Removing white spaces and commenting schemas

[arvados-tutorial.git] / WGS-processing / cwl / helper / bwamem-samtools-view.cwl

diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
index c539325544572fc3968cb979fe4617723f26601a..32eb5ce0ab53cfbc4b421905ba59bff2b52df716 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
+++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
@@ -1,10 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Aligning fastqs with BWA
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Align FASTQs with BWA
 
 requirements:
   DockerRequirement:
@@ -12,16 +8,26 @@ requirements:
   ShellCommandRequirement: {}
   ResourceRequirement:
     ramMin: 50000
-    coresMin: 16 
+    coresMin: 16
 
 hints:
   arv:RuntimeConstraints:
-    keep_cache: 1024 
+    keep_cache: 1024
     outputDirType: keep_output_dir
+  SoftwareRequirement:
+    packages:
+      BWA:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_010910" ]
+        version: [ "0.7.17" ]
+      Samtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+        version: [ "1.10" ]
 
 inputs:
   reference:
     type: File
+    format: edam:format_1929 # FASTA
+    label: Reference genome
     secondaryFiles:
       - .amb
       - .ann
@@ -30,15 +36,25 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  fastq1: File
-  fastq2: File
-  sample: string
+  fastq1:
+    type: File
+    format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R1)
+  fastq2:
+    type: File
+    format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R2)
+  sample:
+    type: string
+    label: Sample Name
 
 stdout: $(inputs.sample).bam
 
 outputs:
   bam:
     type: File
+    format: edam:format_2572 # BAM
+    label: Alignments in BAM format
     outputBinding:
       glob: "*bam"
 
@@ -50,7 +66,7 @@ arguments:
   - $(runtime.cores)
   - $(inputs.reference)
   - -R
-  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
+  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
   - -c
   - '250'
   - $(inputs.fastq1)
@@ -65,3 +81,16 @@ arguments:
   - -S
   - shellQuote: false
     valueFrom: '-'
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl