- fastq1: fastq1
- fastq2: fastq2
- out: [out-html, out-zip]
- bwamem-samtools-view:
- run: bwamem-samtools-view.cwl
- in:
- fastq1: fastq1
- fastq2: fastq2
- reference: reference
- sample: sample
- out: [bam]
- samtools-sort:
- run: samtools-sort.cwl
- in:
- bam: bwamem-samtools-view/bam
- sample: sample
- out: [sortedbam]
- mark-duplicates:
- run: mark-duplicates.cwl
- in:
- bam: samtools-sort/sortedbam
- out: [dupbam,dupmetrics]
- samtools-index:
- run: samtools-index.cwl
- in:
- bam: mark-duplicates/dupbam
- out: [indexedbam]
- haplotypecaller:
- run: scatter-gatk-wf-with-interval.cwl
+ fastqdir: fastqdir
+ out: [fastq1, fastq2, sample]
+
+ bwamem-gatk-report:
+ run: ./helper/bwamem-gatk-report-wf.cwl
+ scatter: [fastq1, fastq2, sample]
+ scatterMethod: dotproduct