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Bugfix .bai secondary file for ApplyBSQR behavior
[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 56efe6545d928b4fafdb6b79bce6f8a821761e44..41c9130e923c35cd86164f404a38db4165225eb4 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)
@@
-26,15
+26,24
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
- knownsites:
+ knownsites
1
:
type: File
format: edam:format_3016 # VCF
type: File
format: edam:format_3016 # VCF
- label: VCF of known
polymorphic
sites for BQSR
+ label: VCF of known
SNPS
sites for BQSR
secondaryFiles:
secondaryFiles:
- - .tbi
+ - .idx
+ knownsites2:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known indel sites for BQSR
+ secondaryFiles:
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
scattercount:
type: string
label: Desired split for variant calling
@@
-47,18
+56,18
@@
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: FASTQ QC reports
label: Footer for HTML report
outputs:
qc-html:
type: File[]
label: FASTQ QC reports
- format: edam:format_
1964
# HTML
+ format: edam:format_
2331
# HTML
outputSource: fastqc/out-html
qc-zip:
type: File[]
outputSource: fastqc/out-html
qc-zip:
type: File[]
@@
-72,7
+81,7
@@
outputs:
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
+100,7
@@
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
@@
-110,21
+119,23
@@
steps:
run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
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
+144,6
@@
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
s: https://schema.org/
edam: http://edamontology.org/
-$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