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| author | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
| commit | d781e42c9adac07253cb928ae66e9b7314710267 (patch) | |
| tree | 4718165cbc069169eaff98080c61c5f07763ffc1 /workflows/fastq2fasta/samtools-faidx.cwl | |
| parent | 1219eaf496c899f3043b90e30eb956f0f363bfb3 (diff) | |
| download | bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.gz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.lz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.zip | |
Move workflows into main repo
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/fastq2fasta/samtools-faidx.cwl')
| -rw-r--r-- | workflows/fastq2fasta/samtools-faidx.cwl | 39 |
1 files changed, 39 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/samtools-faidx.cwl b/workflows/fastq2fasta/samtools-faidx.cwl new file mode 100644 index 0000000..5196607 --- /dev/null +++ b/workflows/fastq2fasta/samtools-faidx.cwl @@ -0,0 +1,39 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.0 +class: CommandLineTool +doc: "samtools sort, sort given bam file" +requirements: + DockerRequirement: + dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11 + InitialWorkDirRequirement: + listing: + - $(inputs.input_fasta) +baseCommand: [samtools, faidx] +inputs: + input_fasta: + type: File + label: "Input fasta" + inputBinding: + position: 1 + secondaryFiles: + - .amb + - .ann + - .bwt + - .pac + - .sa +outputs: + indexed_fasta: + type: File + outputBinding: + glob: "$(inputs.input_fasta.basename)" + secondaryFiles: + - .amb + - .ann + - .bwt + - .pac + - .sa + - .fai + stdout: stdout + stderr: stderr +stdout: samtools-sort-stdout.log +stderr: samtools-sort-stderr.log |