Improve worklow names as shown in Galaxy #517
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@mvdbeek directly into the PR or separate ones? |
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Feel free to push to the PR or comment |
lldelisle
reviewed
Sep 9, 2024
| @@ -554,7 +554,7 @@ | |||
| }, | |||
| "inputs": [], | |||
| "label": "Compute fragment length histogram", | |||
| "name": "Paired-end histogram", | |||
| "name": "paired end histogram", | |||
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Is this change on purpose or a side effect?
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That's the tool name, shouldn't change it
| @@ -11,7 +11,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.11", | |||
| "name": "ChIPseq_PE", | |||
| "name": "ChIPseq: Paired End", | |||
| @@ -11,7 +11,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.11", | |||
| "name": "ChIPseq_SR", | |||
| "name": "ChIPseq: Single Read", | |||
| @@ -82,7 +82,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "1.1", | |||
| "name": "Get Confident Peaks From ChIP_PE replicates", | |||
| "name": "Get Confident Peaks From Paired End ChIP replicates", | |||
| @@ -82,7 +82,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "1.1", | |||
| "name": "Get Confident Peaks From ChIP_SR replicates", | |||
| "name": "Get Confident Peaks From Single Read ChIP replicates", | |||
workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga
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workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
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wm75
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Sep 9, 2024
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Just to avoid redundant work: you are aware of https://training.galaxyproject.org/training-material/workflows/list.html and checked if that's reuseable in some way?
workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga
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| @@ -1,6 +1,6 @@ | |||
| { | |||
| "a_galaxy_workflow": "true", | |||
| "annotation": "Importing demultiplexed data (single-end)", | |||
| "annotation": "Importing demultiplexed data (single read)", | |||
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Shouldn't it be single-end reads instead of single read everywhere?
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https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html uses single read. I don't particularly care but we should choose one.
workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
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mvdbeek
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Sep 9, 2024
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mvdbeek
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mvdbeek
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mvdbeek
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The workflow name change will also benefit this, but I think we want a component that we can embed in the BRC analytics site where we need additional functionality. |
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@Delphine-L could you also take a look at this ? |
Delphine-L
reviewed
Sep 10, 2024
| @@ -21,7 +21,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "release": "0.2.2", | |||
| "name": "Assembly-Hifi-HiC-phasing-VGP4", | |||
| "name": "Contiging Solo with HiC data VGP4", | |||
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Suggested change
| "name": "Contiging Solo with HiC data VGP4", | |
| "name": "Assembly with Hifi reads and Hi-C data VGP4", |
| @@ -16,7 +16,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "release": "0.2.1", | |||
| "name": "Assembly-Hifi-only-VGP3", | |||
| "name": "Contiging Solo VGP3", | |||
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Suggested change
| "name": "Contiging Solo VGP3", | |
| "name": "Assembly with Hifi reads VGP3", |
@Delphine-L you can add suggestions by using this https://stackoverflow.com/questions/54239733/how-can-i-manually-add-suggestions-in-code-reviews-on-github
I changed your suggestion accordingly.
| @@ -15,7 +15,7 @@ | |||
| ], | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "name": "Mitogenome-Assembly-VGP0", | |||
| "name": "Mitogenome Assembly VGP0", | |||
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Suggested change
| "name": "Mitogenome Assembly VGP0", | |
| "name": "Mitogenome Assembly with Hifi data VGP0", |
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is it maybe time to remove the VGPx suffix from all names?
| @@ -16,7 +16,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "release": "0.4", | |||
| "name": "Purge-duplicate-contigs-VGP6", | |||
| "name": "Purge duplicate contigs VGP6", | |||
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Suggested change
| "name": "Purge duplicate contigs VGP6", | |
| "name": "Purge duplicate contigs from two haplotypes VGP6" |
| @@ -16,7 +16,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "release": "0.7.1", | |||
| "name": "Purging-duplicates-one-haplotype-VGP6b ", | |||
| "name": "Purge Duplicate Contigs VGP6b", | |||
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Suggested change
| "name": "Purge Duplicate Contigs VGP6b", | |
| "name": "Purge duplicate contigs from one haplotypes VGP6b" |
| @@ -16,7 +16,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "release": "0.2.7", | |||
| "name": "Scaffolding-HiC-VGP8", | |||
| "name": "Scaffolding with HiC data VGP8", | |||
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Suggested change
| "name": "Scaffolding with HiC data VGP8", | |
| "name": "Scaffolding with Hi-C data VGP8", |
| @@ -15,7 +15,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "CC-BY-4.0", | |||
| "release": "0.1.4", | |||
| "name": "kmer-profiling-hifi-trio-VGP2", | |||
| "name": "K-mer profiling with HiFi trio data VGP2", | |||
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Suggested change
| "name": "K-mer profiling with HiFi trio data VGP2", | |
| "name": "K-mer profiling for PacBio HiFi and Trio data VGP2", |
lldelisle
reviewed
Sep 25, 2024
| @@ -11,7 +11,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.3", | |||
| "name": "cHi-C_fastqToCool_hicup_cooler", | |||
| "name": "Hi-C: fastq to balanced cool using HiCUP and Cooler", | |||
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Suggested change
| "name": "Hi-C: fastq to balanced cool using HiCUP and Cooler", | |
| "name": "capture Hi-C: fastq to balanced cool using HiCUP and Cooler", |
lldelisle
reviewed
Sep 25, 2024
| @@ -11,7 +11,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.5", | |||
| "name": "baredSC_1d_logNorm", | |||
| "name": "baredSC 1D logNorm", | |||
lldelisle
reviewed
Sep 25, 2024
| @@ -11,7 +11,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.5", | |||
| "name": "baredSC_2d_logNorm", | |||
| "name": "baredSC 2D logNorm", | |||
| @@ -31,7 +31,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.4", | |||
| "name": "scRNA-seq_preprocessing_10X_cellPlex", | |||
| "name": "Single-cell RNA-seq fastq to matrix for 10X cellPlex data", | |||
| @@ -31,7 +31,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.4", | |||
| "name": "scRNA-seq_preprocessing_10X_v3_Bundle", | |||
| "name": "Single-cell RNA-seq fastq to bundled matrix for 10X V3 data", | |||
| @@ -1,6 +1,6 @@ | |||
| # Velocyto on 10X data | |||
|
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| 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). | |||
| These workflows simply run velocyto. There are 2 workflows because one can be easily run after the 'fastq-to-matrix-10x' workflows (Velocyto for 10X bundled data). The other can be easily run from uploaded datasets (Velocyto for 10X filtered barcode data). | |||
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Suggested change
| These workflows simply run velocyto. There are 2 workflows because one can be easily run after the 'fastq-to-matrix-10x' workflows (Velocyto for 10X bundled data). The other can be easily run from uploaded datasets (Velocyto for 10X filtered barcode data). | |
| These workflows simply run velocyto. There are 2 workflows because one can be easily run after the 'Single-cell RNA-seq fastq to bundled matrix for 10X ... data' workflows (Velocyto for 10X bundled data). The other can be easily run from uploaded datasets (Velocyto for 10X filtered barcode data). |
| @@ -12,7 +12,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.2", | |||
| "name": "Velocyto-on10X-filtered-barcodes", | |||
| "name": "Velocyto for 10X filtered barcode data", | |||
| @@ -12,7 +12,7 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.2", | |||
| "name": "Velocyto-on10X-from-bundled", | |||
| "name": "Velocyto for 10X bundled data", | |||
| @@ -12,17 +12,17 @@ | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "release": "0.8", | |||
| "name": "RNAseq_PE", | |||
| "name": "RNA-seq Paired End", | |||
| @@ -11,7 +11,7 @@ | |||
| ], | |||
| "format-version": "0.1", | |||
| "license": "MIT", | |||
| "name": "RNAseq_SR", | |||
| "name": "RNA-seq Single Read", | |||
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@dannon is working on a static site listing our workflows, and we'd like to have better workflow names. I've made a first pass here, but I would love input from everyone.