projects
/
arvados-tutorial.git
/ blobdiff
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Updating readme and reorganization
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
bwamem-gatk-report-wf.cwl
diff --git
a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index f601e9549eec665e8ed113103394f1bc57fd52b8..dbe5cf05f88dbdfa6e1014b98306b344f2238589 100644
(file)
--- a/
WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/
WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@
-43,7
+43,7
@@
outputs:
outputSource: generate-report/report
steps:
fastqc:
outputSource: generate-report/report
steps:
fastqc:
- run:
./helper/
fastqc.cwl
+ run: fastqc.cwl
in:
fastq1: fastq1
fastq2: fastq2
in:
fastq1: fastq1
fastq2: fastq2
@@
-57,13
+57,13
@@
steps:
sample: sample
out: [bam]
samtools-sort:
sample: sample
out: [bam]
samtools-sort:
- run:
./helper/
samtools-sort.cwl
+ run: samtools-sort.cwl
in:
bam: bwamem-samtools-view/bam
sample: sample
out: [sortedbam]
mark-duplicates:
in:
bam: bwamem-samtools-view/bam
sample: sample
out: [sortedbam]
mark-duplicates:
- run:
./helper/
mark-duplicates.cwl
+ run: mark-duplicates.cwl
in:
bam: samtools-sort/sortedbam
out: [dupbam,dupmetrics]
in:
bam: samtools-sort/sortedbam
out: [dupbam,dupmetrics]
@@
-73,7
+73,7
@@
steps:
bam: mark-duplicates/dupbam
out: [indexedbam]
haplotypecaller:
bam: mark-duplicates/dupbam
out: [indexedbam]
haplotypecaller:
- run:
./helper/
scatter-gatk-wf-with-interval.cwl
+ run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
bam: samtools-index/indexedbam
in:
reference: reference
bam: samtools-index/indexedbam
@@
-82,7
+82,7
@@
steps:
knownsites1: knownsites
out: [gatheredgvcf]
generate-report:
knownsites1: knownsites
out: [gatheredgvcf]
generate-report:
- run:
./helper/
report-wf.cwl
+ run: report-wf.cwl
in:
gvcf: haplotypecaller/gatheredgvcf
samplename: sample
in:
gvcf: haplotypecaller/gatheredgvcf
samplename: sample