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Merge pull request #982 from tmooney/umi_sequence_align
Convert UMI alignment pipelines to use `sequence_data` custom type.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| #!/usr/bin/env cwl-runner | ||
|
|
||
| cwlVersion: v1.0 | ||
| class: CommandLineTool | ||
| label: "resolve sequence type to a bam" | ||
| baseCommand: ["/bin/bash", "sequence_to_bam_helper.sh"] | ||
| requirements: | ||
| - class: SchemaDefRequirement | ||
| types: | ||
| - $import: ../types/sequence_data.yml | ||
| - class: ResourceRequirement | ||
| ramMin: 6000 | ||
| tmpdirMin: 25000 | ||
| - class: DockerRequirement | ||
| dockerPull: "broadinstitute/picard:2.23.6" | ||
| - class: InlineJavascriptRequirement | ||
| - class: InitialWorkDirRequirement | ||
| listing: | ||
| - entryname: 'sequence_to_bam_helper.sh' | ||
| entry: | | ||
| set -o pipefail | ||
| set -o errexit | ||
| set -o nounset | ||
|
|
||
| if [[ "$1" == 'bam' ]]; then | ||
| cp "$2" sequence.bam | ||
| else | ||
| /usr/bin/java -Xmx4g -jar /usr/picard/picard.jar FastqToSam --OUTPUT sequence.bam "$@" | ||
| fi | ||
| arguments: | ||
| - { valueFrom: "$(inputs.sequence.sequence.hasOwnProperty('bam')? inputs.sequence.sequence.bam : null)", prefix: 'bam', position: -1 } | ||
| - { valueFrom: "$(inputs.sequence.sequence.hasOwnProperty('fastq1')? inputs.sequence.sequence.fastq1 : null)", prefix: '--FASTQ' } | ||
| - { valueFrom: "$(inputs.sequence.sequence.hasOwnProperty('fastq2')? inputs.sequence.sequence.fastq2 : null)", prefix: '--FASTQ2' } | ||
| - valueFrom: | | ||
| ${ | ||
| var x = inputs.sequence.readgroup.split("\t").find(function(tag){ return tag.startsWith("SM:")}); | ||
| if(x) { | ||
| return x.substr(3) | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| prefix: '--SAMPLE_NAME' | ||
| - valueFrom: | | ||
| ${ | ||
| var x = inputs.sequence.readgroup.split("\t").find(function(tag){ return tag.startsWith("LB:")}); | ||
| if(x) { | ||
| return x.substr(3) | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| prefix: '--LIBRARY_NAME' | ||
| - valueFrom: | | ||
| ${ | ||
| var x = inputs.sequence.readgroup.split("\t").find(function(tag){ return tag.startsWith("PU:")}); | ||
| if(x) { | ||
| return x.substr(3) | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| prefix: '--PLATFORM_UNIT' | ||
| - valueFrom: | | ||
| ${ | ||
| var x = inputs.sequence.readgroup.split("\t").find(function(tag){ return tag.startsWith("PL:")}); | ||
| if(x) { | ||
| return x.substr(3) | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| prefix: '--PLATFORM' | ||
| - valueFrom: | | ||
| ${ | ||
| var x = inputs.sequence.readgroup.split("\t").find(function(tag){ return tag.startsWith("ID:")}); | ||
| if(x) { | ||
| return x.substr(3) | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| prefix: '--READ_GROUP_NAME' | ||
| - valueFrom: | | ||
| ${ | ||
| var x = inputs.sequence.readgroup.split("\t").find(function(tag){ return tag.startsWith("CN:")}); | ||
| if(x) { | ||
| return x.substr(3) | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| prefix: '--SEQUENCING_CENTER' | ||
| inputs: | ||
| sequence: | ||
| type: ../types/sequence_data.yml#sequence_data | ||
| output_bam_basename: | ||
| type: string | ||
| default: "sequence" | ||
| outputs: | ||
| bam: | ||
| type: File | ||
| outputBinding: | ||
| glob: sequence.bam |