-
-
Notifications
You must be signed in to change notification settings - Fork 8
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
30 changed files
with
1,452 additions
and
12 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,151 @@ | ||
| class: CommandLineTool | ||
| id: Annotate | ||
| inputs: | ||
| - id: inputFile | ||
| type: File | ||
| - id: annsFile | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: collapse | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: exclude | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: headerLines | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: newId | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: include | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: markSites | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: regions | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: regionsFile | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: renameChrs | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: samplesFile | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: columns | ||
| default: '[]' | ||
| type: string[] | ||
| - id: force | ||
| default: false | ||
| type: boolean | ||
| - id: keepSites | ||
| default: false | ||
| type: boolean | ||
| - id: noVersion | ||
| default: false | ||
| type: boolean | ||
| - id: samples | ||
| default: '[]' | ||
| type: string[] | ||
| - id: singleOverlaps | ||
| default: false | ||
| type: boolean | ||
| - id: removeAnns | ||
| default: '[]' | ||
| type: string[] | ||
| - id: outputPath | ||
| default: output.vcf.gz | ||
| type: string | ||
| - id: threads | ||
| default: 0 | ||
| type: int | ||
| - id: memory | ||
| default: 256M | ||
| type: string | ||
| - id: dockerImage | ||
| default: quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2 | ||
| type: string | ||
| outputs: | ||
| - id: outputVcf | ||
| type: File | ||
| outputBinding: | ||
| glob: $(inputs.outputPath) | ||
| - id: outputVcfIndex | ||
| type: | ||
| - File | ||
| - 'null' | ||
| outputBinding: | ||
| glob: $(inputs.outputPath).tbi | ||
| requirements: | ||
| - class: DockerRequirement | ||
| dockerPull: quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2 | ||
| - class: InitialWorkDirRequirement | ||
| listing: | ||
| - entryname: example.sh | ||
| entry: |4 | ||
|
|
||
| set -e | ||
| mkdir -p "\$(dirname $(inputs.outputPath))" | ||
| bcftools annotate \ | ||
| -o $(inputs.outputPath) \ | ||
| -O \ | ||
| $(inputs.annsFile === null ? "" : "--annotations " + inputs.annsFile.path ) \ | ||
| $(inputs.collapse === null ? "" : "--collapse " + inputs.collapse ) \ | ||
| ${if (inputs.columns.length > 0) {return "--columns";} else {return '';}} $(inputs.columns.join(",")) \ | ||
| $(inputs.exclude === null ? "" : "--exclude " + inputs.exclude ) \ | ||
| $(inputs.force ? "--force" : "") \ | ||
| $(inputs.headerLines === null ? "" : "--header-lines " + inputs.headerLines.path ) \ | ||
| $(inputs.newId === null ? "" : "--set-id " + inputs.newId ) \ | ||
| $(inputs.include === null ? "" : "--include " + inputs.include ) \ | ||
| $(inputs.keepSites ? "--keep-sites" : "") \ | ||
| $(inputs.markSites === null ? "" : "--mark-sites " + inputs.markSites ) \ | ||
| $(inputs.noVersion ? "--no-version" : "") \ | ||
| $(inputs.regions === null ? "" : "--regions " + inputs.regions ) \ | ||
| $(inputs.regionsFile === null ? "" : "--regions-file " + inputs.regionsFile.path ) \ | ||
| $(inputs.renameChrs === null ? "" : "--rename-chrs " + inputs.renameChrs.path ) \ | ||
| ${if (inputs.samples.length > 0) {return "--samples";} else {return '';}} $(inputs.samples.join(",")) \ | ||
| $(inputs.samplesFile === null ? "" : "--samples-file " + inputs.samplesFile.path ) \ | ||
| $(inputs.singleOverlaps ? "--single-overlaps" : "") \ | ||
| ${if (inputs.removeAnns.length > 0) {return "--remove";} else {return '';}} $(inputs.removeAnns.join(",")) \ | ||
| $(inputs.inputFile.path) | ||
|
|
||
| $(inputs.ifcompressedthen'bcftools index --tbi ~{outputPath)'else''} | ||
| - class: InlineJavascriptRequirement | ||
| - class: NetworkAccess | ||
| networkAccess: true | ||
| - class: ResourceRequirement | ||
| ramMin: |- | ||
| ${ | ||
| var unit = inputs.memory.match(/[a-zA-Z]+/g).join(""); | ||
| var value = parseInt(inputs.memory.match(/[0-9]+/g)); | ||
| var memory = ""; | ||
| if(unit==="KiB") memory = value/1024; | ||
| else if(unit==="MiB") memory = value; | ||
| else if(unit==="GiB") memory = value*1024; | ||
| else if(unit==="TiB") memory = value*1024*1024; | ||
| else if(unit==="B") memory = value/(1024*1024); | ||
| else if(unit==="KB" || unit==="K") memory = (value*1000)/(1024*1024); | ||
| else if(unit==="MB" || unit==="M") memory = (value*(1000*1000))/(1024*1024); | ||
| else if(unit==="GB" || unit==="G") memory = (value*(1000*1000*1000))/(1024*1024); | ||
| else if(unit==="TB" || unit==="T") memory = (value*(1000*1000*1000*1000))/(1024*1024); | ||
| return parseInt(memory); | ||
| } | ||
| cwlVersion: v1.2 | ||
| baseCommand: | ||
| - bash | ||
| - example.sh |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,166 @@ | ||
| class: CommandLineTool | ||
| id: Stats | ||
| inputs: | ||
| - id: inputVcf | ||
| type: File | ||
| - id: inputVcfIndex | ||
| type: File | ||
| - id: compareVcf | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: compareVcfIndex | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: afBins | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: afTag | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: collapse | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: depth | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: exclude | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: exons | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: applyFilters | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: fastaRef | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: fastaRefIndex | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: include | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: regions | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: regionsFile | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: samplesFile | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: targets | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: targetsFile | ||
| type: | ||
| - File | ||
| - 'null' | ||
| - id: userTsTv | ||
| type: | ||
| - string | ||
| - 'null' | ||
| - id: outputPath | ||
| default: basename(inputVcf)+.stats | ||
| type: string | ||
| - id: firstAlleleOnly | ||
| default: false | ||
| type: boolean | ||
| - id: splitByID | ||
| default: false | ||
| type: boolean | ||
| - id: samples | ||
| default: '[]' | ||
| type: string[] | ||
| - id: verbose | ||
| default: false | ||
| type: boolean | ||
| - id: threads | ||
| default: 0 | ||
| type: int | ||
| - id: memory | ||
| default: 256M | ||
| type: string | ||
| - id: dockerImage | ||
| default: quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2 | ||
| type: string | ||
| outputs: | ||
| - id: stats | ||
| type: File | ||
| outputBinding: | ||
| glob: $(inputs.outputPath) | ||
| requirements: | ||
| - class: DockerRequirement | ||
| dockerPull: quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2 | ||
| - class: InitialWorkDirRequirement | ||
| listing: | ||
| - entryname: example.sh | ||
| entry: |4 | ||
|
|
||
| set -e | ||
| mkdir -p \$(dirname $(inputs.outputPath)) | ||
| bcftools stats \ | ||
| $(inputs.afBins === null ? "" : "--af-bins " + inputs.afBins ) \ | ||
| $(inputs.afTag === null ? "" : "--af-tag " + inputs.afTag ) \ | ||
| $(inputs.firstAlleleOnly ? "--1st-allele-only" : "") \ | ||
| $(inputs.collapse === null ? "" : "--collapse " + inputs.collapse ) \ | ||
| $(inputs.depth === null ? "" : "--depth " + inputs.depth ) \ | ||
| $(inputs.exclude === null ? "" : "--exclude " + inputs.exclude ) \ | ||
| $(inputs.exons === null ? "" : "--exons " + inputs.exons.path ) \ | ||
| $(inputs.applyFilters === null ? "" : "--apply-filters " + inputs.applyFilters ) \ | ||
| $(inputs.fastaRef === null ? "" : "--fasta-ref " + inputs.fastaRef.path ) \ | ||
| $(inputs.include === null ? "" : "--include " + inputs.include ) \ | ||
| $(inputs.splitByID ? "--split-by-ID" : "") \ | ||
| $(inputs.regions === null ? "" : "--regions " + inputs.regions ) \ | ||
| $(inputs.regionsFile === null ? "" : "--regions-file " + inputs.regionsFile.path ) \ | ||
| ${if (inputs.samples.length > 0) {return "--samples";} else {return '';}} $(inputs.samples.join(",")) \ | ||
| $(inputs.samplesFile === null ? "" : "--samples-file " + inputs.samplesFile.path ) \ | ||
| $(inputs.targets === null ? "" : "--targets " + inputs.targets ) \ | ||
| $(inputs.targetsFile === null ? "" : "--targets-file " + inputs.targetsFile.path ) \ | ||
| $(inputs.userTsTv === null ? "" : "--user-tstv " + inputs.userTsTv ) \ | ||
| --threads $(inputs.threads) \ | ||
| $(inputs.verbose ? "--verbose" : "") \ | ||
| $(inputs.inputVcf.path) $(inputs.compareVcf === null ? "" : inputs.compareVcf.path) > $(inputs.outputPath) | ||
| - class: InlineJavascriptRequirement | ||
| - class: NetworkAccess | ||
| networkAccess: true | ||
| - class: ResourceRequirement | ||
| ramMin: |- | ||
| ${ | ||
| var unit = inputs.memory.match(/[a-zA-Z]+/g).join(""); | ||
| var value = parseInt(inputs.memory.match(/[0-9]+/g)); | ||
| var memory = ""; | ||
| if(unit==="KiB") memory = value/1024; | ||
| else if(unit==="MiB") memory = value; | ||
| else if(unit==="GiB") memory = value*1024; | ||
| else if(unit==="TiB") memory = value*1024*1024; | ||
| else if(unit==="B") memory = value/(1024*1024); | ||
| else if(unit==="KB" || unit==="K") memory = (value*1000)/(1024*1024); | ||
| else if(unit==="MB" || unit==="M") memory = (value*(1000*1000))/(1024*1024); | ||
| else if(unit==="GB" || unit==="G") memory = (value*(1000*1000*1000))/(1024*1024); | ||
| else if(unit==="TB" || unit==="T") memory = (value*(1000*1000*1000*1000))/(1024*1024); | ||
| return parseInt(memory); | ||
| } | ||
| - class: ResourceRequirement | ||
| coresMin: $(inputs.threads + 1) | ||
| cwlVersion: v1.2 | ||
| baseCommand: | ||
| - bash | ||
| - example.sh |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.