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Updating HTML edam comments
[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 f1cfad4cac14af5825c1cd14209e82ed075b1f93..522bd822cdbd7178a9c1f8ee9028ca0a5cf86137 100644
(file)
--- a/
WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/
WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@
-3,14
+3,14
@@
class: Workflow
label: WGS processing workflow for single sample
requirements:
label: WGS processing workflow for single sample
requirements:
- - class: SubworkflowFeatureRequirement
+ SubworkflowFeatureRequirement: {}
inputs:
inputs:
- fastq1:
+ fastq1:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R1)
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R1)
- fastq2:
+ fastq2:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R2)
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R2)
@@
-47,32
+47,32
@@
inputs:
label: Function used to create HTML report
headhtml:
type: File
label: Function used to create HTML report
headhtml:
type: File
- format: edam:format_
1964
# HTML
+ format: edam:format_
2331
# HTML
label: Header for HTML report
tailhtml:
type: File
label: Header for HTML report
tailhtml:
type: File
- format: edam:format_
1964
# HTML
+ format: edam:format_
2331
# HTML
label: Footer for HTML report
outputs:
qc-html:
type: File[]
label: Footer for HTML report
outputs:
qc-html:
type: File[]
- label: FASTQ QC report
- format: edam:format_
1964
# HTML
+ label: FASTQ QC report
s
+ format: edam:format_
2331
# HTML
outputSource: fastqc/out-html
qc-zip:
type: File[]
outputSource: fastqc/out-html
qc-zip:
type: File[]
- label: Zip file of FASTQ QC report and associated data
+ label: Zip file
s
of FASTQ QC report and associated data
outputSource: fastqc/out-zip
gvcf:
type: File
outputSource: haplotypecaller/gatheredgvcf
format: edam:format_3016 # GVCF
outputSource: fastqc/out-zip
gvcf:
type: File
outputSource: haplotypecaller/gatheredgvcf
format: edam:format_3016 # GVCF
- label: GVCF generated from GATK
+ label: GVCF generated from GATK
Haplotype Caller
report:
type: File
outputSource: generate-report/report
report:
type: File
outputSource: generate-report/report
- format: edam:format_
1964
# HTML
+ format: edam:format_
2331
# HTML
label: ClinVar variant report
steps:
label: ClinVar variant report
steps:
@@
-91,7
+91,7
@@
steps:
sample: sample
out: [bam]
samtools-sort:
sample: sample
out: [bam]
samtools-sort:
- run: samtools-sort.cwl
+ run: samtools-sort.cwl
in:
bam: bwamem-samtools-view/bam
sample: sample
in:
bam: bwamem-samtools-view/bam
sample: sample
@@
-113,18
+113,18
@@
steps:
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
- knownsites
1
: knownsites
+ knownsites: knownsites
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl
in:
gvcf: haplotypecaller/gatheredgvcf
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl
in:
gvcf: haplotypecaller/gatheredgvcf
- sample
name
: sample
+ sample: sample
clinvarvcf: clinvarvcf
reportfunc: reportfunc
headhtml: headhtml
tailhtml: tailhtml
clinvarvcf: clinvarvcf
reportfunc: reportfunc
headhtml: headhtml
tailhtml: tailhtml
- out: [report]
+ out: [report]
s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
@@
-133,6
+133,6
@@
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
s: https://schema.org/
edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+
#
$schemas:
+
#
- https://schema.org/version/latest/schema.rdf
+
#
- http://edamontology.org/EDAM_1.18.owl