Removing white spaces and commenting schemas

[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..ee8ae4fdce5682340403ba4070a10fc52e1cb1f6 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -6,11 +6,11 @@ requirements:
   - class: SubworkflowFeatureRequirement
 
 inputs:
-  fastq1: 
+  fastq1:
     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)
@@ -57,18 +57,18 @@ inputs:
 outputs:
   qc-html:
     type: File[]
-    label: FASTQ QC report
+    label: FASTQ QC reports
     format: edam:format_1964 # HTML
     outputSource: fastqc/out-html
   qc-zip:
     type: File[]
-    label: Zip file of FASTQ QC report and associated data
+    label: Zip files of FASTQ QC report and associated data
     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
@@ -91,7 +91,7 @@ steps:
       sample: sample
     out: [bam]
   samtools-sort:
-    run: samtools-sort.cwl 
+    run: samtools-sort.cwl
     in:
       bam: bwamem-samtools-view/bam
       sample: sample
@@ -113,7 +113,7 @@ steps:
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount
-      knownsites1: knownsites
+      knownsites: knownsites
     out: [gatheredgvcf]
   generate-report:
     run: report-wf.cwl
@@ -124,7 +124,7 @@ steps:
       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