From fe7eb4779e15162d9a9b29ecb18ddffab5fb2b83 Mon Sep 17 00:00:00 2001 From: bebatut Date: Fri, 25 Oct 2024 10:05:33 +0000 Subject: [PATCH] deploy: 6400113db7ee2c63a5877b2ad24c50c53456bb73 --- 200.html | 10 +++---- 404.html | 10 +++---- _nuxt/{Q0y6llI6.js => B0PD4Km0.js} | 2 +- _nuxt/{F27H2LTB.js => B1WhW7ou.js} | 2 +- _nuxt/{xr9ovDgs.js => B1lATa-T.js} | 2 +- _nuxt/{BWFr69vb.js => B2WrS4F7.js} | 8 +++--- _nuxt/{BQXauQfw.js => BERYsrTf.js} | 2 +- _nuxt/{BX7HqCxZ.js => BEdrpsNP.js} | 2 +- _nuxt/{CC5qg0QL.js => BLKo9RBc.js} | 2 +- _nuxt/BLuEtH_b.js | 1 + _nuxt/{_94mpdbo.js => BURjpqrp.js} | 2 +- _nuxt/{S7UqX5vQ.js => BWRM-vu7.js} | 2 +- _nuxt/{C_bLDgeg.js => BYqfWOoo.js} | 2 +- _nuxt/{CVNjsBHF.js => Bbvx-Str.js} | 2 +- _nuxt/{DcKXAc_F.js => BhoOjUja.js} | 2 +- _nuxt/{CW33h0F2.js => BszVJK1C.js} | 2 +- _nuxt/{71TKAreg.js => Bve-TeOP.js} | 2 +- _nuxt/{BEZhSL6r.js => Bw42aofy.js} | 2 +- _nuxt/{Bnt4ApqC.js => C1nP_51f.js} | 2 +- _nuxt/{D22yXe-6.js => C5EiAhOE.js} | 2 +- _nuxt/{Ciq3B0k2.js => C5II8VSl.js} | 2 +- _nuxt/{BLbNJEyJ.js => C6qH28So.js} | 2 +- _nuxt/{COiwL07E.js => C6q_xaH0.js} | 2 +- _nuxt/{JsvSxmzB.js => C8w-YsAR.js} | 2 +- _nuxt/{B3XhLCAH.js => CaMSfWu1.js} | 2 +- _nuxt/{DfriSdLw.js => CdFWB3il.js} | 2 +- _nuxt/{B2F4_ro1.js => CgUvvjOG.js} | 2 +- _nuxt/{Cq4pZBKz.js => CgfUIu8a.js} | 2 +- _nuxt/{BdEtlRiI.js => Cir98oUc.js} | 2 +- _nuxt/{FcJJd0cX.js => CuxHF_lL.js} | 10 +++++-- _nuxt/{tTsFKelM.js => D2PIAtkT.js} | 2 +- _nuxt/{Dc4k6aeh.js => D3w5GROP.js} | 2 +- _nuxt/{CeLOlcvx.js => DDQEN5Di.js} | 2 +- _nuxt/{COLHc7Zo.js => DVW6mKyd.js} | 4 +-- _nuxt/{BtGFNHrc.js => DWRm9IlE.js} | 2 +- _nuxt/{CxkkcxVM.js => DYIZCnub.js} | 2 +- _nuxt/{DP0Z4RhT.js => D_6HmeRe.js} | 2 +- _nuxt/{d0YDmE97.js => Dac-UKi4.js} | 2 +- _nuxt/{DUflpUzs.js => DalHd6Nl.js} | 2 +- _nuxt/{zfhR0ja8.js => DoKgMDk6.js} | 2 +- _nuxt/{18CYxNv1.js => DoUFXegS.js} | 2 +- _nuxt/{DOLdywvx.js => Dxu4LSA8.js} | 2 +- _nuxt/Dy9f9J-B.js | 1 - _nuxt/{BtI4KRFq.js => DzQFcFQp.js} | 2 +- _nuxt/{RTgJfHXf.js => Hkiugypu.js} | 4 +-- _nuxt/J70ZNwtt.js | 1 - _nuxt/O6Xu1IQQ.js | 1 + _nuxt/{BExog0Tt.js => ONKJz15c.js} | 2 +- _nuxt/{2PylcXyw.js => QH42LMdf.js} | 2 +- _nuxt/{BCbsI-Go.js => RPMs3HYD.js} | 2 +- _nuxt/builds/latest.json | 2 +- .../b8a78d58-5881-4bc0-a7c5-872044ec2b26.json | 1 - .../bb7db555-9293-47bc-863a-1f12b0a23ffc.json | 1 + _nuxt/{Cgpi_DlH.js => jVx4GdQ1.js} | 2 +- _nuxt/{DuOuDy0-.js => tahdbQxN.js} | 2 +- _nuxt/{HS1jbzzA.js => yiPl5MDX.js} | 2 +- _payload.json | 2 +- api/_content/cache.1729842628168.json | 1 - api/_content/cache.1729850709749.json | 1 + index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 28 +++++++++++-------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- .../_payload.json | 2 +- .../index.html | 20 ++++++------- workflow_manifest.json | 22 +++++++-------- 211 files changed, 928 insertions(+), 916 deletions(-) rename _nuxt/{Q0y6llI6.js => B0PD4Km0.js} (85%) rename _nuxt/{F27H2LTB.js => B1WhW7ou.js} (64%) rename _nuxt/{xr9ovDgs.js => B1lATa-T.js} (86%) rename _nuxt/{BWFr69vb.js => B2WrS4F7.js} (98%) rename _nuxt/{BQXauQfw.js => BERYsrTf.js} (64%) rename _nuxt/{BX7HqCxZ.js => BEdrpsNP.js} (87%) rename _nuxt/{CC5qg0QL.js => BLKo9RBc.js} (85%) create mode 100644 _nuxt/BLuEtH_b.js rename _nuxt/{_94mpdbo.js => BURjpqrp.js} (81%) rename _nuxt/{S7UqX5vQ.js => BWRM-vu7.js} (84%) rename _nuxt/{C_bLDgeg.js => BYqfWOoo.js} (99%) rename _nuxt/{CVNjsBHF.js => Bbvx-Str.js} (99%) rename _nuxt/{DcKXAc_F.js => BhoOjUja.js} (63%) rename _nuxt/{CW33h0F2.js => BszVJK1C.js} (79%) rename _nuxt/{71TKAreg.js => Bve-TeOP.js} (77%) rename _nuxt/{BEZhSL6r.js => Bw42aofy.js} (58%) rename _nuxt/{Bnt4ApqC.js => C1nP_51f.js} (65%) rename _nuxt/{D22yXe-6.js => C5EiAhOE.js} (89%) rename _nuxt/{Ciq3B0k2.js => C5II8VSl.js} (85%) rename _nuxt/{BLbNJEyJ.js => C6qH28So.js} (78%) rename _nuxt/{COiwL07E.js => C6q_xaH0.js} (63%) rename _nuxt/{JsvSxmzB.js => C8w-YsAR.js} (97%) rename _nuxt/{B3XhLCAH.js => CaMSfWu1.js} (93%) rename _nuxt/{DfriSdLw.js => CdFWB3il.js} (97%) rename _nuxt/{B2F4_ro1.js => CgUvvjOG.js} (58%) rename _nuxt/{Cq4pZBKz.js => CgfUIu8a.js} (96%) rename _nuxt/{BdEtlRiI.js => Cir98oUc.js} (85%) rename _nuxt/{FcJJd0cX.js => CuxHF_lL.js} (99%) rename _nuxt/{tTsFKelM.js => D2PIAtkT.js} (63%) rename _nuxt/{Dc4k6aeh.js => D3w5GROP.js} (63%) rename _nuxt/{CeLOlcvx.js => DDQEN5Di.js} (97%) rename _nuxt/{COLHc7Zo.js => DVW6mKyd.js} (74%) rename _nuxt/{BtGFNHrc.js => DWRm9IlE.js} (64%) rename _nuxt/{CxkkcxVM.js => DYIZCnub.js} (85%) rename _nuxt/{DP0Z4RhT.js => D_6HmeRe.js} (65%) rename _nuxt/{d0YDmE97.js => Dac-UKi4.js} (92%) rename _nuxt/{DUflpUzs.js => DalHd6Nl.js} (85%) rename _nuxt/{zfhR0ja8.js => DoKgMDk6.js} (99%) rename _nuxt/{18CYxNv1.js => DoUFXegS.js} (64%) rename _nuxt/{DOLdywvx.js => Dxu4LSA8.js} (82%) delete mode 100644 _nuxt/Dy9f9J-B.js rename _nuxt/{BtI4KRFq.js => DzQFcFQp.js} (53%) rename _nuxt/{RTgJfHXf.js => Hkiugypu.js} (95%) delete mode 100644 _nuxt/J70ZNwtt.js create mode 100644 _nuxt/O6Xu1IQQ.js rename _nuxt/{BExog0Tt.js => ONKJz15c.js} (98%) rename _nuxt/{2PylcXyw.js => QH42LMdf.js} (99%) rename _nuxt/{BCbsI-Go.js => RPMs3HYD.js} (63%) delete mode 100644 _nuxt/builds/meta/b8a78d58-5881-4bc0-a7c5-872044ec2b26.json create mode 100644 _nuxt/builds/meta/bb7db555-9293-47bc-863a-1f12b0a23ffc.json rename _nuxt/{Cgpi_DlH.js => jVx4GdQ1.js} (64%) rename _nuxt/{DuOuDy0-.js => tahdbQxN.js} (63%) rename _nuxt/{HS1jbzzA.js => yiPl5MDX.js} (63%) delete mode 100644 api/_content/cache.1729842628168.json create mode 100644 api/_content/cache.1729850709749.json diff --git a/200.html b/200.html index 03c38999e..1fc99063f 100644 --- a/200.html +++ b/200.html @@ -2,9 +2,9 @@ - - - -
- \ No newline at end of file + \ No newline at end of file diff --git a/404.html b/404.html index 03c38999e..1fc99063f 100644 --- a/404.html +++ b/404.html @@ -2,9 +2,9 @@ - - - -
- \ No newline at end of file + \ No newline at end of file diff --git a/_nuxt/Q0y6llI6.js b/_nuxt/B0PD4Km0.js similarity index 85% rename from _nuxt/Q0y6llI6.js rename to _nuxt/B0PD4Km0.js index 9756be2c7..ef00c9050 100644 --- a/_nuxt/Q0y6llI6.js +++ b/_nuxt/B0PD4Km0.js @@ -1 +1 @@ -import{h as i,a3 as c,k as p,o as s,c as n,D as u,r as t}from"./BWFr69vb.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 0:o.anchorLinks)==null?void 0:e.h3)});return(e,m)=>(s(),n("h3",{id:e.id},[e.id&&u(d)?(s(),n("a",{key:0,href:`#${e.id}`},[t(e.$slots,"default")],8,l)):t(e.$slots,"default",{key:1})],8,f))}});export{k as default}; +import{h as i,a3 as c,k as p,o as s,c as n,D as u,r as t}from"./B2WrS4F7.js";const f=["id"],l=["href"],k=i({__name:"ProseH3",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 0:o.anchorLinks)==null?void 0:e.h3)});return(e,m)=>(s(),n("h3",{id:e.id},[e.id&&u(d)?(s(),n("a",{key:0,href:`#${e.id}`},[t(e.$slots,"default")],8,l)):t(e.$slots,"default",{key:1})],8,f))}});export{k as default}; diff --git a/_nuxt/F27H2LTB.js b/_nuxt/B1WhW7ou.js similarity index 64% rename from _nuxt/F27H2LTB.js rename to _nuxt/B1WhW7ou.js index 17a1dc63c..838f89c3e 100644 --- a/_nuxt/F27H2LTB.js +++ b/_nuxt/B1WhW7ou.js @@ -1 +1 @@ -import{_ as r,o,c as t,r as n}from"./BWFr69vb.js";const s={};function c(e,a){return o(),t("strong",null,[n(e.$slots,"default")])}const _=r(s,[["render",c]]);export{_ as default}; +import{_ as r,o,c as t,r as n}from"./B2WrS4F7.js";const s={};function c(e,a){return o(),t("strong",null,[n(e.$slots,"default")])}const _=r(s,[["render",c]]);export{_ as default}; diff --git a/_nuxt/xr9ovDgs.js b/_nuxt/B1lATa-T.js similarity index 86% rename from _nuxt/xr9ovDgs.js rename to _nuxt/B1lATa-T.js index a9897e117..6fa93f246 100644 --- a/_nuxt/xr9ovDgs.js +++ b/_nuxt/B1lATa-T.js @@ -1 +1 @@ -import{h as o,D as s,o as n,c as r,d as e,x as a,a as t}from"./BWFr69vb.js";const c={key:0},i=t("code",null,"script",-1),d=t("code",null,"ProseScript",-1),f=o({__name:"ProseScript",props:{src:{type:String,default:""}},setup(l){return(_,m)=>s(!1)?(n(),r("div",c,[e(" Rendering the "),i,e(" element is dangerous and is disabled by default. Consider implementing your own "),d,e(" element to have control over script rendering. ")])):a("",!0)}});export{f as default}; +import{h as o,D as s,o as n,c as r,d as e,x as a,a as t}from"./B2WrS4F7.js";const c={key:0},i=t("code",null,"script",-1),d=t("code",null,"ProseScript",-1),f=o({__name:"ProseScript",props:{src:{type:String,default:""}},setup(l){return(_,m)=>s(!1)?(n(),r("div",c,[e(" Rendering the "),i,e(" element is dangerous and is disabled by default. Consider implementing your own "),d,e(" element to have control over script rendering. ")])):a("",!0)}});export{f as default}; diff --git a/_nuxt/BWFr69vb.js b/_nuxt/B2WrS4F7.js similarity index 98% rename from _nuxt/BWFr69vb.js rename to _nuxt/B2WrS4F7.js index d8d52c244..bee56d1ff 100644 --- a/_nuxt/BWFr69vb.js +++ b/_nuxt/B2WrS4F7.js @@ -1,4 +1,4 @@ -const __vite__fileDeps=["./DfriSdLw.js","./FcJJd0cX.js","./C_bLDgeg.js","./BQkc-AXV.js","./Icon.8lQfE3Ql.css","./DvDH6DOc.js","./2PylcXyw.js","./_id_.CQoIg8OE.css","./BX7HqCxZ.js","./S7UqX5vQ.js","./CVNjsBHF.js","./C-v3KzvZ.js","./BExog0Tt.js","./d0YDmE97.js","./RTgJfHXf.js","./BLbNJEyJ.js","./COLHc7Zo.js","./Dy9f9J-B.js","./BEZhSL6r.js","./Cq4pZBKz.js","./J70ZNwtt.js","./CW33h0F2.js","./ProsePre.CchFRBtv.css","./DOLdywvx.js","./B3XhLCAH.js","./IconCSS.Z2BAHt_z.css","./JsvSxmzB.js","./error-404.JekaaCis.css","./CeLOlcvx.js","./error-500.CNP9nqm1.css"],__vite__mapDeps=i=>i.map(i=>__vite__fileDeps[i]); +const __vite__fileDeps=["./CdFWB3il.js","./CuxHF_lL.js","./BYqfWOoo.js","./BQkc-AXV.js","./Icon.8lQfE3Ql.css","./DvDH6DOc.js","./QH42LMdf.js","./_id_.CQoIg8OE.css","./BEdrpsNP.js","./BWRM-vu7.js","./Bbvx-Str.js","./C-v3KzvZ.js","./ONKJz15c.js","./Dac-UKi4.js","./Hkiugypu.js","./C6qH28So.js","./DVW6mKyd.js","./BLuEtH_b.js","./Bw42aofy.js","./CgfUIu8a.js","./O6Xu1IQQ.js","./BszVJK1C.js","./ProsePre.CchFRBtv.css","./Dxu4LSA8.js","./CaMSfWu1.js","./IconCSS.Z2BAHt_z.css","./C8w-YsAR.js","./error-404.JekaaCis.css","./DDQEN5Di.js","./error-500.CNP9nqm1.css"],__vite__mapDeps=i=>i.map(i=>__vite__fileDeps[i]); /** * @vue/shared v3.4.27 * (c) 2018-present Yuxi (Evan) You and Vue contributors @@ -15,11 +15,11 @@ const __vite__fileDeps=["./DfriSdLw.js","./FcJJd0cX.js","./C_bLDgeg.js","./BQkc- * @vue/runtime-dom v3.4.27 * (c) 2018-present Yuxi (Evan) You and Vue contributors * @license MIT -**/const $f="http://www.w3.org/2000/svg",Nf="http://www.w3.org/1998/Math/MathML",Tt=typeof 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o}from"./Bbvx-Str.js";import"./B2WrS4F7.js";import"./C-v3KzvZ.js";import"./ONKJz15c.js";import"./DvDH6DOc.js";export{o as default}; diff --git a/_nuxt/_94mpdbo.js b/_nuxt/BURjpqrp.js similarity index 81% rename from _nuxt/_94mpdbo.js rename to _nuxt/BURjpqrp.js index 9abdaa3ff..152756c2d 100644 --- a/_nuxt/_94mpdbo.js +++ b/_nuxt/BURjpqrp.js @@ -1 +1 @@ -import{h as a,o as n,s as o,w as s,r as f,e as u}from"./BWFr69vb.js";const _=a({__name:"ProseA",props:{href:{type:String,default:""},target:{type:String,default:void 0,required:!1}},setup(e){return(t,c)=>{const r=u;return n(),o(r,{href:e.href,target:e.target},{default:s(()=>[f(t.$slots,"default")]),_:3},8,["href","target"])}}});export{_ as default}; +import{h as a,o as n,s as o,w as s,r as f,e as u}from"./B2WrS4F7.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 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a/_nuxt/DcKXAc_F.js +++ b/_nuxt/BhoOjUja.js @@ -1 +1 @@ -import{_ as r,o,c as t,r as s}from"./BWFr69vb.js";const c={};function n(e,a){return o(),t("td",null,[s(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; +import{_ as r,o,c as t,r as s}from"./B2WrS4F7.js";const c={};function n(e,a){return o(),t("td",null,[s(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; diff --git a/_nuxt/CW33h0F2.js b/_nuxt/BszVJK1C.js similarity index 79% rename from _nuxt/CW33h0F2.js rename to _nuxt/BszVJK1C.js index 1a65d2f8f..edc16a9b0 100644 --- a/_nuxt/CW33h0F2.js +++ b/_nuxt/BszVJK1C.js @@ -1 +1 @@ -import{h as t,r}from"./BWFr69vb.js";const o=t({__name:"ProseCode",props:{code:{type:String,default:""},language:{type:String,default:null},filename:{type:String,default:null},highlights:{type:Array,default:()=>[]},meta:{type:String,default:null}},setup(n){return(e,a)=>r(e.$slots,"default")}});export{o as _}; +import{h as t,r}from"./B2WrS4F7.js";const o=t({__name:"ProseCode",props:{code:{type:String,default:""},language:{type:String,default:null},filename:{type:String,default:null},highlights:{type:Array,default:()=>[]},meta:{type:String,default:null}},setup(n){return(e,a)=>r(e.$slots,"default")}});export{o as _}; diff --git a/_nuxt/71TKAreg.js b/_nuxt/Bve-TeOP.js similarity index 77% rename from _nuxt/71TKAreg.js rename to _nuxt/Bve-TeOP.js index 47c0f16b9..04a1590df 100644 --- a/_nuxt/71TKAreg.js +++ b/_nuxt/Bve-TeOP.js @@ -1 +1 @@ -import{h as n,N as e}from"./BWFr69vb.js";const r=n({name:"DocumentDrivenEmpty",props:{value:{type:Object,required:!0}},render({value:t}){return e("div",void 0,[e("p","Document is empty"),e("p",`Add content to it by opening ${t._source}/${t._file} file.`)])}});export{r as default}; +import{h as n,N as e}from"./B2WrS4F7.js";const r=n({name:"DocumentDrivenEmpty",props:{value:{type:Object,required:!0}},render({value:t}){return e("div",void 0,[e("p","Document is empty"),e("p",`Add content to it by opening 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_nuxt/Bnt4ApqC.js rename to _nuxt/C1nP_51f.js index 3690c7418..39b54f8d9 100644 --- a/_nuxt/Bnt4ApqC.js +++ b/_nuxt/C1nP_51f.js @@ -1 +1 @@ -import{_ as o,o as r,c as t,r as s}from"./BWFr69vb.js";const c={};function n(e,a){return r(),t("tbody",null,[s(e.$slots,"default")])}const _=o(c,[["render",n]]);export{_ as default}; +import{_ as o,o as r,c as t,r as s}from"./B2WrS4F7.js";const c={};function n(e,a){return r(),t("tbody",null,[s(e.$slots,"default")])}const _=o(c,[["render",n]]);export{_ as default}; diff --git a/_nuxt/D22yXe-6.js b/_nuxt/C5EiAhOE.js similarity index 89% rename from _nuxt/D22yXe-6.js rename to _nuxt/C5EiAhOE.js index cb70647f1..618de9246 100644 --- a/_nuxt/D22yXe-6.js +++ b/_nuxt/C5EiAhOE.js @@ -1 +1 @@ -import{h as r,k as n,ad as c,a5 as h,a3 as o,ae as d,o as l,c as u,D as f}from"./BWFr69vb.js";const g=["src","alt","width","height"],p=r({__name:"ProseImg",props:{src:{type:String,default:""},alt:{type:String,default:""},width:{type:[String,Number],default:void 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a/_nuxt/Ciq3B0k2.js b/_nuxt/C5II8VSl.js similarity index 85% rename from _nuxt/Ciq3B0k2.js rename to _nuxt/C5II8VSl.js index 9f22d27ce..eb2a5b158 100644 --- a/_nuxt/Ciq3B0k2.js +++ b/_nuxt/C5II8VSl.js @@ -1 +1 @@ -import{h as i,a3 as c,k as p,o as s,c as n,D as u,r as t}from"./BWFr69vb.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.$slots,"default",{key:1})],8,f))}});export{k as default}; +import{h as i,a3 as c,k as p,o as s,c as n,D as u,r as t}from"./B2WrS4F7.js";const f=["id"],l=["href"],k=i({__name:"ProseH2",props:{id:{}},setup(r){const a=r,{headings:o}=c().public.mdc,d=p(()=>{var e;return a.id&&((e=o==null?void 0:o.anchorLinks)==null?void 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p(d,m,{default:t!=null&&t.default?({data:e,refresh:o,isPartial:n})=>t.default({list:e,refresh:o,isPartial:n,...this.$attrs}):e=>u("default",e.data),empty:e=>t!=null&&t.empty?t.empty(e):u("default",e==null?void 0:e.data),"not-found":e=>{var o;return t!=null&&t["not-found"]?(o=t==null?void 0:t["not-found"])==null?void 0:o.call(t,e):u("not-found",e==null?void 0:e.data)}})}}),N=l;export{N as default}; diff --git a/_nuxt/COiwL07E.js b/_nuxt/C6q_xaH0.js similarity index 63% rename from _nuxt/COiwL07E.js rename to _nuxt/C6q_xaH0.js index 33a78fba1..6c64e530d 100644 --- a/_nuxt/COiwL07E.js +++ b/_nuxt/C6q_xaH0.js @@ -1 +1 @@ -import{_ as r,o,c as t,r as s}from"./BWFr69vb.js";const c={};function n(e,a){return o(),t("th",null,[s(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; +import{_ as r,o,c as t,r as s}from"./B2WrS4F7.js";const c={};function n(e,a){return o(),t("th",null,[s(e.$slots,"default")])}const _=r(c,[["render",n]]);export{_ as default}; diff --git 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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. 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"ConnectedValue"}, "gff_file_path": {"__class__": "ConnectedValue"}, "origin": {"origin": "true", "__current_case__": 0, "analysis_software_version": null}, "reference_database_version": {"__class__": "ConnectedValue"}}}]}, "__page__": null, "__rerun_remap_job_id__": null}',tool_version:"0.9.1+galaxy1",type:"tool",uuid:"678bdbfe-7a3a-4a91-8ea7-1cb17f53daa6",when:null,workflow_outputs:[{label:"tooldistillator_results",output_name:"output_json",uuid:"a8db4b4d-8573-45bf-990c-304868ad5150"}]},9:{annotation:"ToolDistillator summarize groups all JSON file into a unique JSON file",content_id:"toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1",errors:null,id:9,input_connections:{summarize_data:{id:8,output_name:"output_json"}},inputs:[],label:"ToolDistillator summarize",name:"ToolDistillator Summarize",outputs:[{name:"summary_json",type:"json"}],position:{left:1999.7866424448703,top:1179.174084225585},post_job_actions:{RenameDatasetActionsummary_json:{action_arguments:{newname:"tooldistillator_summarize"},action_type:"RenameDatasetAction",output_name:"summary_json"},TagDatasetActionsummary_json:{action_arguments:{tags:"tooldistillator_summarize"},action_type:"TagDatasetAction",output_name:"summary_json"}},tool_id:"toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1",tool_shed_repository:{changeset_revision:"24eec94e6dfc",name:"tooldistillator_summarize",owner:"iuc",tool_shed:"toolshed.g2.bx.psu.edu"},tool_state:'{"summarize_data": {"__class__": "ConnectedValue"}, "__page__": null, "__rerun_remap_job_id__": null}',tool_version:"0.9.1+galaxy1",type:"tool",uuid:"3427b1f1-79ce-4ade-a350-baf15ac250c2",when:null,workflow_outputs:[{label:"tooldistillator_summarize",output_name:"summary_json",uuid:"96d63721-4cb5-4879-8984-4eeba8dec36b"}]}},tags:["Genomics","fasta","ABRomics","bacterial-genomics","Annotation","genome-annotation"],uuid:"d55a9e46-a205-4143-b92f-3783499063ed",version:1},readme:`# Bacterial genome annotation workflow (v1.0) This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps: 1. Genomic annotation @@ -114,6 +114,12 @@ This workflow uses assembled bacterial genome fasta files (but can be any fasta 5. Aggregating outputs: - JSON file with information about the outputs of **Bakta**, **IntegronFinder2**, **Plasmidfinder**, **ISEScan**`,changelog:`# Changelog +## [1.1.7] 2024-10-21 + +### Automatic update +- \`toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0\` was updated to \`toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1\` +- \`toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0\` was updated to \`toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1\` + ## [1.1.6] 2024-10-11 ### Manual update diff --git a/_nuxt/tTsFKelM.js b/_nuxt/D2PIAtkT.js similarity index 63% rename from _nuxt/tTsFKelM.js rename to _nuxt/D2PIAtkT.js index 91baf3520..7e7d35dac 100644 --- a/_nuxt/tTsFKelM.js +++ b/_nuxt/D2PIAtkT.js @@ -1 +1 @@ -import{_ as r,o,c as s,r as t}from"./BWFr69vb.js";const c={};function n(e,a){return 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IWC LogoGalaxy IWC - Workflow Library
AboutDevelopment
  • 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
  • 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
  • BREW3R
  • RNAseq_PE
  • 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
  • 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

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. @@ -60,5 +60,5 @@ 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/0608c7f4-767c-47b3-ae45-4e98c7c83bec/_payload.json b/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/_payload.json index 31e2a081c..dd1a37b64 100644 --- a/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/_payload.json +++ b/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649840] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731117] \ No newline at end of file diff --git a/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/index.html b/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/index.html index 52a17d7c6..b890b0160 100644 --- a/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/index.html +++ b/workflow/0608c7f4-767c-47b3-ae45-4e98c7c83bec/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Velocyto-on10X-from-bundled

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

  • Author(s):
  • Lucille Delisle
  • Release: 0.2
  • License: MIT
  • UniqueID: 0608c7f4-767c-47b3-ae45-4e98c7c83bec

Velocyto on 10X data

These workflows simply run velocyto. There are 2 workflows because one can be easily run after the 'fastq-to-matrix-10x' workflows (Velocyto-on10X-from-bundled). The other can be easily run from uploaded datasets (Velocyto-on10X-filtered-barcodes).

Input datasets

@@ -68,5 +68,5 @@

Automatic update

[0.1] 2024-01-26

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/_payload.json b/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/_payload.json index b824742be..d871f85ea 100644 --- a/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/_payload.json +++ b/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650092] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731359] \ No newline at end of file diff --git a/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/index.html b/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/index.html index b549dff00..1e4cd5873 100644 --- a/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/index.html +++ b/workflow/06dc40a7-99f2-4b3c-ae21-b3dcb239306f/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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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.

  • Author(s):
  • Wolfgang Maier
  • Release: 0.4.2
  • License: MIT
  • UniqueID: 06dc40a7-99f2-4b3c-ae21-b3dcb239306f

COVID-19: consensus construction

This workflow aims at generating reliable consensus sequences from variant @@ -181,5 +181,5 @@

[0.1]

  • Initial version of COVID-19: consensus construction
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/_payload.json b/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/_payload.json index 196bc887e..c1a37de1b 100644 --- a/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/_payload.json +++ b/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650445] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731651] \ No newline at end of file diff --git a/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/index.html b/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/index.html index 73b2a452c..8291c79ce 100644 --- a/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/index.html +++ b/workflow/0808b15a-7e3e-4b06-b804-f3d2cc73981a/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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kmer-profiling-hifi-VGP1

  • Author(s):
  • VGP
  • Galaxy
  • Release: 0.1.7
  • License: CC-BY-4.0
  • UniqueID: 0808b15a-7e3e-4b06-b804-f3d2cc73981a

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

@@ -109,5 +109,5 @@

Added

  • First version of the workflow.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/_payload.json b/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/_payload.json index 49ae959c8..b249bd1e0 100644 --- a/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/_payload.json +++ b/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649819] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731099] \ No newline at end of file diff --git a/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/index.html b/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/index.html index a1eee0d09..27db8ba81 100644 --- a/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/index.html +++ b/workflow/0b976704-e1e0-4cc3-9e75-38bda67c01ff/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Nanopore Preprocessing

Microbiome - QC and Contamination Filtering

Nanopore Preprocessing

Before starting any analysis, it is always a good idea to assess the quality of your input data and to discard poor-quality base content by trimming and filtering reads.

Generally, we are not interested in the host sequences, but rather only those originating from the pathogen itself. It is important to get rid of all host sequences and to only retain sequences that might include a pathogen, both in order to speed up further steps and to avoid host sequences compromising the analysis.

@@ -64,5 +64,5 @@

Output Datasets

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/_payload.json b/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/_payload.json index 5ec73aef1..538292935 100644 --- a/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/_payload.json +++ b/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650558] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731788] \ No newline at end of file diff --git a/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/index.html b/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/index.html index a1f84f212..8a76e4c5a 100644 --- a/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/index.html +++ b/workflow/11d717f8-92ef-4dd7-bda7-c193175fece2/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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dada2 amplicon analysis pipeline - for paired end data

dada2 amplicon analysis for paired end data The workflow has three main outputs: @@ -101,5 +101,5 @@

Automatic update

[0.1] 2024-01-09

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/_payload.json b/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/_payload.json index 5512f9596..7d4ef964b 100644 --- a/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/_payload.json +++ b/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649828] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731101] \ No newline at end of file diff --git a/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/index.html b/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/index.html index de387f89b..68a4ef1eb 100644 --- a/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/index.html +++ b/workflow/15c3229d-8786-457f-a020-7aa64c0cf6e8/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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.

  • Author(s):
  • Marius van den Beek
  • IWC
  • Release: 0.1.14
  • License: MIT
  • UniqueID: 15c3229d-8786-457f-a020-7aa64c0cf6e8

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, and is therefore @@ -126,5 +126,5 @@

Added

  • Initial version of Parallel Accession Download workflow.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/16455667-cdef-4979-9603-f338e09aa2a1/_payload.json b/workflow/16455667-cdef-4979-9603-f338e09aa2a1/_payload.json index 80a102090..1d230a3f6 100644 --- a/workflow/16455667-cdef-4979-9603-f338e09aa2a1/_payload.json +++ b/workflow/16455667-cdef-4979-9603-f338e09aa2a1/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650111] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731378] \ No newline at end of file diff --git a/workflow/16455667-cdef-4979-9603-f338e09aa2a1/index.html b/workflow/16455667-cdef-4979-9603-f338e09aa2a1/index.html index b5eff6319..62f522314 100644 --- a/workflow/16455667-cdef-4979-9603-f338e09aa2a1/index.html +++ b/workflow/16455667-cdef-4979-9603-f338e09aa2a1/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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MMGBSA calculations with GROMACS

MMGBSA simulation and calculation

  • Author(s):
  • Simon Bray
  • Release: 0.1.5
  • License: MIT
  • UniqueID: 16455667-cdef-4979-9603-f338e09aa2a1

GROMACS MMGBSA free energy calculation

Perform an ensemble of MD simulations of a user-specified size using GROMACS, and calculate MMGBSA free energies using AmberTools. An ensemble average is @@ -90,5 +90,5 @@

[0.1]

  • Initial version of GROMACS MMGBSA workflow.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/_payload.json b/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/_payload.json index a103c7c53..f9babc900 100644 --- a/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/_payload.json +++ b/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650302] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731535] \ No newline at end of file diff --git a/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/index.html b/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/index.html index e54a0967b..66dd6d530 100644 --- a/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/index.html +++ b/workflow/1834d09c-c683-4424-bc8d-57df156c2fc8/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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ChIPseq_PE

This workflow takes as input a collection of paired fastqs. Remove adapters with cutadapt, map pairs with bowtie2. Keep MAPQ30 and concordant pairs. MACS2 for paired bam.

  • Author(s):
  • Lucille Delisle
  • Release: 0.12
  • License: MIT
  • UniqueID: 1834d09c-c683-4424-bc8d-57df156c2fc8

ChIP-seq paired-end Workflow

Inputs dataset

    @@ -145,5 +145,5 @@

    2022-10-20

    ChIPseq_PE has been renamed chipseq-pe (still version 0.1)

    [0.1] 2022-10-06

    First release.

    -
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/1936816b-958a-4140-b839-58be4cdae1a5/_payload.json b/workflow/1936816b-958a-4140-b839-58be4cdae1a5/_payload.json index 4c326b82d..f1f9234fc 100644 --- a/workflow/1936816b-958a-4140-b839-58be4cdae1a5/_payload.json +++ b/workflow/1936816b-958a-4140-b839-58be4cdae1a5/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650054] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731297] \ No newline at end of file diff --git a/workflow/1936816b-958a-4140-b839-58be4cdae1a5/index.html b/workflow/1936816b-958a-4140-b839-58be4cdae1a5/index.html index 69e4dfba7..c607b7ef3 100644 --- a/workflow/1936816b-958a-4140-b839-58be4cdae1a5/index.html +++ b/workflow/1936816b-958a-4140-b839-58be4cdae1a5/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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baredSC_2d_logNorm

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

  • Author(s):
  • Lucille Delisle
  • Release: 0.5
  • License: MIT
  • UniqueID: 1936816b-958a-4140-b839-58be4cdae1a5

BaredSC Workflows

These workflows allow to run a baredSC analysis from a table with counts in a single click. It uses models from 1 to N Gaussians and combine them. It uses the logNorm scale, 100 bins for 1 dimension and 25 bins on each axis in 2 dimensions.

Inputs dataset

@@ -114,5 +114,5 @@

Automatic update

[0.1] 2023-10-03

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/_payload.json b/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/_payload.json index 3aab2e363..e76bbaaab 100644 --- a/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/_payload.json +++ b/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650023] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731292] \ No newline at end of file diff --git a/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/index.html b/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/index.html index 83b9d2312..317a311fb 100644 --- a/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/index.html +++ b/workflow/1ea0b92d-d863-435a-96ac-1e547fdbc994/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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baredSC_1d_logNorm

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

  • Author(s):
  • Lucille Delisle
  • Release: 0.5
  • License: MIT
  • UniqueID: 1ea0b92d-d863-435a-96ac-1e547fdbc994

BaredSC Workflows

These workflows allow to run a baredSC analysis from a table with counts in a single click. It uses models from 1 to N Gaussians and combine them. It uses the logNorm scale, 100 bins for 1 dimension and 25 bins on each axis in 2 dimensions.

Inputs dataset

@@ -114,5 +114,5 @@

Automatic update

[0.1] 2023-10-03

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/2196fbff-317e-437d-a022-696a1f95a850/_payload.json b/workflow/2196fbff-317e-437d-a022-696a1f95a850/_payload.json index 137cd4955..668191c95 100644 --- a/workflow/2196fbff-317e-437d-a022-696a1f95a850/_payload.json +++ b/workflow/2196fbff-317e-437d-a022-696a1f95a850/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650309] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731540] \ No newline at end of file diff --git a/workflow/2196fbff-317e-437d-a022-696a1f95a850/index.html b/workflow/2196fbff-317e-437d-a022-696a1f95a850/index.html index 141a3d915..78464147c 100644 --- a/workflow/2196fbff-317e-437d-a022-696a1f95a850/index.html +++ b/workflow/2196fbff-317e-437d-a022-696a1f95a850/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Hi-C_fastqToCool_hicup_cooler

This workflow takes as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file using the middle of the fragment as coordinates. The pairs are filtered for MAPQ and sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.

  • Author(s):
  • Lucille Delisle
  • Release: 0.3
  • License: MIT
  • UniqueID: 2196fbff-317e-437d-a022-696a1f95a850

Hi-C (hic_fastq_to_cool_hicup_cooler) and region capture Hi-C (chic_fastq_to_cool_hicup_cooler) Workflows

This can also be used for Hi-ChIP experiments, in that case the output with matrix with iced values is ignored and the matrix to use is matrix with raw values.

Input datasets

@@ -123,5 +123,5 @@

Manual update

[0.1] 2023-01-16

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/_payload.json b/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/_payload.json index 1fa17f47c..70007f597 100644 --- a/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/_payload.json +++ b/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650399] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731608] \ No newline at end of file diff --git a/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/index.html b/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/index.html index 25ac6d9b1..0dd475e6c 100644 --- a/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/index.html +++ b/workflow/242ed0e9-f1fc-4eb0-af99-8328211f5998/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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RNAseq_PE

This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.

  • Author(s):
  • Lucille Delisle
  • Release: 0.9
  • License: MIT
  • UniqueID: 242ed0e9-f1fc-4eb0-af99-8328211f5998

RNA-seq paired-end Workflow

Inputs dataset

    @@ -154,5 +154,5 @@

    Automatic update

[0.1] 2022-10-21

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/_payload.json b/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/_payload.json index 179112a8c..1363eb9d6 100644 --- a/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/_payload.json +++ b/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650530] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731752] \ No newline at end of file diff --git a/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/index.html b/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/index.html index 5d39fd02d..5fea13f3e 100644 --- a/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/index.html +++ b/workflow/2988562a-fa7a-4135-bf67-943ab03d1517/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Assembly-Hifi-only-VGP3

  • Author(s):
  • Galaxy
  • VGP
  • Release: 0.2.1
  • License: CC-BY-4.0
  • UniqueID: 2988562a-fa7a-4135-bf67-943ab03d1517

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

@@ -157,5 +157,5 @@

[0.1.1] 2023-11-20

[0.1] - 2023-09-26

Addition of the workflow to the iwc repository.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/_payload.json b/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/_payload.json index 5918c02ef..4c2a6a111 100644 --- a/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/_payload.json +++ b/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650315] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731545] \ No newline at end of file diff --git a/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/index.html b/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/index.html index 00835d6ca..5dffc51d5 100644 --- a/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/index.html +++ b/workflow/2a89cbe4-a69f-4bff-9465-2e04b0217e35/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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cHi-C_fastqToCool_hicup_cooler

This workflow take as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. The pairs are filtered for MAPQ and for the region captured. Then, they are sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.

  • Author(s):
  • Lucille Delisle
  • Release: 0.3
  • License: MIT
  • UniqueID: 2a89cbe4-a69f-4bff-9465-2e04b0217e35

Hi-C (hic_fastq_to_cool_hicup_cooler) and region capture Hi-C (chic_fastq_to_cool_hicup_cooler) Workflows

This can also be used for Hi-ChIP experiments, in that case the output with matrix with iced values is ignored and the matrix to use is matrix with raw values.

Input datasets

@@ -123,5 +123,5 @@

Manual update

[0.1] 2023-01-16

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/_payload.json b/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/_payload.json index 9a69c847e..c6140c0f2 100644 --- a/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/_payload.json +++ b/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650623] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731853] \ No newline at end of file diff --git a/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/index.html b/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/index.html index 73cecf2bb..bf32dd4be 100644 --- a/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/index.html +++ b/workflow/300b5a7d-f763-486a-a8ea-87ea84571f19/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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QIIME2 VI: Diversity metrics and estimations

The first step in hypothesis testing in microbial ecology is typically to look at within- (alpha) and between-sample (beta) diversity. We can calculate diversity metrics, apply appropriate statistical tests, and visualize the data using the q2-diversity plugin.

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.1
  • License: MIT
  • UniqueID: 300b5a7d-f763-486a-a8ea-87ea84571f19

QIIME2 workflows

Available workflows

    @@ -118,5 +118,5 @@

    Outputs

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/3163175d-7673-42d9-8aae-505afbd74946/_payload.json b/workflow/3163175d-7673-42d9-8aae-505afbd74946/_payload.json index ec8fba618..f3dd5e92b 100644 --- a/workflow/3163175d-7673-42d9-8aae-505afbd74946/_payload.json +++ b/workflow/3163175d-7673-42d9-8aae-505afbd74946/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650618] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731844] \ No newline at end of file diff --git a/workflow/3163175d-7673-42d9-8aae-505afbd74946/index.html b/workflow/3163175d-7673-42d9-8aae-505afbd74946/index.html index 228445772..d96f5fb5f 100644 --- a/workflow/3163175d-7673-42d9-8aae-505afbd74946/index.html +++ b/workflow/3163175d-7673-42d9-8aae-505afbd74946/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis

This workflow - Reconstruct phylogeny (insert fragments in a reference) - Alpha rarefaction analysis @@ -121,5 +121,5 @@

Outputs

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/33862923-af05-48ba-aec5-14393981cee2/_payload.json b/workflow/33862923-af05-48ba-aec5-14393981cee2/_payload.json index b14552e25..1b19c1dbc 100644 --- a/workflow/33862923-af05-48ba-aec5-14393981cee2/_payload.json +++ b/workflow/33862923-af05-48ba-aec5-14393981cee2/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650001] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731273] \ No newline at end of file diff --git a/workflow/33862923-af05-48ba-aec5-14393981cee2/index.html b/workflow/33862923-af05-48ba-aec5-14393981cee2/index.html index 8befc9a02..dc55ff8bf 100644 --- a/workflow/33862923-af05-48ba-aec5-14393981cee2/index.html +++ b/workflow/33862923-af05-48ba-aec5-14393981cee2/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Velocyto-on10X-filtered-barcodes

Run velocyto to get loom with counts of spliced and unspliced

  • Author(s):
  • Lucille Delisle
  • Release: 0.2
  • License: MIT
  • UniqueID: 33862923-af05-48ba-aec5-14393981cee2

Velocyto on 10X data

These workflows simply run velocyto. There are 2 workflows because one can be easily run after the 'fastq-to-matrix-10x' workflows (Velocyto-on10X-from-bundled). The other can be easily run from uploaded datasets (Velocyto-on10X-filtered-barcodes).

Input datasets

@@ -68,5 +68,5 @@

Automatic update

[0.1] 2024-01-26

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/_payload.json b/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/_payload.json index 4e88128b2..6c4f4f72e 100644 --- a/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/_payload.json +++ b/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649830] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731103] \ No newline at end of file diff --git a/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/index.html b/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/index.html index 44e6c6644..705b6a6b5 100644 --- a/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/index.html +++ b/workflow/363898af-e598-4f0e-abd9-e6ded395ce66/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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.

SRA manifest to concatenated fastqs

This workflow takes as input a SRA manifest from SRA Run Selector (or a tabular with a header line), downloads all sequencing run data from the SRA and arranges it into per-sample fastq or pairs of fastq datasets.

It will work out the relationship between runs and samples from the user-indicated run and sample columns in the input and will concatenate sequencing run data as needed to obtain per-sample datasets.

@@ -134,5 +134,5 @@

Automatic update

[0.1] 2023-10-23

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/_payload.json b/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/_payload.json index 3bd75e25b..fc31b940c 100644 --- a/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/_payload.json +++ b/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650491] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731721] \ No newline at end of file diff --git a/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/index.html b/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/index.html index 8427f23b6..a85011754 100644 --- a/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/index.html +++ b/workflow/3cacf798-0f32-43b9-82c0-2d8f76312c80/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Assembly-Hifi-Trio-phasing-VGP5

  • Author(s):
  • Galaxy
  • VGP
  • Release: 0.2
  • License: CC-BY-4.0
  • UniqueID: 3cacf798-0f32-43b9-82c0-2d8f76312c80

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

@@ -155,5 +155,5 @@

[0.1.1] 2023-11-20

[0.1] - 2023-09-27

Creation of workflow for Trio assembly.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/_payload.json b/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/_payload.json index 31d19d907..a24f89210 100644 --- a/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/_payload.json +++ b/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650068] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731336] \ No newline at end of file diff --git a/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/index.html b/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/index.html index b6d05a6af..c5870e42e 100644 --- a/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/index.html +++ b/workflow/3d86e5fc-cad1-4e21-8ecc-d0e6637899bc/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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

  • Author(s):
  • Peter van Heusden
  • Release: 0.2.3
  • License: MIT
  • UniqueID: 3d86e5fc-cad1-4e21-8ecc-d0e6637899bc

COVID-19 sequence analysis on Illumina Amplicon PE data

This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf, covid-19-signal and the Thiagen Titan workflow. These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK, CanCOGeN and some US state public health laboratories.

@@ -109,5 +109,5 @@

[0.1] - 2021-06-20

  • Initial version of SARS-CoV-2 Illumina Amplicon pipeline - iVar based for IWC
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/_payload.json b/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/_payload.json index ca6587903..ba9c34a7f 100644 --- a/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/_payload.json +++ b/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650472] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731712] \ No newline at end of file diff --git a/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/index.html b/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/index.html index b775b221a..26ea141eb 100644 --- a/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/index.html +++ b/workflow/40c0a173-1805-46c6-9005-5ead67bc9f48/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Generate Nx and Size plots for multiple assemblies

  • Author(s):
  • VGP
  • Delphine Lariviere
  • Release: 0.1.1
  • License:
  • UniqueID: 40c0a173-1805-46c6-9005-5ead67bc9f48

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

@@ -62,5 +62,5 @@

Automatic update

[0.1] - 2024-05-11

Addition of the workflow to the iwc repository.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/_payload.json b/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/_payload.json index 33e48a156..28452f756 100644 --- a/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/_payload.json +++ b/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649817] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731098] \ No newline at end of file diff --git a/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/index.html b/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/index.html index 925396b46..72f10bb76 100644 --- a/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/index.html +++ b/workflow/435875a1-72c4-4fda-8943-3a78f25c6574/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Allele-based Pathogen Identification

Microbiome - Variant calling and Consensus Building

Allele-based Pathogen Identification

This workflow identifies pathogens using an allelic approach, detecting Single Nucleotide Polymorphisms (SNPs) to track emerging variants, i.e. markers showing evolutionary histories of homogeneous strains. This process includes SNP calling, aimed at identifying novel pathogen strains and elucidating discrepancies compared to reference sequences, thereby facilitating the tracking of emerging variants. Within this workflow, both variants and SNPs are discerned, serving as crucial elements for subsequent pathogen identification and variant tracking purposes.

Input Datasets

@@ -68,5 +68,5 @@

Automatic update

[0.1] 2024-06-19

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/_payload.json b/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/_payload.json index 010a851c4..3602cf633 100644 --- a/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/_payload.json +++ b/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649832] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731105] \ No newline at end of file diff --git a/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/index.html b/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/index.html index 1c0ab0620..899f71687 100644 --- a/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/index.html +++ b/workflow/470536e7-ac58-4859-94d6-2085be9c2e17/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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 RNA-seq fastq to matrix for 10X data

These workflows are inspired by the training material. Except that the output is in a 'bundle' format: three files (one matrix, one with genes, one with barcodes) which is similar to the cellranger output format.

Both are designed for fastqs from 10X libraries v3. One is for regular 10X library (one library per sample), while the other one is for CellPlex 10X library which allows to multiplex samples using CMOs (see this blog article).

@@ -140,5 +140,5 @@

Tool updates

[0.1] 2023-12-21

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/_payload.json b/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/_payload.json index 48fa5ab6d..f3cc07f7b 100644 --- a/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/_payload.json +++ b/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650334] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731555] \ No newline at end of file diff --git a/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/index.html b/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/index.html index 6f8bf5c22..01b90b198 100644 --- a/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/index.html +++ b/workflow/48733b55-4cde-45d4-a69e-78faff0db3f5/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Hi-C_juicermediumtabixToCool_cooler

This workflow uses as input a collection of juicer medium tabix files and a genome name. It builds balanced cool file to the desired resolution.

  • Author(s):
  • Lucille Delisle
  • Release: 0.3
  • License: MIT
  • UniqueID: 48733b55-4cde-45d4-a69e-78faff0db3f5

Hi-C (hic_fastq_to_cool_hicup_cooler) and region capture Hi-C (chic_fastq_to_cool_hicup_cooler) Workflows

This can also be used for Hi-ChIP experiments, in that case the output with matrix with iced values is ignored and the matrix to use is matrix with raw values.

Input datasets

@@ -123,5 +123,5 @@

Manual update

[0.1] 2023-01-16

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/_payload.json b/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/_payload.json index 5d58120f8..7982ea012 100644 --- a/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/_payload.json +++ b/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650341] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731561] \ No newline at end of file diff --git a/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/index.html b/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/index.html index 3f6131e34..2fd636ae0 100644 --- a/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/index.html +++ b/workflow/48f579ea-eaac-49ee-b38f-93c82f8b7d76/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Hi-C_fastqToPairs_hicup

This workflow takes as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. First truncate the fastq using the cutting sequence to guess the fill-in. Then map the truncated fastq. Then asign to fragment and filter the self-ligated and dandling ends or internal (it can also filter for the size). Then it removes the duplicates. Convert the output to be compatible with juicebox or cooler using the middle of the fragment as coordinates. Finally filter for mapping quality

  • Author(s):
  • Lucille Delisle
  • Release: 0.3
  • License: MIT
  • UniqueID: 48f579ea-eaac-49ee-b38f-93c82f8b7d76

Hi-C (hic_fastq_to_cool_hicup_cooler) and region capture Hi-C (chic_fastq_to_cool_hicup_cooler) Workflows

This can also be used for Hi-ChIP experiments, in that case the output with matrix with iced values is ignored and the matrix to use is matrix with raw values.

Input datasets

@@ -123,5 +123,5 @@

Manual update

[0.1] 2023-01-16

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/_payload.json b/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/_payload.json index 0267bd32f..efbc0dc25 100644 --- a/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/_payload.json +++ b/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650641] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731866] \ No newline at end of file diff --git a/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/index.html b/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/index.html index cd59de89c..45a3c6c97 100644 --- a/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/index.html +++ b/workflow/4b4dda98-7422-4207-b9bd-62c11ce8e0f0/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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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). @@ -89,5 +89,5 @@

Main steps

All notable changes to this project will be documented in this file.

[1.0] - 2023-11-22

First release

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/5171bc59-590c-4e97-8db8-004f73928627/_payload.json b/workflow/5171bc59-590c-4e97-8db8-004f73928627/_payload.json index 092140a62..cb2d74e65 100644 --- a/workflow/5171bc59-590c-4e97-8db8-004f73928627/_payload.json +++ b/workflow/5171bc59-590c-4e97-8db8-004f73928627/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650075] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731342] \ No newline at end of file diff --git a/workflow/5171bc59-590c-4e97-8db8-004f73928627/index.html b/workflow/5171bc59-590c-4e97-8db8-004f73928627/index.html index 0a0c9898f..beb38813a 100644 --- a/workflow/5171bc59-590c-4e97-8db8-004f73928627/index.html +++ b/workflow/5171bc59-590c-4e97-8db8-004f73928627/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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

  • Author(s):
  • Wolfgang Maier
  • Release: 0.1.5
  • License: MIT
  • UniqueID: 5171bc59-590c-4e97-8db8-004f73928627

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 and variant @@ -82,5 +82,5 @@

[0.1]

  • Initial version of COVID-19: variation analysis on WGS SE data workflow
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/_payload.json b/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/_payload.json index 362a3089c..c1a5d8e26 100644 --- a/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/_payload.json +++ b/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650500] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731748] \ No newline at end of file diff --git a/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/index.html b/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/index.html index c081aae9a..af4a51b50 100644 --- a/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/index.html +++ b/workflow/57920bf9-1741-4170-badf-39fdfcdaa2e9/index.html @@ -31,22 +31,22 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Mitogenome-Assembly-VGP0

  • Author(s):
  • VGP
  • Galaxy
  • Release: 0.1
  • License: CC-BY-4.0
  • UniqueID: 57920bf9-1741-4170-badf-39fdfcdaa2e9

No README available.

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/_payload.json b/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/_payload.json index db09cacd7..808c19f9b 100644 --- a/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/_payload.json +++ b/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650610] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731836] \ No newline at end of file diff --git a/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/index.html b/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/index.html index 23e958278..ead20f1ef 100644 --- a/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/index.html +++ b/workflow/5a57f873-52f8-4c51-9e8d-e747d32d183a/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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QIIME2 Ic: Demultiplexed data (single-end)

Importing demultiplexed data (single-end)

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.2
  • License: MIT
  • UniqueID: 5a57f873-52f8-4c51-9e8d-e747d32d183a

QIIME2 import workflows

Available workflows

Import of fastqsanger.gz data into QIIME artifact files.

@@ -101,5 +101,5 @@

[0.1] 2024-04-08

First release.

[0.2] 2024-05-23

Fix dockstore.yml and test.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/_payload.json b/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/_payload.json index 9fb53b45e..ec75fc961 100644 --- a/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/_payload.json +++ b/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650097] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731364] \ No newline at end of file diff --git a/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/index.html b/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/index.html index 67107ea9a..40df074c8 100644 --- a/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/index.html +++ b/workflow/6695eb16-30a5-42ea-8591-56f2630cf8bf/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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

  • Author(s):
  • Wolfgang Maier
  • Release: 0.2.4
  • License: MIT
  • UniqueID: 6695eb16-30a5-42ea-8591-56f2630cf8bf

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 and variant @@ -84,5 +84,5 @@

[0.1]

  • Initial version of COVID-19: variation analysis on WGS PE data workflow
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/_payload.json b/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/_payload.json index 917beb667..e42905d86 100644 --- a/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/_payload.json +++ b/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650144] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731402] \ No newline at end of file diff --git a/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/index.html b/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/index.html index b6a07d1e0..68090a6fc 100644 --- a/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/index.html +++ b/workflow/68d6270a-bfd1-452a-abc9-4a314e13af85/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Assembly polishing with long reads

Racon polish with long reads, x4

  • Author(s):
  • Anna Syme
  • Release: 0.1
  • License: MIT
  • UniqueID: 68d6270a-bfd1-452a-abc9-4a314e13af85

Assembly polishing with Racon workflow

Inputs

    @@ -76,5 +76,5 @@

    Outputs

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/_payload.json b/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/_payload.json index 4d38a7144..2af865313 100644 --- a/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/_payload.json +++ b/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650351] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731581] \ No newline at end of file diff --git a/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/index.html b/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/index.html index 1cd062b95..f42493dc8 100644 --- a/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/index.html +++ b/workflow/6a424c0e-eb24-4f61-8750-adc09f4db1b1/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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RNAseq_SR

This workflow takes as input a list of single-reads fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.

  • Author(s):
  • Lucille Delisle
  • Release: 0.9
  • License: MIT
  • UniqueID: 6a424c0e-eb24-4f61-8750-adc09f4db1b1

RNA-seq single-read Workflow

Inputs dataset

    @@ -157,5 +157,5 @@

    Automatic update

[0.1] 2022-10-12

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/_payload.json b/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/_payload.json index 04fb62f50..34fd1df5e 100644 --- a/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/_payload.json +++ b/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650584] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731808] \ No newline at end of file diff --git a/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/index.html b/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/index.html index 91378b253..595a299a7 100644 --- a/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/index.html +++ b/workflow/718df5b9-9cbb-4792-be50-604e18ef0548/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)

Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.2
  • License: MIT
  • UniqueID: 718df5b9-9cbb-4792-be50-604e18ef0548

QIIME2 workflows

Available workflows

Denoising (using qiime2's dada2 integration for paired / single end data.

@@ -78,5 +78,5 @@

[0.1] 2024-04-08

First release.

[0.2] 2024-05-23

Fix dockstore.yml.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/_payload.json b/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/_payload.json index 5bb927d91..9575b2fa2 100644 --- a/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/_payload.json +++ b/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650458] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731698] \ No newline at end of file diff --git a/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/index.html b/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/index.html index 23e16a20c..198bba7cb 100644 --- a/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/index.html +++ b/workflow/727b2b8c-3ff1-4736-952d-b2c215c0faa1/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Purging-duplicates-one-haplotype-VGP6b

  • Author(s):
  • Galaxy
  • VGP
  • Release: 0.7.1
  • License: CC-BY-4.0
  • UniqueID: 727b2b8c-3ff1-4736-952d-b2c215c0faa1

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

@@ -128,5 +128,5 @@

Added

  • Workflow for purging duplication in contigs in single haplotype
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/_payload.json b/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/_payload.json index 136bc584a..8c68f5c21 100644 --- a/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/_payload.json +++ b/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650103] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731370] \ No newline at end of file diff --git a/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/index.html b/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/index.html index b2d166f58..6a396883a 100644 --- a/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/index.html +++ b/workflow/7950b716-2bc9-4cb6-8472-6506c702adea/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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dcTMD calculations with GROMACS

Perform dcTMD free energy simulations and calculations

  • Author(s):
  • Simon Bray
  • Release: 0.1.5
  • License: MIT
  • UniqueID: 7950b716-2bc9-4cb6-8472-6506c702adea

GROMACS dcTMD free energy calculation

Perform an ensemble of targeted MD simulations of a user-specified size using the GROMACS PULL code and calculate dcTMD free energy and friction profiles @@ -94,5 +94,5 @@

[0.1]

  • Initial version of GROMACS dcTMD workflow.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/_payload.json b/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/_payload.json index 35018bcc1..097690012 100644 --- a/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/_payload.json +++ b/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650250] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731470] \ No newline at end of file diff --git a/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/index.html b/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/index.html index 144ac4439..4cf41b228 100644 --- a/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/index.html +++ b/workflow/83ef6fdc-b8a9-41af-a824-0225f0199e63/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Genome assembly with Flye

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

  • Author(s):
  • Anna Syme
  • Release: 0.2
  • License: MIT
  • UniqueID: 83ef6fdc-b8a9-41af-a824-0225f0199e63

Genome assembly with Flye workflow

Why use this workflow?

    @@ -88,5 +88,5 @@

    Automatic update

    and this project adheres to Semantic Versioning.

    [0.1] 2023-07-14

    First release.

    -
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/_payload.json b/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/_payload.json index f79c29c36..50f52a7fb 100644 --- a/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/_payload.json +++ b/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650087] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731354] \ No newline at end of file diff --git a/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/index.html b/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/index.html index b28c79262..865dcf73a 100644 --- a/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/index.html +++ b/workflow/864427b0-d25a-499c-b437-f83f2d6b83f2/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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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.

  • Author(s):
  • Wolfgang Maier
  • Release: 0.5.3
  • License: MIT
  • UniqueID: 864427b0-d25a-499c-b437-f83f2d6b83f2

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but @@ -219,5 +219,5 @@

[0.1]

  • Initial version of COVID-19: variation analysis on ARTIC PE data workflow
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/_payload.json b/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/_payload.json index dc4e59796..953eb06d3 100644 --- a/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/_payload.json +++ b/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649833] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731106] \ No newline at end of file diff --git a/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/index.html b/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/index.html index 338842374..5826397db 100644 --- a/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/index.html +++ b/workflow/87f25ddb-a663-4582-9ec6-d0b4bef4109c/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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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 RNA-seq fastq to matrix for 10X data

These workflows are inspired by the training material. Except that the output is in a 'bundle' format: three files (one matrix, one with genes, one with barcodes) which is similar to the cellranger output format.

Both are designed for fastqs from 10X libraries v3. One is for regular 10X library (one library per sample), while the other one is for CellPlex 10X library which allows to multiplex samples using CMOs (see this blog article).

@@ -140,5 +140,5 @@

Tool updates

[0.1] 2023-12-21

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/_payload.json b/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/_payload.json index da2045606..f94a77d1b 100644 --- a/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/_payload.json +++ b/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650589] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731812] \ No newline at end of file diff --git a/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/index.html b/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/index.html index 00e71fb25..06eb92d19 100644 --- a/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/index.html +++ b/workflow/8b8c4f4c-7cc0-422d-9a6f-47357faa0082/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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QIIME2 IIb: Denoising (sequence quality control) and feature table creation (paired-end)

Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.2
  • License: MIT
  • UniqueID: 8b8c4f4c-7cc0-422d-9a6f-47357faa0082

QIIME2 workflows

Available workflows

Denoising (using qiime2's dada2 integration for paired / single end data.

@@ -78,5 +78,5 @@

[0.1] 2024-04-08

First release.

[0.2] 2024-05-23

Fix dockstore.yml.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/_payload.json b/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/_payload.json index 0b8308d17..ef46b399a 100644 --- a/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/_payload.json +++ b/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649810] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731090] \ No newline at end of file diff --git a/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/index.html b/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/index.html index a3d16a8db..f655d887a 100644 --- a/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/index.html +++ b/workflow/8c2d765b-2764-4b66-8542-adc2109c24f2/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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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

  • Author(s):
  • Leonid Kostrykin
  • Release: 0.1
  • License: MIT
  • UniqueID: 8c2d765b-2764-4b66-8542-adc2109c24f2

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

@@ -60,5 +60,5 @@

[0.1] - 2024-02-29

  • Creation of workflow for segmentation and counting of cell nuclei in fluorescence microscopy images.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/_payload.json b/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/_payload.json index c3c308613..8bec886ed 100644 --- a/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/_payload.json +++ b/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650594] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731816] \ No newline at end of file diff --git a/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/index.html b/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/index.html index b5369cbdf..f9eb18e88 100644 --- a/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/index.html +++ b/workflow/951c418e-f57e-491d-af38-f2c44c6089ce/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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QIIME2 Ia: multiplexed data (single-end)

Importing single-end multiplexed data (not demultiplexed yet)

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.2
  • License: MIT
  • UniqueID: 951c418e-f57e-491d-af38-f2c44c6089ce

QIIME2 import workflows

Available workflows

Import of fastqsanger.gz data into QIIME artifact files.

@@ -101,5 +101,5 @@

[0.1] 2024-04-08

First release.

[0.2] 2024-05-23

Fix dockstore.yml and test.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/_payload.json b/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/_payload.json index b1dedb024..7b8ffabca 100644 --- a/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/_payload.json +++ b/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650295] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731529] \ No newline at end of file diff --git a/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/index.html b/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/index.html index 82e02f113..22932a82b 100644 --- a/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/index.html +++ b/workflow/98e9e34b-b203-43db-9a23-5fa72963fa6d/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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CUTandRUN

This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.

  • Author(s):
  • Lucille Delisle
  • Release: 0.13
  • License: MIT
  • UniqueID: 98e9e34b-b203-43db-9a23-5fa72963fa6d

CUT&RUN (and CUT&TAG) Workflow

Inputs dataset

    @@ -146,5 +146,5 @@

    Automatic update

[0.1] 2022-10-06

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/_payload.json b/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/_payload.json index 67df95f9f..ba9d7f8f9 100644 --- a/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/_payload.json +++ b/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650288] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731524] \ No newline at end of file diff --git a/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/index.html b/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/index.html index 7f4b74718..2eaf4b292 100644 --- a/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/index.html +++ b/workflow/9debc3c9-ccbd-4ce6-a7de-80580e663cac/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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ATACseq

This workflow takes as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will compute 2 normalization for coverage: normalized by million reads and normalized by million reads in peaks. Will plot the number of reads for each fragment length.

  • Author(s):
  • Lucille Delisle
  • Release: 0.17
  • License: MIT
  • UniqueID: 9debc3c9-ccbd-4ce6-a7de-80580e663cac

ATACseq Workflow

This workflow is highly concordant with the corresponding training material. You can have more information about ATAC-seq analysis in the slides and the tutorial.

@@ -191,5 +191,5 @@

Automatic update

[0.1] 2022-10-12

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/_payload.json b/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/_payload.json index bff1550b0..4de7d2189 100644 --- a/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/_payload.json +++ b/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650548] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731779] \ No newline at end of file diff --git a/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/index.html b/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/index.html index 27ef3fbbc..5bf8dc542 100644 --- a/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/index.html +++ b/workflow/9e94da53-d8ab-4713-8aac-7c6674fa1d39/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Generic 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.

  • Author(s):
  • Wolfgang Maier
  • Release: 0.1.1
  • License: MIT
  • UniqueID: 9e94da53-d8ab-4713-8aac-7c6674fa1d39

Generic variation analysis reporting

This workflow takes table of variants produced by any of the variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/variant-calling @@ -59,5 +59,5 @@

[0.1]

  • Initial version generic variation analysis reporting workflow
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/_payload.json b/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/_payload.json index a1bc3a5f9..b2c617fc7 100644 --- a/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/_payload.json +++ b/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650464] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731703] \ No newline at end of file diff --git a/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/index.html b/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/index.html index f65bd4ac3..6cd5e0cd0 100644 --- a/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/index.html +++ b/workflow/9fd3c0de-a497-47dc-96e3-0f3e1998173d/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Scaffolding-BioNano-VGP7

  • Author(s):
  • Galaxy
  • VGP
  • Release: 0.1.4
  • License: CC-BY-4.0
  • UniqueID: 9fd3c0de-a497-47dc-96e3-0f3e1998173d

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

@@ -86,5 +86,5 @@

Automatic update

[0.1] - 2023-11-01

Addition of the workflow to the iwc repository.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/_payload.json b/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/_payload.json index 9142072d5..175f88be4 100644 --- a/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/_payload.json +++ b/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650060] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731303] \ No newline at end of file diff --git a/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/index.html b/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/index.html index fa5371e9c..5f50ba07a 100644 --- a/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/index.html +++ b/workflow/a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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.

  • Author(s):
  • Wolfgang Maier
  • Release: 0.3.2
  • License: MIT
  • UniqueID: a1ceaf35-f3d7-452d-b5ed-53a4f429d1cf

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. 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.

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/_payload.json b/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/_payload.json index 241f01656..60626cc58 100644 --- a/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/_payload.json +++ b/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650637] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731857] \ No newline at end of file diff --git a/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/index.html b/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/index.html index 25f208211..fc8d03281 100644 --- a/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/index.html +++ b/workflow/a2b0d4f7-164c-40d3-ac34-f248db18bbef/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Mass spectrometry: GCMS with metaMS

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics. https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gcms/tutorial.html

  • Author(s):
  • workflow4metabolomics
  • Release: 0.1
  • License: MIT
  • UniqueID: a2b0d4f7-164c-40d3-ac34-f248db18bbef

Mass spectrometry: GCMS with metaMS

@@ -86,5 +86,5 @@

Main steps

All notable changes to this project will be documented in this file.

[0.1] - 2023-11-22

First release

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/_payload.json b/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/_payload.json index febda7602..eac5b2c10 100644 --- a/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/_payload.json +++ b/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650268] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731484] \ No newline at end of file diff --git a/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/index.html b/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/index.html index 2c55a932e..96053dec8 100644 --- a/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/index.html +++ b/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Get Confident Peaks From ChIP_PE replicates

This workflow takes as input PE BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using all subsets combined. Only peaks called using a combination of all subsets which have summits intersecting the intersection of at least x replicates will be kept.

  • Author(s):
  • Lucille Delisle
  • Release: 1.2
  • License: MIT
  • UniqueID: a2f66906-e9e3-42f9-8629-390017ed2db0

Consensus peaks Workflow

The goal of this workflow is to get a list of confident peaks with summits from n replicates.

Inputs dataset

@@ -140,5 +140,5 @@

Automatic update

[0.1] 2023-08-31

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/_payload.json b/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/_payload.json index 04d9e872f..364edb2cd 100644 --- a/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/_payload.json +++ b/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649826] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731100] \ No newline at end of file diff --git a/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/index.html b/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/index.html index 65aab7b8a..2c90be3a8 100644 --- a/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/index.html +++ b/workflow/a55428c8-9934-4941-93c4-3920b4ba3366/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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Taxonomy Profiling and Visualization with Krona

Microbiome - Taxonomy Profiling

Taxonomy Profiling and Visualisation with Krona

In this workflow, we identify the different organisms found in our samples by assigning taxonomy levels to the reads starting from the kingdom level down to the species level and visualise the result.

It’s important to check what might be the species of a possible pathogen to be found, it gets us closer to the investigation as well as discovering possible multiple pathogenetic infections if any existed.

@@ -62,5 +62,5 @@

Output Datasets

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/_payload.json b/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/_payload.json index 745aa21cd..6ace4e2e1 100644 --- a/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/_payload.json +++ b/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650450] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731657] \ No newline at end of file diff --git a/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/index.html b/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/index.html index 0ed0af260..aa0a9f33a 100644 --- a/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/index.html +++ b/workflow/aa4960d9-198d-4990-a393-a98efcd3070a/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Assembly-decontamination-VGP9

  • Author(s):
  • Nadolina Brajuka
  • Release: 0.3
  • License: BSD-3-Clause
  • UniqueID: aa4960d9-198d-4990-a393-a98efcd3070a

No README available.

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/_payload.json b/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/_payload.json index c62bb5141..66fe0923e 100644 --- a/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/_payload.json +++ b/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650382] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731587] \ No newline at end of file diff --git a/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/index.html b/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/index.html index e8cb340e4..724abd56c 100644 --- a/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/index.html +++ b/workflow/ac8ef6cb-1621-4b73-9362-8a460ef3c3a2/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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BREW3R

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

  • Author(s):
  • Lucille Delisle
  • Release: 0.2
  • License: GPL-3.0-or-later
  • UniqueID: ac8ef6cb-1621-4b73-9362-8a460ef3c3a2

BREW3R

BREW3R logo

BREW3R stands for Bulk RNA-seq Evidence-based Workflow for 3' UTR Reannotation.

@@ -76,5 +76,5 @@

Automatic update

[0.1] 2024-06-17

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/_payload.json b/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/_payload.json index 8f589faf0..56e2f6641 100644 --- a/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/_payload.json +++ b/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650468] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731708] \ No newline at end of file diff --git a/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/index.html b/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/index.html index 942d0185d..e4cf3ed50 100644 --- a/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/index.html +++ b/workflow/af01815b-5b66-4578-ade7-6e2caed0c19a/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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kmer-profiling-hifi-trio-VGP2

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

  • Author(s):
  • VGP
  • Galaxy
  • Release: 0.1.4
  • License: CC-BY-4.0
  • UniqueID: af01815b-5b66-4578-ade7-6e2caed0c19a

VGP Workflow #1

This workflow collects the metrics on the properties of the genome under consideration by analyzing the k-mer frequencies. It provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality. It uses reads from two parental genomes to partition long reads from the offspring into haplotype-specific k-mer databases.

Inputs

@@ -109,5 +109,5 @@

Added

  • First version of the workflow.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/_payload.json b/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/_payload.json index 64cc7a5e5..e03c7eb91 100644 --- a/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/_payload.json +++ b/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649808] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731088] \ No newline at end of file diff --git a/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/index.html b/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/index.html index 7db08fc87..5f68e57aa 100644 --- a/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/index.html +++ b/workflow/b03da1a7-fc6f-419f-aa2c-431a670f9a96/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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MetaProSIP OpenMS 2.8

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

  • Author(s):
  • Matthias Bernt
  • Release: 0.2
  • License: MIT
  • UniqueID: b03da1a7-fc6f-419f-aa2c-431a670f9a96

MetaProSIP: automated inference of elemental fluxes in microbial communities

Inputs dataset

    @@ -88,5 +88,5 @@

    Automatic update

[0.1] 2023-04-13

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/_payload.json b/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/_payload.json index 64ff08ac2..2085b6f4d 100644 --- a/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/_payload.json +++ b/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650081] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731347] \ No newline at end of file diff --git a/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/index.html b/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/index.html index 22d9cefed..0b1ae32ea 100644 --- a/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/index.html +++ b/workflow/b08c744d-7c61-4b58-ac5f-4b5886c3c643/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
IWC LogoGalaxy IWC - Workflow Library
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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.

  • Author(s):
  • Wolfgang Maier
  • Release: 0.3.4
  • License: MIT
  • UniqueID: b08c744d-7c61-4b58-ac5f-4b5886c3c643

COVID-19: variation analysis reporting

This workflow takes VCF datasets of variants produced by any of the "*-variant-calling" workflows in @@ -147,5 +147,5 @@

[0.1]

  • Initial version of COVID-19: variation analysis reporting
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/_payload.json b/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/_payload.json index a67dd5b13..96fee443c 100644 --- a/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/_payload.json +++ b/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650606] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731819] \ No newline at end of file diff --git a/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/index.html b/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/index.html index be7a518e5..c33fa007e 100644 --- a/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/index.html +++ b/workflow/b09b5420-bb7c-4f27-9c90-7e2031889379/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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QIIME2 Ib: multiplexed data (paired-end)

Importing paired-end multiplexed data (not demultiplexed yet)

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.2
  • License: MIT
  • UniqueID: b09b5420-bb7c-4f27-9c90-7e2031889379

QIIME2 import workflows

Available workflows

Import of fastqsanger.gz data into QIIME artifact files.

@@ -101,5 +101,5 @@

[0.1] 2024-04-08

First release.

[0.2] 2024-05-23

Fix dockstore.yml and test.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/_payload.json b/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/_payload.json index aee1585d6..8f12f5af9 100644 --- a/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/_payload.json +++ b/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650454] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731661] \ No newline at end of file diff --git a/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/index.html b/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/index.html index b2e5cefca..40a3406db 100644 --- a/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/index.html +++ b/workflow/b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Purge-duplicate-contigs-VGP6

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

  • Author(s):
  • Galaxy
  • VGP
  • Release: 0.4
  • License: CC-BY-4.0
  • UniqueID: b5d0e4ae-3041-4cbe-9d0e-a1140e5469dd

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

@@ -162,5 +162,5 @@

Added

  • Workflow for purging duplication in contigs
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/_payload.json b/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/_payload.json index beacc5882..9161e9c63 100644 --- a/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/_payload.json +++ b/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650107] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731374] \ No newline at end of file diff --git a/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/index.html b/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/index.html index bd137c66f..9b3baeb12 100644 --- a/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/index.html +++ b/workflow/bb767af6-3641-4a5e-843d-78508fd7577a/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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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

Fragment-based virtual screening with docking and pose scoring

Dock a compound library against a target protein with rDock and validate the poses generated against a reference fragment using SuCOS to compare the feature @@ -87,5 +87,5 @@

[0.1]

  • Initial version of fragment-based docking and scoring workflow.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/_payload.json b/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/_payload.json index 632b958b9..ec3c89ae5 100644 --- a/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/_payload.json +++ b/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650544] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731756] \ No newline at end of file diff --git a/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/index.html b/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/index.html index dd277aef6..137e9a59f 100644 --- a/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/index.html +++ b/workflow/be0d055d-25ac-422a-ae9c-b0efdfb5bf86/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Generic variation analysis on WGS PE data

Workflow for variant analysis against a reference genome in GenBank format

  • Author(s):
  • Anton Nekrutenko
  • Release: 0.1.1
  • License: MIT
  • UniqueID: be0d055d-25ac-422a-ae9c-b0efdfb5bf86

Generic 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 and variant @@ -59,5 +59,5 @@

[0.1]

  • Initial version of Generic variation analysis on WGS PE data workflow
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/_payload.json b/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/_payload.json index 86b0c81f0..fe81763b1 100644 --- a/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/_payload.json +++ b/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650149] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731418] \ No newline at end of file diff --git a/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/index.html b/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/index.html index 2cacd85d3..b2e56b6ba 100644 --- a/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/index.html +++ b/workflow/bfe7f341-07ef-4bfe-9b50-2bc7628d6c55/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Bacterial Genome Assembly using Shovill

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

  • Author(s):
  • abromics-consortium
  • ABRomics
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.4
  • License: GPL-3.0-or-later
  • UniqueID: bfe7f341-07ef-4bfe-9b50-2bc7628d6c55

Bacterial genome assembly workflow for paired end data (v1.0)

This workflow uses paired-end illumina trimmed reads fastq(.gz) files and executes the following steps:

    @@ -122,5 +122,5 @@

    [1.0] - 05-06-2024

    • First release
    -
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/_payload.json b/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/_payload.json index edb88f188..b404f1381 100644 --- a/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/_payload.json +++ b/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650256] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731475] \ No newline at end of file diff --git a/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/index.html b/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/index.html index 82c02ac91..830d865df 100644 --- a/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/index.html +++ b/workflow/c6ed4b0e-d719-4997-9860-ba99488ec332/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Average Bigwig between replicates

We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: @@ -104,5 +104,5 @@

Automatic update

[0.1] 2023-09-22

First release.

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/_payload.json b/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/_payload.json index 90e5d6a88..e57b75ecb 100644 --- a/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/_payload.json +++ b/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650477] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731716] \ No newline at end of file diff --git a/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/index.html b/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/index.html index b46d2919c..9a54c89fb 100644 --- a/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/index.html +++ b/workflow/cb0e2983-13df-451c-85a2-ee78c94a2bd2/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Assembly-Hifi-HiC-phasing-VGP4

  • Author(s):
  • Galaxy
  • VGP
  • Delphine Lariviere
  • Release: 0.2.2
  • License: CC-BY-4.0
  • UniqueID: cb0e2983-13df-451c-85a2-ee78c94a2bd2

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

@@ -167,5 +167,5 @@

[0.1] - 2023-09-27

  • Creation of workflow for HiFi assembly with Hi-C phasing.
-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/cb26018e-9d2f-4513-a372-122474df703e/_payload.json b/workflow/cb26018e-9d2f-4513-a372-122474df703e/_payload.json index b5464c372..3e53664f5 100644 --- a/workflow/cb26018e-9d2f-4513-a372-122474df703e/_payload.json +++ b/workflow/cb26018e-9d2f-4513-a372-122474df703e/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649816] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731096] \ No newline at end of file diff --git a/workflow/cb26018e-9d2f-4513-a372-122474df703e/index.html b/workflow/cb26018e-9d2f-4513-a372-122474df703e/index.html index 134da27ef..46518614b 100644 --- a/workflow/cb26018e-9d2f-4513-a372-122474df703e/index.html +++ b/workflow/cb26018e-9d2f-4513-a372-122474df703e/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation

Pathogens of all samples report generation and visualization

Pathogen Detection: PathoGFAIR Samples Aggregation and Visualisation

In this workflow, we will aggregate results and use the results from 3 workflows (Nanopore Preprocessing, Gene-based Pathogen Identification and Nanopore Allele-based Pathogen Identification) to help track pathogens among samples and visualise all performed analysis by:

    @@ -58,5 +58,5 @@
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/d55a9e46-a205-4143-b92f-3783499063ed/_payload.json b/workflow/d55a9e46-a205-4143-b92f-3783499063ed/_payload.json index b5e96a805..0a3d0c695 100644 --- a/workflow/d55a9e46-a205-4143-b92f-3783499063ed/_payload.json +++ b/workflow/d55a9e46-a205-4143-b92f-3783499063ed/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649812] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731092] \ No newline at end of file diff --git a/workflow/d55a9e46-a205-4143-b92f-3783499063ed/index.html b/workflow/d55a9e46-a205-4143-b92f-3783499063ed/index.html index 1f19b2b5d..eb5b0e0c2 100644 --- a/workflow/d55a9e46-a205-4143-b92f-3783499063ed/index.html +++ b/workflow/d55a9e46-a205-4143-b92f-3783499063ed/index.html @@ -31,22 +31,22 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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bacterial_genome_annotation

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

  • Author(s):
  • ABRomics
  • abromics-consortium
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.6
  • License: GPL-3.0-or-later
  • UniqueID: d55a9e46-a205-4143-b92f-3783499063ed

Bacterial genome annotation workflow (v1.0)

+ + +
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bacterial_genome_annotation

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

  • Author(s):
  • ABRomics
  • abromics-consortium
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.7
  • License: GPL-3.0-or-later
  • UniqueID: d55a9e46-a205-4143-b92f-3783499063ed

Bacterial genome annotation workflow (v1.0)

This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:

  1. Genomic annotation
      @@ -104,6 +104,12 @@

      Outputs

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/_payload.json b/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/_payload.json index 5af6cbf89..22c834b88 100644 --- a/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/_payload.json +++ b/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649815] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731095] \ No newline at end of file diff --git a/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/index.html b/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/index.html index 40ce7e4f6..4c8204a7a 100644 --- a/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/index.html +++ b/workflow/d6795753-1562-4ccc-8f9c-f598acd5404e/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Gene-based Pathogen Identification

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

Gene-based Pathogen Identification

In this workflow, we determine whether the samples are pathogenic or not, by looking for genes known to be linked to pathogenicity or to the pathogenecity character of the organism.

    @@ -72,5 +72,5 @@

    Output Datasets

- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/_payload.json b/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/_payload.json index 1586350b4..2fcf5cbde 100644 --- a/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/_payload.json +++ b/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650496] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731731] \ No newline at end of file diff --git a/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/index.html b/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/index.html index 4eb975a47..e43b6967e 100644 --- a/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/index.html +++ b/workflow/dbe64df1-13fc-49fa-8a14-ead72f9d7ea1/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Scaffolding with Hi-C data VGP8

Scaffolding using HiC data with YAHS.

  • Author(s):
  • VGP
  • Galaxy
  • Release: 0.2.8
  • License: CC-BY-4.0
  • UniqueID: dbe64df1-13fc-49fa-8a14-ead72f9d7ea1

Scaffolding with HiC data

This workflow perfoms scaffolding using HiC data with YAHS. It is designed to be run as part of one the VGP analysis trajectories. Example of trajectory :

@@ -140,5 +140,5 @@

[0.1.1] - 2023-10-26

Added tags for better visibility of outputs in the history, and exposure of the BUSCO lineage parameter

[0.1] - 2023-09-27

Creation of the workflow and tests

-
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/_payload.json b/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/_payload.json index 1b244c4d5..b654f94fd 100644 --- a/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/_payload.json +++ b/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649814] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731094] \ No newline at end of file diff --git a/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/index.html b/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/index.html index 8095e6d12..622512cfa 100644 --- a/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/index.html +++ b/workflow/dfcedd6a-9dc1-4dcd-8b15-dbd21482f463/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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amr_gene_detection

Antimicrobial resistance gene detection from assembled bacterial genomes

  • Author(s):
  • ABRomics
  • abromics-consortium
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.4
  • License: GPL-3.0-or-later
  • UniqueID: dfcedd6a-9dc1-4dcd-8b15-dbd21482f463

AMR gene detection workflow in an assembled bacterial genome (v1.0)

This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:

    @@ -125,5 +125,5 @@

    [1.0] - 05-06-2024

    • First release
    -
- \ No newline at end of file +
+ \ No newline at end of file diff --git a/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/_payload.json b/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/_payload.json index f1fbeb5e9..d1e53cd31 100644 --- a/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/_payload.json +++ b/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842649805] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731086] \ No newline at end of file diff --git a/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/index.html b/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/index.html index 5af5fef04..8ffd952c2 100644 --- a/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/index.html +++ b/workflow/e21d954c-bb46-46f3-8081-0095b6b0de1f/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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Clinical Metaproteomics Quantitation

Clinical Metaproteomics 4: Quantitation

  • Author(s):
  • GalaxyP
  • Release: 0.1
  • License: CC-BY-4.0
  • UniqueID: e21d954c-bb46-46f3-8081-0095b6b0de1f

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.

In this current workflow, we perform Quantification using the MaxQuant tool. A GTN has been developed for this workflow. @@ -69,5 +69,5 @@

Processing

  • Grouping duplicates using the Group tool
    • - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/_payload.json b/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/_payload.json index 6639d61d0..38ee8cc2b 100644 --- a/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/_payload.json +++ b/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650138] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731397] \ No newline at end of file diff --git a/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/index.html b/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/index.html index 380983616..d407198e6 100644 --- a/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/index.html +++ b/workflow/eb1c667d-639d-4403-a2b4-1cb6683e0fa5/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
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    Quality and Contamination Control For Genome Assembly

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

    • Author(s):
    • ABRomics
    • abromics-consortium
    • Pierre Marin
    • Clea Siguret
    • Release: 1.1.5
    • License: GPL-3.0-or-later
    • UniqueID: eb1c667d-639d-4403-a2b4-1cb6683e0fa5

    Quality and Contamination control workflow for paired end data (v1.0)

    This workflow uses paired-end illumina fastq(.gz) files and executes the following steps:

      @@ -138,5 +138,5 @@

      [1.0] - 04-06-2024

      • First release
      -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/_payload.json b/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/_payload.json index 3ac2558f5..b5a44cd28 100644 --- a/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/_payload.json +++ b/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650126] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731384] \ No newline at end of file diff --git a/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/index.html b/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/index.html index ea2ab2176..7428b4e8c 100644 --- a/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/index.html +++ b/workflow/f1aea424-b536-496f-a0e6-fe46df8e6e18/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    Create GRO and TOP complex files

    • Author(s):
    • Simon Bray
    • Release: 0.1.4
    • License: MIT
    • UniqueID: f1aea424-b536-496f-a0e6-fe46df8e6e18

    Protein-ligand complex parameterization

    Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS.

    @@ -77,5 +77,5 @@

    [0.1]

    • Initial version of protein-ligand parameterization workflow.
    -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/f25be8fa-7823-456f-9707-a497703f48d7/_payload.json b/workflow/f25be8fa-7823-456f-9707-a497703f48d7/_payload.json index b72d53b14..b48e461dd 100644 --- a/workflow/f25be8fa-7823-456f-9707-a497703f48d7/_payload.json +++ b/workflow/f25be8fa-7823-456f-9707-a497703f48d7/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650674] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731870] \ No newline at end of file diff --git a/workflow/f25be8fa-7823-456f-9707-a497703f48d7/index.html b/workflow/f25be8fa-7823-456f-9707-a497703f48d7/index.html index 26ddbdb70..5f8f71460 100644 --- a/workflow/f25be8fa-7823-456f-9707-a497703f48d7/index.html +++ b/workflow/f25be8fa-7823-456f-9707-a497703f48d7/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    Repeat masking with RepeatModeler and RepeatMasker

    • Author(s):
    • Romane Libouban
    • Release: 0.1
    • License: MIT
    • UniqueID: f25be8fa-7823-456f-9707-a497703f48d7

    RepeatMasking Workflow

    This workflow uses RepeatModeler and RepeatMasker for genome analysis.

      @@ -84,5 +84,5 @@

      Outputs datasets for RepeatMasker

    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/f4887024-6f68-4d53-a889-5635366dd18d/_payload.json b/workflow/f4887024-6f68-4d53-a889-5635366dd18d/_payload.json index 8b35c8d1a..47dd10ed4 100644 --- a/workflow/f4887024-6f68-4d53-a889-5635366dd18d/_payload.json +++ b/workflow/f4887024-6f68-4d53-a889-5635366dd18d/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650614] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731840] \ No newline at end of file diff --git a/workflow/f4887024-6f68-4d53-a889-5635366dd18d/index.html b/workflow/f4887024-6f68-4d53-a889-5635366dd18d/index.html index 529939c3a..7f8e78021 100644 --- a/workflow/f4887024-6f68-4d53-a889-5635366dd18d/index.html +++ b/workflow/f4887024-6f68-4d53-a889-5635366dd18d/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    QIIME2 Id: Demultiplexed data (paired-end)

    Importing demultiplexed data (paired-end)

    • Author(s):
    • Debjyoti Ghosh
    • Helmholtz-Zentrum für Umweltforschung - UFZ
    • Release: 0.2
    • License: MIT
    • UniqueID: f4887024-6f68-4d53-a889-5635366dd18d

    QIIME2 import workflows

    Available workflows

    Import of fastqsanger.gz data into QIIME artifact files.

    @@ -101,5 +101,5 @@

    [0.1] 2024-04-08

    First release.

    [0.2] 2024-05-23

    Fix dockstore.yml and test.

    -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/_payload.json b/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/_payload.json index da5c414f3..49eee9a19 100644 --- a/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/_payload.json +++ b/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650274] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731496] \ No newline at end of file diff --git a/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/index.html b/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/index.html index ab92fac6b..92044c4cc 100644 --- a/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/index.html +++ b/workflow/f58371cd-2e2d-41da-b1ca-ef10f7330047/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    Get Confident Peaks From ATAC or CUTandRUN replicates

    This workflow takes as input BAM from ATAC-seq or CUT&amp;RUN. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using all subsets combined. Only peaks called using a combination of all subsets which have summits intersecting the intersection of at least x replicates will be kept.

    • Author(s):
    • Lucille Delisle
    • Release: 1.2
    • License: MIT
    • UniqueID: f58371cd-2e2d-41da-b1ca-ef10f7330047

    Consensus peaks Workflow

    The goal of this workflow is to get a list of confident peaks with summits from n replicates.

    Inputs dataset

    @@ -140,5 +140,5 @@

    Automatic update

    [0.1] 2023-08-31

    First release.

    -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/f71eee25-8402-41da-8284-5298656ab379/_payload.json b/workflow/f71eee25-8402-41da-8284-5298656ab379/_payload.json index 8795cb053..264fde122 100644 --- a/workflow/f71eee25-8402-41da-8284-5298656ab379/_payload.json +++ b/workflow/f71eee25-8402-41da-8284-5298656ab379/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650262] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731479] \ No newline at end of file diff --git a/workflow/f71eee25-8402-41da-8284-5298656ab379/index.html b/workflow/f71eee25-8402-41da-8284-5298656ab379/index.html index 498cff379..6de9b932c 100644 --- a/workflow/f71eee25-8402-41da-8284-5298656ab379/index.html +++ b/workflow/f71eee25-8402-41da-8284-5298656ab379/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    Get Confident Peaks From ChIP_SR replicates

    This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using all subsets combined. Only peaks called using a combination of all subsets which have summits intersecting the intersection of at least x replicates will be kept.

    • Author(s):
    • Lucille Delisle
    • Release: 1.2
    • License: MIT
    • UniqueID: f71eee25-8402-41da-8284-5298656ab379

    Consensus peaks Workflow

    The goal of this workflow is to get a list of confident peaks with summits from n replicates.

    Inputs dataset

    @@ -140,5 +140,5 @@

    Automatic update

    [0.1] 2023-08-31

    First release.

    -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/f8552617-4af2-4fa6-883f-0d605225939e/_payload.json b/workflow/f8552617-4af2-4fa6-883f-0d605225939e/_payload.json index d581a43be..8be400d08 100644 --- a/workflow/f8552617-4af2-4fa6-883f-0d605225939e/_payload.json +++ b/workflow/f8552617-4af2-4fa6-883f-0d605225939e/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650441] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731645] \ No newline at end of file diff --git a/workflow/f8552617-4af2-4fa6-883f-0d605225939e/index.html b/workflow/f8552617-4af2-4fa6-883f-0d605225939e/index.html index 18cc126a8..ad9a8411c 100644 --- a/workflow/f8552617-4af2-4fa6-883f-0d605225939e/index.html +++ b/workflow/f8552617-4af2-4fa6-883f-0d605225939e/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    Pox Virus Illumina Amplicon Workflow from half-genomes

    A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach

    Pox Virus Illumina Amplicon Workflow for half-genomes sequencing data

    This workflow generates consensus sequences from Illumina PE-sequenced ARTIC data of pox virus samples.

    It requires that all samples have been sequenced in two halves in two separate sequencing runs, and utilizes this property to resolve the inverted terminal repeat (ITR) sequences of pox virus genomes.

    @@ -69,5 +69,5 @@

    Tool version updates

    [0.1]

    Initial version of Pox Virus Illumina Amplicon workflow (iVar based) for half-genomes sequencing data

    -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/_payload.json b/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/_payload.json index 56cbfa827..9524db9c3 100644 --- a/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/_payload.json +++ b/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/_payload.json @@ -1 +1 @@ -[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729842650282] \ No newline at end of file +[{"data":1,"prerenderedAt":3},["Reactive",2],{},1729850731517] \ No newline at end of file diff --git a/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/index.html b/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/index.html index 6acb13d5b..a5a2905a0 100644 --- a/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/index.html +++ b/workflow/fe6bda9f-1fc2-4a86-bf8d-e779c79466fc/index.html @@ -31,21 +31,21 @@ --color-primary-DEFAULT: var(--color-primary-400); } - + - - - - + + + + - - -
    IWC LogoGalaxy IWC - Workflow Library
    AboutDevelopment

    ChIPseq_SR

    This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.

    • Author(s):
    • Lucille Delisle
    • Release: 0.12
    • License: MIT
    • UniqueID: fe6bda9f-1fc2-4a86-bf8d-e779c79466fc

    ChIP-seq single-read Workflow

    Inputs dataset

      @@ -138,5 +138,5 @@

      Automatic update

    [0.1] 2022-10-18

    First release.

    -
    - \ No newline at end of file +
    + \ No newline at end of file diff --git a/workflow_manifest.json b/workflow_manifest.json index 5c3d8ec63..10e506c86 100644 --- a/workflow_manifest.json +++ b/workflow_manifest.json @@ -1592,7 +1592,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.6", + "release": "1.1.7", "name": "bacterial_genome_annotation", "steps": { "0": { @@ -2547,7 +2547,7 @@ }, "8": { "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1", "errors": null, "id": 8, "input_connections": { @@ -2685,15 +2685,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1", "tool_shed_repository": { - "changeset_revision": "8d6686664021", + "changeset_revision": "ea93df4b3df2", "name": "tooldistillator", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"plasmidfinder\", \"__current_case__\": 14, \"input\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_result_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"genome_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.6\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"isescan\", \"__current_case__\": 11, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_faa_path\": {\"__class__\": \"ConnectedValue\"}, \"is_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.7.2.3\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"integronfinder2\", \"__current_case__\": 10, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.0.5\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bakta\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"annotation_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_genbank_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_embl_path\": {\"__class__\": \"ConnectedValue\"}, \"contig_sequences_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_protein_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"plot_file_path\": {\"__class__\": \"ConnectedValue\"}, \"summary_result_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"amino_acid_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"gff_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.9.4\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.1+galaxy0", + "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"plasmidfinder\", \"__current_case__\": 14, \"input\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_result_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"genome_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"true\", \"__current_case__\": 0, \"analysis_software_version\": null}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"isescan\", \"__current_case__\": 11, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_faa_path\": {\"__class__\": \"ConnectedValue\"}, \"is_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"true\", \"__current_case__\": 0, \"analysis_software_version\": null}, \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"integronfinder2\", \"__current_case__\": 10, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_file_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"true\", \"__current_case__\": 0, \"analysis_software_version\": null}, \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bakta\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"annotation_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_genbank_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_embl_path\": {\"__class__\": \"ConnectedValue\"}, \"contig_sequences_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_protein_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"plot_file_path\": {\"__class__\": \"ConnectedValue\"}, \"summary_result_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"amino_acid_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"gff_file_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"true\", \"__current_case__\": 0, \"analysis_software_version\": null}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.9.1+galaxy1", "type": "tool", "uuid": "678bdbfe-7a3a-4a91-8ea7-1cb17f53daa6", "when": null, @@ -2707,7 +2707,7 @@ }, "9": { "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -2745,15 +2745,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1", "tool_shed_repository": { - "changeset_revision": "f3233d395549", + "changeset_revision": "24eec94e6dfc", "name": "tooldistillator_summarize", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.1+galaxy0", + "tool_version": "0.9.1+galaxy1", "type": "tool", "uuid": "3427b1f1-79ce-4ade-a350-baf15ac250c2", "when": null, @@ -2778,7 +2778,7 @@ "version": 1 }, "readme": "# Bacterial genome annotation workflow (v1.0)\n\nThis workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:\n1. Genomic annotation\n - **Bakta** to predict CDS and small proteins (sORF)\n2. Integron identification\n - **IntegronFinder2** to identify CALIN elements, In0 elements, and complete integrons\n3. Plasmid gene identification\n - **Plasmidfinder** to identify and typing plasmid sequences\n4. Inserted sequence (IS) detection\n - **ISEScan** to detect IS elements\n5. Aggregating outputs into a single JSON file\n - **ToolDistillator** to extract and aggregate information from different tool outputs to JSON parsable files\n\n## Inputs\n\n1. Assembled bacterial genome in fasta format.\n\n## Outputs\n\n1. Genomic annotation:\n - genome annotation in tabular, gff and several other formats\n - annotation plot\n - nucleotide and protein sequences identified\n - summary of genomic identified elements\n2. Integron identification:\n - integron identification in tabular format and a summary\n3. Plasmid gene identification:\n - plasmid gene identified and associated blast hits\n4. Inserted Element (IS) detection:\n - IS element list in tabular format\n - is hits in fasta format\n - ORF hits in protein and nucleotide fasta format\n - IS annotation gff format\n5. Aggregating outputs:\n - JSON file with information about the outputs of **Bakta**, **IntegronFinder2**, **Plasmidfinder**, **ISEScan**", - "changelog": "# Changelog\n\n## [1.1.6] 2024-10-11\n\n### Manual update\n\n- Changed input parameters to select databases in WFs. Use \"Attempt restriction based on connections\" instead of \"Provide list of suggested values\".\n\n## [1.1.5] 2024-09-30\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0`\n\n## [1.1.4] 2024-09-19\n\n### Manual update\n\n- Updated the tool versions manually in the ToolDistillator parameters\n\n## [1.1.3] 2024-09-09\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0`\n\n## [1.1.2] - 2024-07-19\n\n- PlasmidFinder database correction in .ga\n\n## [1.1.1] 2024-07-08\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.8.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.8.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0`\n\n## [1.1] 2024-06-24\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0`\n\n## [1.0] - 14-06-2024\n\n- First release\n", + "changelog": "# Changelog\n\n## [1.1.7] 2024-10-21\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1`\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1`\n\n## [1.1.6] 2024-10-11\n\n### Manual update\n\n- Changed input parameters to select databases in WFs. Use \"Attempt restriction based on connections\" instead of \"Provide list of suggested values\".\n\n## [1.1.5] 2024-09-30\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0`\n\n## [1.1.4] 2024-09-19\n\n### Manual update\n\n- Updated the tool versions manually in the ToolDistillator parameters\n\n## [1.1.3] 2024-09-09\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0`\n\n## [1.1.2] - 2024-07-19\n\n- PlasmidFinder database correction in .ga\n\n## [1.1.1] 2024-07-08\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.8.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0`\n- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.8.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0`\n\n## [1.1] 2024-06-24\n\n### Automatic update\n- `toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0`\n\n## [1.0] - 14-06-2024\n\n- First release\n", "trsID": "#workflow/github.com/iwc-workflows/bacterial_genome_annotation/main", "tests": [ {