steps:
fastqc:
- run: bio-cwl-tools/fastqc/fastqc_2.cwl
+ run: fastqc_2.cwl
in:
reads_file: fq
out: [html_file]
requirements:
ResourceRequirement:
ramMin: 9000
- run: bio-cwl-tools/STAR/STAR-Align.cwl
+ run: STAR-Align.cwl
in:
RunThreadN: {default: 4}
GenomeDir: genome
OutSAMtype: {default: BAM}
SortedByCoordinate: {default: true}
OutSAMunmapped: {default: Within}
- ### 1. Expressions on step inputs
OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
out: [alignment]
samtools:
- run: bio-cwl-tools/samtools/samtools_index.cwl
+ run: samtools_index.cwl
in:
bam_sorted: STAR/alignment
out: [bam_sorted_indexed]