677d8555fd4", @@ -59902,7 +59898,7 @@ } }, "tags": [], - "uuid": "7a36b35e-4487-49d8-b6e1-45a2063a5fff" + "uuid": "4e0fb735-1e3f-4948-8991-001ef7d7e7c0" }, "tool_id": null, "type": "subworkflow", @@ -59930,7 +59926,7 @@ "version": 1 }, "readme": "# RNA-seq paired-end Workflow\n\n## Inputs dataset\n\n- Collection paired FASTQ files: The workflow needs a list of dataset pairs of fastqsanger.\n- GTF file of annotation: A gtf file with genes annotation.\n- GTF with regions to exclude from FPKM normalization with Cufflinks: Optional, but recommended. A gtf file with regions to exclude from normalization in Cufflinks.\n\n - For instance a gtf that masks chrM for the mm10 genome:\n\n```\nchrM\tchrM_gene\texon\t0\t16299\t.\t+\t.\tgene_id \"chrM_gene_plus\"; transcript_id \"chrM_tx_plus\"; exon_id \"chrM_ex_plus\";\nchrM\tchrM_gene\texon\t0\t16299\t.\t-\t.\tgene_id \"chrM_gene_minus\"; transcript_id \"chrM_tx_minus\"; exon_id \"chrM_ex_minus\";\n```\n\n## Inputs values\n\n- Forward and Reverse adapter (optional): By default, fastp will try to overlap both reads and will only use these sequences if R1/R2 are found not overlapped. Their sequences depends on the library preparation. Usually classical Illumina RNA libraries is Truseq and ISML (relatively new Illumina library) is Nextera.\n- Generate additional QC reports: whether to compute additional QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes.\n- Reference genome: this field will be adapted to the genomes available for STAR.\n- Strandedness: For stranded RNA, reverse means that the first read in a pair is complementary to the coding sequence, forward means that the first read in a pair is in the same orientation as the coding sequence. This will only count alignments that are compatible with your library preparation strategy. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie.\n- Use featureCounts for generating count tables: Whether to use count tables from featureCounts instead of from STAR.\n- Compute Cufflinks FPKM: Whether you want to get FPKM with Cufflinks (pretty long).\n- Compute StringTie FPKM: Whether you want to get FPKM/TPM etc... with StringTie.\n\n## Processing\n\n- The workflow will remove adapters and low quality bases and filter out any read smaller than 15bp.\n- The filtered reads are mapped with STAR with ENCODE parameters (for long RNA-seq but I use it for short also). STAR is also used to count reads per gene and generate strand-specific normalized coverage (on uniquely mapped reads).\n- Optionally featureCounts is used to generate count files when this option enabled.\n- Optionally FastQC, Picard, read_distribution, geneBody_coverage, samtools idxstats, Picard are run to get additional QC.\n- A multiQC is run to have an overview of the QC. This can also be used to get the strandedness.\n- FPKM values for genes and transcripts are computed with cufflinks using correction for multi-mapped reads (this step is optionnal).\n- FPKM/TPM values for genes are computed with StringTie (this step is optional).\n- The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1).\n- Unstranded coverage is computed with bedtools and normalized to the number of million uniquely mapped reads.\n- The three coverage files are converted to bigwig.\n\n### Warning\n\n- The coverage stranded output depends on the strandedness of the library:\n - If you have an unstranded library, stranded coverages are useless\n - If you have a forward stranded library, the label matches the orientation of the first read in pairs.\n - If you have a reverse stranded library, the label matches the orientation of the second read in pairs.\n", - "changelog": "# Changelog\n\n## [1.0] 2024-09-23\n\n### Changes in workflows\n- Add an optional subworkflow with more QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes.\n- Add featureCounts as an alternative way to generate count files\n- Use fastp instead of cutadapt which uses pair overlap and allows to have optional adapter sequences\n\n### Tool update\n- `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4`\n\n### Test dataset\n- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631\n\n## [0.9] 2024-09-23\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`\n\n## [0.8] 2024-07-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0`\n\n## [0.7] 2024-06-25\n\n### Automatic update (triggered manually)\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0`\n\n## [0.6] 2024-02-05\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0`\n\n## [0.5] 2023-09-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4`\n\n### Manual update\n- Use STAR to compute normalized strand-specific coverage\n- Add an option to use StringTie to compute FPKM\n- Make cufflinks step optional\n\n## [0.4.1] 2023-09-14\n- add author in dockstore file\n\n## [0.4] 2023-01-16\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1`\n\n## [0.3] 2022-12-17\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1`\n\n## [0.2] 2022-11-02\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1`\n\n## [0.1] 2022-10-21\n\nFirst release.\n", + "changelog": "# Changelog\n\n## [1.1] 2024-11-18\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3`\n- `toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0`\n\n## [1.0] 2024-09-23\n\n### Changes in workflows\n- Add an optional subworkflow with more QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes.\n- Add featureCounts as an alternative way to generate count files\n- Use fastp instead of cutadapt which uses pair overlap and allows to have optional adapter sequences\n\n### Tool update\n- `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4`\n\n### Test dataset\n- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631\n\n## [0.9] 2024-09-23\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`\n\n## [0.8] 2024-07-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0`\n\n## [0.7] 2024-06-25\n\n### Automatic update (triggered manually)\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0`\n\n## [0.6] 2024-02-05\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0`\n\n## [0.5] 2023-09-15\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4`\n\n### Manual update\n- Use STAR to compute normalized strand-specific coverage\n- Add an option to use StringTie to compute FPKM\n- Make cufflinks step optional\n\n## [0.4.1] 2023-09-14\n- add author in dockstore file\n\n## [0.4] 2023-01-16\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1`\n\n## [0.3] 2022-12-17\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1`\n\n## [0.2] 2022-11-02\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1`\n\n## [0.1] 2022-10-21\n\nFirst release.\n", "trsID": "#workflow/github.com/iwc-workflows/rnaseq-pe/main", "tests": [ {