SDAP-1261-refactor-k2

tools/bypass-trimgalore-pe.cwl

@@ -19,6 +19,9 @@ inputs:
     type: string?
     default: |
       #!/bin/bash
+      exec 1> error_msg.txt 2>&1
+      printf "bypass-trimgalore-pe.cwl\n$(date)\n"
+
       ORIGINAL_FASTQ_1=$0
       TRIMMED_FASTQ_1=$1
       TRIMMING_REPORT_1=$2
@@ -93,6 +96,16 @@ inputs:
 
 outputs:
 
+  error_msg:
+    type: File?
+    outputBinding:
+      glob: "error_msg.txt"
+
+  error_report:
+    type: File?
+    outputBinding:
+      glob: "error_report.txt"
+
   selected_fastq_file_1:
     type: File
     outputBinding:
@@ -117,55 +130,8 @@ outputs:
 baseCommand: ["bash", "-c"]
 
 
-$namespaces:
-  s: http://schema.org/
-
-$schemas:
-- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
-
-
-s:name: "bypass-trimgalore-pe"
-s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/bypass-trimgalore-pe.cwl
-s:codeRepository: https://github.com/Barski-lab/workflows
-s:license: http://www.apache.org/licenses/LICENSE-2.0
-
-s:isPartOf:
-  class: s:CreativeWork
-  s:name: Common Workflow Language
-  s:url: http://commonwl.org/
-
-s:creator:
-- class: s:Organization
-  s:legalName: "Cincinnati Children's Hospital Medical Center"
-  s:location:
-  - class: s:PostalAddress
-    s:addressCountry: "USA"
-    s:addressLocality: "Cincinnati"
-    s:addressRegion: "OH"
-    s:postalCode: "45229"
-    s:streetAddress: "3333 Burnet Ave"
-    s:telephone: "+1(513)636-4200"
-  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
-  s:department:
-  - class: s:Organization
-    s:legalName: "Allergy and Immunology"
-    s:department:
-    - class: s:Organization
-      s:legalName: "Barski Research Lab"
-      s:member:
-      - class: s:Person
-        s:name: Michael Kotliar
-        s:email: mailto:[email protected]
-        s:sameAs:
-        - id: http://orcid.org/0000-0002-6486-3898
-
+label: "bypass-trimgalore-pe"
 doc: |
-  If the number of reads in the trimmed_fastq_file_1 is less then min_reads_count, tool
-  will return original_fastq_file_1/2 and nulls as selected_report_file_1/2. Otherwise,
-  the trimmed_fastq_file_1/2 and trimming_report_file_1/2 will be returned. Might be
-  usefull in case of trimgalore removed all reads from the original_fastq_file_1/2.
-
-s:about: |
   If the number of reads in the trimmed_fastq_file_1 is less then min_reads_count, tool
   will return original_fastq_file_1/2 and nulls as selected_report_file_1/2. Otherwise,
   the trimmed_fastq_file_1/2 and trimming_report_file_1/2 will be returned. Might be

tools/bypass-trimgalore-se.cwl

@@ -19,6 +19,9 @@ inputs:
     type: string?
     default: |
       #!/bin/bash
+      exec 1> error_msg.txt 2>&1
+      printf "bypass-trimgalore-se.cwl\n$(date)\n"
+
       ORIGINAL_FASTQ=$0
       TRIMMED_FASTQ=$1
       TRIMMING_REPORT=$2
@@ -79,55 +82,8 @@ outputs:
 baseCommand: ["bash", "-c"]
 
 
-$namespaces:
-  s: http://schema.org/
-
-$schemas:
-- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
-
-
-s:name: "bypass-trimgalore-se"
-s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/bypass-trimgalore-se.cwl
-s:codeRepository: https://github.com/Barski-lab/workflows
-s:license: http://www.apache.org/licenses/LICENSE-2.0
-
-s:isPartOf:
-  class: s:CreativeWork
-  s:name: Common Workflow Language
-  s:url: http://commonwl.org/
-
-s:creator:
-- class: s:Organization
-  s:legalName: "Cincinnati Children's Hospital Medical Center"
-  s:location:
-  - class: s:PostalAddress
-    s:addressCountry: "USA"
-    s:addressLocality: "Cincinnati"
-    s:addressRegion: "OH"
-    s:postalCode: "45229"
-    s:streetAddress: "3333 Burnet Ave"
-    s:telephone: "+1(513)636-4200"
-  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
-  s:department:
-  - class: s:Organization
-    s:legalName: "Allergy and Immunology"
-    s:department:
-    - class: s:Organization
-      s:legalName: "Barski Research Lab"
-      s:member:
-      - class: s:Person
-        s:name: Michael Kotliar
-        s:email: mailto:[email protected]
-        s:sameAs:
-        - id: http://orcid.org/0000-0002-6486-3898
-
+label: "bypass-trimgalore-se"
 doc: |
-  If the number of reads in the trimmed_fastq_file is less then min_reads_count, tool
-  will return original_fastq_file and null as selected_report_file. Otherwise, the
-  trimmed_fastq_file and trimming_report_file will be returned. Might be usefull in
-  case of trimgalore removed all reads from the original_fastq_file
-
-s:about: |
   If the number of reads in the trimmed_fastq_file is less then min_reads_count, tool
   will return original_fastq_file and null as selected_report_file. Otherwise, the
   trimmed_fastq_file and trimming_report_file will be returned. Might be usefull in

tools/extract-fastq.cwl

@@ -15,10 +15,16 @@ hints:
 
 inputs:
 
-  script:
+  script_command:
     type: string?
     default: |
       #!/bin/bash
+      exec 1> error_msg.txt 2>&1
+      printf "extract-fastq.cwl\n$(date)\n"
+      printf "INPUTS:\n"
+      printf "\$0 - $0\n"
+      printf "\$1 - $1\n\n"
+
       shopt -s nocaseglob
 
       COMBINED="$0".fastq
@@ -35,7 +41,7 @@ inputs:
             cat "${FILE}" >> "${COMBINED}" || true
             ;;
           *)
-            echo "Error: file type unknown"
+            echo "Error: file type '${T}' unknown" > error_report.txt
             rm -f "${COMBINED}"
             exit 1
         esac
@@ -48,16 +54,14 @@ inputs:
 
     inputBinding:
       position: 5
-    doc: |
-      Bash script to extract compressed FASTQ file
+    doc: "Bash script to extract compressed FASTQ file"
 
   output_prefix:
     type: string?
     inputBinding:
       position: 6
     default: "merged"
-    doc: |
-      Output prefix for extracted file
+    doc: "Output prefix for extracted file"
 
   compressed_file:
     type:
@@ -66,61 +70,31 @@ inputs:
       items: File
     inputBinding:
       position: 7
-    doc: |
-      Compressed or uncompressed FASTQ file(s)
+    doc: "Compressed or uncompressed FASTQ file(s)"
 
 
 outputs:
 
+  error_msg:
+    type: File?
+    outputBinding:
+      glob: "error_msg.txt"
+
+  error_report:
+    type: File?
+    outputBinding:
+      glob: "error_report.txt"
+
   fastq_file:
     type: File
     outputBinding:
-      glob: "*"
+      glob: "*.fastq"
 
-baseCommand: [bash, '-c']
 
+baseCommand: [bash, '-c']
 
-$namespaces:
-  s: http://schema.org/
-
-$schemas:
-- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
-
-s:name: "extract-fastq"
-s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/extract-fastq.cwl
-s:codeRepository: https://github.com/Barski-lab/workflows
-s:license: http://www.apache.org/licenses/LICENSE-2.0
-
-s:isPartOf:
-  class: s:CreativeWork
-  s:name: Common Workflow Language
-  s:url: http://commonwl.org/
-
-s:creator:
-- class: s:Organization
-  s:legalName: "Cincinnati Children's Hospital Medical Center"
-  s:location:
-  - class: s:PostalAddress
-    s:addressCountry: "USA"
-    s:addressLocality: "Cincinnati"
-    s:addressRegion: "OH"
-    s:postalCode: "45229"
-    s:streetAddress: "3333 Burnet Ave"
-    s:telephone: "+1(513)636-4200"
-  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
-  s:department:
-  - class: s:Organization
-    s:legalName: "Allergy and Immunology"
-    s:department:
-    - class: s:Organization
-      s:legalName: "Barski Research Lab"
-      s:member:
-      - class: s:Person
-        s:name: Michael Kotliar
-        s:email: mailto:[email protected]
-        s:sameAs:
-        - id: http://orcid.org/0000-0002-6486-3898
 
+label: "extract-fastq"
 doc: |
   Tool to decompress input FASTQ file(s).
   If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input.
@@ -131,6 +105,3 @@ doc: |
   - check file type, decompress if needed
   - return 1, if file type is not recognized
   This script also works of input file doesn't have any extension at all
-
-s:about: |
-  Tool to decompress input FASTQ file

tools/fastx-quality-stats.cwl

@@ -72,6 +72,17 @@ inputs:
       Output file to store generated statistics. If not provided - return from default_output_filename function
 
 outputs:
+
+  error_msg:
+    type: File?
+    outputBinding:
+      glob: "error_msg.txt"
+
+  error_report:
+    type: File?
+    outputBinding:
+      glob: "error_report.txt"
+
   statistics_file:
     type: File
     outputBinding:
@@ -88,56 +99,12 @@ outputs:
 baseCommand: [fastx_quality_stats]
 
 
-$namespaces:
-  s: http://schema.org/
-
-$schemas:
-- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
-
-s:mainEntity:
-  $import: ./metadata/fastx-toolkit-metadata.yaml
-
-s:name: "fastx-quality-stats"
-s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/fastx-quality-stats.cwl
-s:codeRepository: https://github.com/Barski-lab/workflows
-s:license: http://www.apache.org/licenses/LICENSE-2.0
-
-s:isPartOf:
-  class: s:CreativeWork
-  s:name: Common Workflow Language
-  s:url: http://commonwl.org/
-
-s:creator:
-- class: s:Organization
-  s:legalName: "Cincinnati Children's Hospital Medical Center"
-  s:location:
-  - class: s:PostalAddress
-    s:addressCountry: "USA"
-    s:addressLocality: "Cincinnati"
-    s:addressRegion: "OH"
-    s:postalCode: "45229"
-    s:streetAddress: "3333 Burnet Ave"
-    s:telephone: "+1(513)636-4200"
-  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
-  s:department:
-  - class: s:Organization
-    s:legalName: "Allergy and Immunology"
-    s:department:
-    - class: s:Organization
-      s:legalName: "Barski Research Lab"
-      s:member:
-      - class: s:Person
-        s:name: Michael Kotliar
-        s:email: mailto:[email protected]
-        s:sameAs:
-        - id: http://orcid.org/0000-0002-6486-3898
-
+label: "fastx-quality-stats"
 doc: |
   Tool calculates statistics on the base of FASTQ file quality scores.
   If `output_filename` is not provided call function `default_output_filename` to return default output file name
   generated as `input_file` basename + `.fastxstat` extension.
 
-s:about: |
   usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE]
   Part of FASTX Toolkit 0.0.14 by A. Gordon ([email protected])
      [-h] = This helpful help screen.