- 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]
+
+ bwamem-gatk-report:
+ run: ./helper/bwamem-gatk-report-wf.cwl
+ scatter: [fastq1, fastq2]
+ scatterMethod: dotproduct