git.arvados.org - arvados-tutorial.git/commit

projects / arvados-tutorial.git / commit

author	Sarah Wait Zaranek <swz@curii.com>
	Wed, 17 Jun 2020 16:20:39 +0000 (16:20 +0000)
committer	Ward Vandewege <ward@jhvc.com>
	Thu, 18 Jun 2020 15:16:40 +0000 (11:16 -0400)
commit	cec9a7f6a83fc2596e042e8adc6179b202f92a6e
tree	6e53d838224928b0c96e5476f3cb9b8df952ea90	tree \| snapshot
parent	aa289173560cd4466d890f3a63927650e37d8aa7	commit \| diff

Rearranging for clarity
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

72 files changed:

WGS-processing/cwl/helper/annotate-vcf.cwl	[moved from cwl/helper/annotate-vcf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/bwa-gatk-report-wf.cwl	[moved from cwl/helper/bwa-gatk-report-wf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/bwa-gatk-wf.cwl	[moved from cwl/helper/bwa-gatk-wf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/bwamem-samtools-view.cwl	[moved from cwl/helper/bwamem-samtools-view.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/fastqc.cwl	[moved from cwl/helper/fastqc.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gather-array-vcf.cwl	[moved from cwl/helper/gather-array-vcf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gather-vcf-try2.cwl	[moved from cwl/helper/gather-vcf-try2.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gather-vcf.cwl	[moved from cwl/helper/gather-vcf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-applyBQSR.cwl	[moved from cwl/helper/gatk-applyBQSR.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl	[moved from cwl/helper/gatk-applyBSQR-with-interval.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl	[moved from cwl/helper/gatk-baserecalibrator-with-interval.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-baserecalibrator.cwl	[moved from cwl/helper/gatk-baserecalibrator.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl	[moved from cwl/helper/gatk-haplotypecaller-with-interval.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-haplotypecaller.cwl	[moved from cwl/helper/gatk-haplotypecaller.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-selectvariants.cwl	[moved from cwl/helper/gatk-selectvariants.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-splitintervals.cwl	[moved from cwl/helper/gatk-splitintervals.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl	[moved from cwl/helper/gatk-wf-with-interval.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/generate-report.cwl	[moved from cwl/helper/generate-report.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/getfastq.cwl	[moved from cwl/helper/getfastq.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/getgvcfs.cwl	[moved from cwl/helper/getgvcfs.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/gvcf-to-vcf.cwl	[moved from cwl/helper/gvcf-to-vcf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/mark-duplicates.cwl	[moved from cwl/helper/mark-duplicates.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/bwa-gatk-wf.cwl	[moved from cwl/helper/not-in-use/bwa-gatk-wf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/bwamem-samtools-sort.cwl	[moved from cwl/helper/not-in-use/bwamem-samtools-sort.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/calc-coverage.cwl	[moved from cwl/helper/not-in-use/calc-coverage.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/check-sam.cwl	[moved from cwl/helper/not-in-use/check-sam.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/fix-groups.cwl	[moved from cwl/helper/not-in-use/fix-groups.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/samtools-fixmate.cwl	[moved from cwl/helper/not-in-use/samtools-fixmate.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/not-in-use/samtools-sort.cwl	[moved from cwl/helper/not-in-use/samtools-sort.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/report-wf.cwl	[moved from cwl/helper/report-wf.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/samtools-index.cwl	[moved from cwl/helper/samtools-index.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/samtools-sort.cwl	[moved from cwl/helper/samtools-sort.cwl with 100% similarity]	blob \| history
WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl	[moved from cwl/helper/scatter-gatk-wf-with-interval.cwl with 100% similarity]	blob \| history
WGS-processing/docker/bwa/Dockerfile	[moved from docker/bwa/Dockerfile with 100% similarity]	blob \| history
WGS-processing/docker/clinvar-report/Dockerfile	[moved from docker/clinvar-report/Dockerfile with 100% similarity]	blob \| history
WGS-processing/docker/fastqc/Dockerfile	[moved from docker/fastqc/Dockerfile with 100% similarity]	blob \| history
WGS-processing/src/annotation/generatereport.py	[moved from src/annotation/generatereport.py with 100% similarity]	blob \| history
WGS-processing/src/annotation/head.html	[moved from src/annotation/head.html with 100% similarity]	blob \| history
WGS-processing/src/annotation/runcommand	[moved from src/annotation/runcommand with 100% similarity]	blob \| history
WGS-processing/src/annotation/sample.html	[moved from src/annotation/sample.html with 100% similarity]	blob \| history
WGS-processing/src/annotation/samplelist	[moved from src/annotation/samplelist with 100% similarity]	blob \| history
WGS-processing/src/annotation/tail.html	[moved from src/annotation/tail.html with 100% similarity]	blob \| history
WGS-processing/src/annotation/test.html	[moved from src/annotation/test.html with 100% similarity]	blob \| history
WGS-processing/yml/annotate-vcf.yml	[moved from yml/annotate-vcf.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwa-gatk-report-wf-UK.yml	[moved from yml/bwa-gatk-report-wf-UK.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwa-gatk-wf-WGC071838D.yml	[moved from yml/bwa-gatk-wf-WGC071838D.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwa-gatk-wf-WGC074701D.yml	[moved from yml/bwa-gatk-wf-WGC074701D.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwa-gatk-wf-chr19.yml	[moved from yml/bwa-gatk-wf-chr19.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwa-gatk-wf-report.yml	[moved from yml/bwa-gatk-wf-report.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwa-gatk-wf.yml	[moved from yml/bwa-gatk-wf.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwamem-samtools-sort.yml	[moved from yml/bwamem-samtools-sort.yml with 100% similarity]	blob \| history
WGS-processing/yml/bwamem-samtools-view.yml	[moved from yml/bwamem-samtools-view.yml with 100% similarity]	blob \| history
WGS-processing/yml/check-sam.yml	[moved from yml/check-sam.yml with 100% similarity]	blob \| history
WGS-processing/yml/gather-vcf.yml	[moved from yml/gather-vcf.yml with 100% similarity]	blob \| history
WGS-processing/yml/gather-vcf2.yml	[moved from yml/gather-vcf2.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-applyBQSR.yml	[moved from yml/gatk-applyBQSR.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-baserecalibrator.yml	[moved from yml/gatk-baserecalibrator.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-haplotypecaller-with-interval.yml	[moved from yml/gatk-haplotypecaller-with-interval.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-haplotypecaller.yml	[moved from yml/gatk-haplotypecaller.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-selectvariants.yml	[moved from yml/gatk-selectvariants.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-splitintervals.yml	[moved from yml/gatk-splitintervals.yml with 100% similarity]	blob \| history
WGS-processing/yml/gatk-wf-with-interval.yml	[moved from yml/gatk-wf-with-interval.yml with 100% similarity]	blob \| history
WGS-processing/yml/generate-report.yml	[moved from yml/generate-report.yml with 100% similarity]	blob \| history
WGS-processing/yml/getfastq.yml	[moved from yml/getfastq.yml with 100% similarity]	blob \| history
WGS-processing/yml/getgvcfs.yml	[moved from yml/getgvcfs.yml with 100% similarity]	blob \| history
WGS-processing/yml/gvcf-to-vcf.yml	[moved from yml/gvcf-to-vcf.yml with 100% similarity]	blob \| history
WGS-processing/yml/mark-duplicates.yml	[moved from yml/mark-duplicates.yml with 100% similarity]	blob \| history
WGS-processing/yml/report-wf.yml	[moved from yml/report-wf.yml with 100% similarity]	blob \| history
WGS-processing/yml/samtools-index.yml	[moved from yml/samtools-index.yml with 100% similarity]	blob \| history
WGS-processing/yml/samtools-sort-WGC069888D.yml	[moved from yml/samtools-sort-WGC069888D.yml with 100% similarity]	blob \| history
WGS-processing/yml/scatter-gatk-wf-with-interval.yml	[moved from yml/scatter-gatk-wf-with-interval.yml with 100% similarity]	blob \| history
docker/bam2fastq/Dockerfile	[deleted file]	blob \| history

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