adding helper directory for structure, may reorg later
adding cwl to do intervals and scattering
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
- [DH] cwl/helper/annotate-vcf.cwl
- [DH] cwl/helper/bwa-gatk-wf.cwl
- [DH] cwl/helper/bwamem-samtools-sort.cwl
- [DH] cwl/helper/bwamem-samtools-view.cwl
- [DH] cwl/helper/calc-coverage.cwl
- [DH] cwl/helper/check-sam.cwl
- [DH] cwl/helper/fastqc.cwl
- [DH] cwl/helper/fix-groups.cwl
- [DH] cwl/helper/gatk-applyBQSR.cwl
- [DH] cwl/helper/gatk-applyBSQR-with-interval.cwl
- [DH] cwl/helper/gatk-baserecalibrator-with-interval.cwl
- [DH] cwl/helper/gatk-baserecalibrator.cwl
- [DH] cwl/helper/gatk-haplotypecaller-with-interval.cwl
- [DH] cwl/helper/gatk-haplotypecaller.cwl
- [DH] cwl/helper/gatk-splitintervals.cwl
- [DH] cwl/helper/gatk-wf-with-interval.cwl
- [DH] cwl/helper/generate-report.cwl
- [DH] cwl/helper/gvcf-to-vcf.cwl
- [DH] cwl/helper/mark-duplicates.cwl
- [DH] cwl/helper/old/bwa-gatk-wf.cwl
- [DH] cwl/helper/old/samtools-sort.cwl
- [DH] cwl/helper/report-wf.cwl
- [DH] cwl/helper/samtools-fixmate.cwl
- [DH] cwl/helper/samtools-index.cwl
- [DH] cwl/helper/samtools-sort.cwl
- [DH] cwl/helper/scatter-gatk-wf-with-interval.cwl