Merge pull request #124 from mskcc/dev

nikhil · web-flow · commit dbff0c5ae06a · 2025-05-20T11:02:06.000-04:00
Release 12.12.1
diff --git a/cwl/add_af.cwl b/cwl/add_af.cwl
@@ -8,7 +8,9 @@ baseCommand: ['add_af.py']
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
-
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 inputs:
   input_file:
     type: File
diff --git a/cwl/add_header.cwl b/cwl/add_header.cwl
@@ -10,7 +10,9 @@ requirements:
         entry: |-
           echo "$1"
           cat "$2"
-
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 inputs:
   header_str:
     type: string
diff --git a/cwl/add_is_in_impact.cwl b/cwl/add_is_in_impact.cwl
@@ -8,6 +8,9 @@ baseCommand: ['add_is_in_impact.py', '--include-assay']
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   input_file:
diff --git a/cwl/add_msi_status.cwl b/cwl/add_msi_status.cwl
@@ -6,6 +6,9 @@ baseCommand: [ "add_msi_status.py" ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   input_filename:
diff --git a/cwl/bgzip.cwl b/cwl/bgzip.cwl
@@ -7,6 +7,9 @@ baseCommand: [ "bgzip" ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:igv-reports-1.0.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 stdout: $(inputs.output_filename)
 
diff --git a/cwl/calc-tmb.cwl b/cwl/calc-tmb.cwl
@@ -7,6 +7,9 @@ baseCommand: ["calc-tmb.py", 'from-file']
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   input_file:
diff --git a/cwl/cat.cwl b/cwl/cat.cwl
@@ -6,6 +6,9 @@ baseCommand: [ cat ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 stdout: output.txt
 inputs:
   input_files:
diff --git a/cwl/concat-mafs.cwl b/cwl/concat-mafs.cwl
@@ -40,6 +40,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: inputs_dir
diff --git a/cwl/concat-mafs_all_cols.cwl b/cwl/concat-mafs_all_cols.cwl
@@ -17,6 +17,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: inputs_dir
diff --git a/cwl/concat-tables.cwl b/cwl/concat-tables.cwl
@@ -6,6 +6,9 @@ baseCommand: [ "concat-tables.py", "--no-carriage-returns" ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 inputs:
   output_filename:
     type: string
diff --git a/cwl/concat-tables_dir.cwl b/cwl/concat-tables_dir.cwl
@@ -9,6 +9,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: inputs_dir
diff --git a/cwl/concat.cwl b/cwl/concat.cwl
@@ -11,6 +11,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 # echo ${return item['path'] for item in inputs.input_files}
 inputs:
diff --git a/cwl/concat_with_comments.cwl b/cwl/concat_with_comments.cwl
@@ -9,6 +9,9 @@ baseCommand: [ 'concat_with_comments.sh' ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   comment_label:
diff --git a/cwl/convert_TNMafPileupPair_to_TMBInputPair.cwl b/cwl/convert_TNMafPileupPair_to_TMBInputPair.cwl
@@ -4,6 +4,7 @@ class: ExpressionTool
 requirements:
 - $import: types.yml
 
+
 inputs:
   pairs: "types.yml#TNMafPileupPair[]"
 
diff --git a/cwl/copy_number.cwl b/cwl/copy_number.cwl
@@ -19,6 +19,9 @@ requirements:
     dockerPull: mskcc/roslin-variant-facets:1.6.3
     # TODO: switch to this container when it is working;
     # dockerPull: mskcc/helix_filters_01:facets-1.6.3
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   output_cna_filename:
diff --git a/cwl/cp.cwl b/cwl/cp.cwl
@@ -6,6 +6,9 @@ baseCommand: cp
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 inputs:
   input_file:
     type: File
diff --git a/cwl/cut.cwl b/cwl/cut.cwl
@@ -6,6 +6,9 @@ baseCommand: [ cut ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 stdout: output.txt
 inputs:
   field_indexes:
diff --git a/cwl/deduplicate-maf.cwl b/cwl/deduplicate-maf.cwl
@@ -30,6 +30,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: run.deduplicate_maf.sh
diff --git a/cwl/env_container.cwl b/cwl/env_container.cwl
@@ -8,6 +8,9 @@ doc: "CWL to save a copy of the execution environment for debugging"
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 stdout: env.container.txt
 
diff --git a/cwl/fillout_clinical_filter.cwl b/cwl/fillout_clinical_filter.cwl
@@ -17,6 +17,9 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: DockerRequirement
     dockerPull: mskcc/helix_filters_01:21.4.1
+  - class: ResourceRequirement
+    ramMin: 8000
+    coresMin: 3
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.fillout_vcf)
diff --git a/cwl/fillout_get_samples_with_without_maf.cwl b/cwl/fillout_get_samples_with_without_maf.cwl
@@ -6,6 +6,9 @@ doc: separate the samples list into samples with and without .maf files
 requirements:
   - class: InlineJavascriptRequirement
   - $import: types.yml
+  - class: ResourceRequirement
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   samples:
diff --git a/cwl/fillout_index_prefilter.cwl b/cwl/fillout_index_prefilter.cwl
@@ -42,6 +42,7 @@ steps:
       requirements:
         ResourceRequirement:
           coresMin: 4
+          ramMin: 8000
         DockerRequirement:
           dockerPull: mskcc/helix_filters_01:samtools-1.9
         InitialWorkDirRequirement:
diff --git a/cwl/fillout_maf2vcf.cwl b/cwl/fillout_maf2vcf.cwl
@@ -12,6 +12,9 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: DockerRequirement
     dockerPull: mskcc/helix_filters_01:21.4.1
+  - class: ResourceRequirement
+    ramMin: 8000
+    coresMin: 3
   - class: InitialWorkDirRequirement
     listing:
     # NOTE: might need dos2unix for some that give errors ERROR: Your MAF uses CR line breaks, which we can't support. Please use LF or CRLF.
diff --git a/cwl/fillout_post_processing.cwl b/cwl/fillout_post_processing.cwl
@@ -71,6 +71,7 @@ steps:
       baseCommand: [ "sh", "run.vcf_to_maf.sh" ]
       requirements:
         ResourceRequirement:
+          ramMin: 8000
           coresMin: 8
         DockerRequirement:
           dockerPull: mskcc/roslin-variant-vcf2maf:1.6.17
diff --git a/cwl/filterUncalledMutations.cwl b/cwl/filterUncalledMutations.cwl
@@ -14,6 +14,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix:21.5.3
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: run.filterUncalledMutations.sh
diff --git a/cwl/full-outer-join.cwl b/cwl/full-outer-join.cwl
@@ -6,6 +6,9 @@ baseCommand: [ "full-outer-join.R" ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:R-3.5.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 inputs:
   table1:
     type: File
diff --git a/cwl/fusion_filter.cwl b/cwl/fusion_filter.cwl
@@ -9,6 +9,9 @@ baseCommand: ["fusion_filter.py"]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   fusions_file:
diff --git a/cwl/fusion_to_sv.cwl b/cwl/fusion_to_sv.cwl
@@ -6,6 +6,9 @@ baseCommand: ["fusion_to_sv_converter.py"]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.6.0
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 inputs:
   fusion_file:
     type: File
diff --git a/cwl/generate_cBioPortal_file.cwl b/cwl/generate_cBioPortal_file.cwl
@@ -7,6 +7,9 @@ baseCommand: [ "generate_cbioPortal_files.py" ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.6.0
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   # required for every invocation
diff --git a/cwl/getbasecountsmultisample.cwl b/cwl/getbasecountsmultisample.cwl
@@ -22,6 +22,7 @@ baseCommand: [
 requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
+    ramMin: 8000
     coresMin: 4
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:getbasecountsmultisample-1.2.2
diff --git a/cwl/head.cwl b/cwl/head.cwl
@@ -6,6 +6,9 @@ baseCommand: [ head ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 stdout: $(inputs.input_file.basename).head.txt
 inputs:
   num_lines:
diff --git a/cwl/igv-reports.cwl b/cwl/igv-reports.cwl
@@ -20,6 +20,9 @@ requirements:
   InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:igv-reports-1.0.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 arguments:
   - valueFrom: ${ return inputs.vcf_gz_files.map((a) => a.path).join(' ') + ' ' + inputs.bam_files.map((a) => a.path).join(' '); }
diff --git a/cwl/index_bam.cwl b/cwl/index_bam.cwl
@@ -8,7 +8,7 @@ label: cmo-index
 requirements:
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 2
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-cmo-utils:1.9.15
   InitialWorkDirRequirement:
diff --git a/cwl/index_sample_bam.cwl b/cwl/index_sample_bam.cwl
@@ -7,6 +7,7 @@ requirements:
   - $import: types.yml
   - class: InlineJavascriptRequirement
   - class: ResourceRequirement
+    ramMin: 16000
     coresMin: 4 # make sure this matches what is in the command below!
   - class: DockerRequirement
     dockerPull: mskcc/helix_filters_01:samtools-1.9
diff --git a/cwl/index_vcf.cwl b/cwl/index_vcf.cwl
@@ -7,6 +7,9 @@ baseCommand: [ "tabix", "-p", "vcf" ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:igv-reports-1.0.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   # tabix does not work unless you stage the input file here
   InitialWorkDirRequirement:
     listing: [ $(inputs.input_file) ]
diff --git a/cwl/ls.cwl b/cwl/ls.cwl
@@ -7,6 +7,9 @@ doc: "CWL to save a copy of the execution Directory for debugging"
 
 requirements:
   InlineJavascriptRequirement: {}
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 stdout: ls.txt
 
diff --git a/cwl/ls_dir.cwl b/cwl/ls_dir.cwl
@@ -9,6 +9,9 @@ requirements:
   InlineJavascriptRequirement: {}
   # DockerRequirement:
   #   dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: some_dir
diff --git a/cwl/maf2bed.cwl b/cwl/maf2bed.cwl
@@ -5,6 +5,9 @@ class: CommandLineTool
 baseCommand: [ "bash", "run.maf2bed.sh" ]
 
 requirements:
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
   InitialWorkDirRequirement:
     listing:
       - entryname: run.maf2bed.sh
diff --git a/cwl/maf2vcf.cwl b/cwl/maf2vcf.cwl
@@ -7,6 +7,9 @@ baseCommand: [ "maf2vcf.pl", "--output-dir", "." ]
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:igv-reports-1.0.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   maf_file:
diff --git a/cwl/maf_col_filter.cwl b/cwl/maf_col_filter.cwl
@@ -9,6 +9,9 @@ baseCommand: ['maf_col_filter.py']
 requirements:
   DockerRequirement:
     dockerPull: mskcc/helix_filters_01:21.4.1
+  ResourceRequirement:
+    ramMin: 8000
+    coresMin: 3
 
 inputs:
   input_file:
diff --git a/cwl/maf_filter.cwl b/cwl/maf_filter.cwl
diff --git a/cwl/merge-tables.cwl b/cwl/merge-tables.cwl
diff --git a/cwl/mergebed.cwl b/cwl/mergebed.cwl
diff --git a/cwl/paste-col-wrapper.cwl b/cwl/paste-col-wrapper.cwl
diff --git a/cwl/paste-col.cwl b/cwl/paste-col.cwl
diff --git a/cwl/reduce_sig_figs.cwl b/cwl/reduce_sig_figs.cwl
diff --git a/cwl/replace.cwl b/cwl/replace.cwl
diff --git a/cwl/replace_colname.cwl b/cwl/replace_colname.cwl
diff --git a/cwl/report.cwl b/cwl/report.cwl
diff --git a/cwl/run-facets-legacy-wrapper.cwl b/cwl/run-facets-legacy-wrapper.cwl
diff --git a/cwl/run-facets-wrapper.cwl b/cwl/run-facets-wrapper.cwl
diff --git a/cwl/sleep.cwl b/cwl/sleep.cwl
diff --git a/cwl/snp-pileup-wrapper.cwl b/cwl/snp-pileup-wrapper.cwl
diff --git a/cwl/strip.cwl b/cwl/strip.cwl
diff --git a/cwl/tail.cwl b/cwl/tail.cwl
diff --git a/cwl/tmb_variant_filter.cwl b/cwl/tmb_variant_filter.cwl
diff --git a/cwl/updateCaseList.cwl b/cwl/updateCaseList.cwl
diff --git a/cwl/update_cBioPortal_data.cwl b/cwl/update_cBioPortal_data.cwl
diff --git a/cwl/vcf_sort.cwl b/cwl/vcf_sort.cwl
diff --git a/cwl/write-str.cwl b/cwl/write-str.cwl
