Merge branch 'release/1.2.4'

msk-access · Aug 8, 2023 · d9bbc74 · d9bbc74
2 parents 18a44c5 + a493b7f
commit d9bbc74
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diff --git a/command_line_tools b/command_line_tools
diff --git a/qc_duplex_bam/qc_duplex_bam_v2.0.cwl b/qc_duplex_bam/qc_duplex_bam_v2.0.cwl
@@ -381,7 +381,7 @@ steps:
       - id: sequence_qc_noise_n
       - id: sequence_qc_noise_del
       - id: sequence_qc_figures
-    run: ../command_line_tools/sequence_qc/0.2.3/sequence_qc_0.2.3.cwl
+    run: ../command_line_tools/sequence_qc/0.2.4/sequence_qc_0.2.4.cwl
     'sbg:x': 353.515625
     'sbg:y': 1426.328125
   - id: biometrics_extract_0_2_14

diff --git a/qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl b/qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl
@@ -2140,13 +2140,13 @@
         },
         {
             "class": "CommandLineTool",
-            "id": "#sequence_qc_0.2.3.cwl",
+            "id": "#sequence_qc_0.2.4.cwl",
             "baseCommand": [
                 "calculate_noise"
             ],
             "inputs": [
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/reference",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/reference",
                     "type": "File",
                     "inputBinding": {
                         "position": 0,
@@ -2158,7 +2158,7 @@
                     "doc": "Path to reference fasta, containing all regions in bed_file"
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/bam_file",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/bam_file",
                     "type": "File",
                     "inputBinding": {
                         "position": 0,
@@ -2170,7 +2170,7 @@
                     "doc": "Path to BAM file for calculating noise  [required]"
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/bed_file",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/bed_file",
                     "type": "File",
                     "inputBinding": {
                         "position": 0,
@@ -2179,7 +2179,7 @@
                     "doc": "Path to BED file containing regions over which to calculate noise  [required]"
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sample_id",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sample_id",
                     "type": "string",
                     "inputBinding": {
                         "position": 0,
@@ -2188,7 +2188,7 @@
                     "doc": "Prefix to include in all output file names"
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/threshold",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/threshold",
                     "type": [
                         "null",
                         "float"
@@ -2200,7 +2200,7 @@
                     "doc": "Alt allele frequency past which to ignore positions from the calculation."
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/truncate",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/truncate",
                     "type": [
                         "null",
                         "int"
@@ -2212,7 +2212,7 @@
                     "doc": "Whether to exclude trailing bases from reads that only partially overlap the bed file (0 or 1)"
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/min_mapq",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/min_mapq",
                     "type": [
                         "null",
                         "int"
@@ -2224,7 +2224,7 @@
                     "doc": "Exclude reads with a lower mapping quality"
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/min_basq",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/min_basq",
                     "type": [
                         "null",
                         "int"
@@ -2238,49 +2238,49 @@
             ],
             "outputs": [
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_pileup",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_pileup",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_pileup.tsv'\n}"
                     }
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_positions",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_positions",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_noise_positions.tsv'\n}"
                     }
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_by_substitution",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_by_substitution",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_noise_by_substitution.tsv'\n}"
                     }
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_acgt",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_acgt",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_noise_acgt.tsv'\n}"
                     }
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_n",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_n",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_noise_n.tsv'\n}"
                     }
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_del",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_del",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_noise_del.tsv'\n}"
                     }
                 },
                 {
-                    "id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_figures",
+                    "id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_figures",
                     "type": "File",
                     "outputBinding": {
                         "glob": "${\n    return inputs.sample_id + '_noise.html'\n}"
@@ -2295,7 +2295,7 @@
                 },
                 {
                     "class": "DockerRequirement",
-                    "dockerPull": "ghcr.io/msk-access/sequence_qc:0.2.3"
+                    "dockerPull": "ghcr.io/msk-access/sequence_qc:0.2.4"
                 },
                 {
                     "class": "InlineJavascriptRequirement"
@@ -2320,8 +2320,8 @@
                     "http://xmlns.com/foaf/0.1/member": [
                         {
                             "class": "http://xmlns.com/foaf/0.1/Person",
-                            "http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org",
-                            "http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
+                            "http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org",
+                            "http://xmlns.com/foaf/0.1/name": "Ronak Shah"
                         }
                     ],
                     "http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
@@ -2344,7 +2344,7 @@
                 {
                     "class": "http://usefulinc.com/ns/doap#Version",
                     "http://usefulinc.com/ns/doap#name": "sesquence_qc",
-                    "http://usefulinc.com/ns/doap#revision": "0.2.3"
+                    "http://usefulinc.com/ns/doap#revision": "0.2.4"
                 }
             ]
         },
@@ -3031,7 +3031,7 @@
                             "id": "#main/calculate_noise/sequence_qc_figures"
                         }
                     ],
-                    "run": "#sequence_qc_0.2.3.cwl",
+                    "run": "#sequence_qc_0.2.4.cwl",
                     "https://www.sevenbridges.com/x": 353.515625,
                     "https://www.sevenbridges.com/y": 1426.328125
                 },

diff --git a/vardict_workflow/run_processed_vardict.cwl b/vardict_workflow/run_processed_vardict.cwl
@@ -59,6 +59,24 @@ outputs:
     type: File
     'sbg:x': 1064.255126953125
     'sbg:y': 213.53125
+  - id: vardict_output
+    outputSource:
+      - vardict/output
+    type: File
+    'sbg:x': 397.9921875
+    'sbg:y': 590.5
+  - id: single_filter_vcf
+    outputSource:
+      - pv_vardict_single_filter/vcf
+    type: File
+    'sbg:x': 688.9921875
+    'sbg:y': 587.5
+  - id: single_filter_vcf_complex
+    outputSource:
+      - pv_vardict_single_filter/vcf_complex
+    type: File
+    'sbg:x': 942.9921875
+    'sbg:y': 552.5
 steps:
   - id: vardict
     in:
@@ -113,8 +131,8 @@ steps:
       - id: vcf
     run: >-
       ../command_line_tools/postprocessing_variant_calls/0.1.5/pv_vardict_single_filter.cwl
-    'sbg:x': 513.37158203125
-    'sbg:y': 213.53125
+    'sbg:x': 483
+    'sbg:y': 220
   - id: variants_concat
     in:
       - id: fastaRef

diff --git a/vardict_workflow/run_processed_vardict__packed.cwl b/vardict_workflow/run_processed_vardict__packed.cwl
@@ -1731,6 +1731,33 @@
                     "type": "File",
                     "https://www.sevenbridges.com/x": 1064.255126953125,
                     "https://www.sevenbridges.com/y": 213.53125
+                },
+                {
+                    "id": "#main/vardict_output",
+                    "outputSource": [
+                        "#main/vardict/output"
+                    ],
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 397.9921875,
+                    "https://www.sevenbridges.com/y": 590.5
+                },
+                {
+                    "id": "#main/single_filter_vcf",
+                    "outputSource": [
+                        "#main/pv_vardict_single_filter/vcf"
+                    ],
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 688.9921875,
+                    "https://www.sevenbridges.com/y": 587.5
+                },
+                {
+                    "id": "#main/single_filter_vcf_complex",
+                    "outputSource": [
+                        "#main/pv_vardict_single_filter/vcf_complex"
+                    ],
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 942.9921875,
+                    "https://www.sevenbridges.com/y": 552.5
                 }
             ],
             "steps": [
@@ -1837,8 +1864,8 @@
                         }
                     ],
                     "run": "#pv_vardict_single_filter.cwl",
-                    "https://www.sevenbridges.com/x": 513.37158203125,
-                    "https://www.sevenbridges.com/y": 213.53125
+                    "https://www.sevenbridges.com/x": 483,
+                    "https://www.sevenbridges.com/y": 220
                 },
                 {
                     "id": "#main/variants_concat",

diff --git a/variant_annotation/README.md b/variant_annotation/README.md
@@ -6,16 +6,25 @@
 
 - [snpift](https://msk-access.gitbook.io/command-line-tools-cwl/snpsift_annotate_5.0/)
 - [vcf2maf](https://msk-access.gitbook.io/command-line-tools-cwl/vcf2maf_1.6.21/)
+- [maf_annotated_by_bed](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.0/maf_annotated_by_bed/)
 
 #### Usage
 
 ```bash
-usage: variant_annotation.cwl [-h]  --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
+usage: variant_annotation.cwl
+       [-h] --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
        --vardict_input_vcf VARDICT_INPUT_VCF --input_cosmicprevalenceDB_vcf
        INPUT_COSMICPREVALENCEDB_VCF [--min_hom_vaf MIN_HOM_VAF]
-       [--output_mafName OUTPUT_MAFNAME] [--retain_info RETAIN_INFO]
+       [--output_vcf2mafName OUTPUT_VCF2MAFNAME] [--retain_info RETAIN_INFO]
        [--tumor_id TUMOR_ID] [--snpsift_countOpName SNPSIFT_COUNTOPNAME]
-       [--snpsift_prevalOpName SNPSIFT_PREVALOPNAME]
+       [--snpsift_prevalOpName SNPSIFT_PREVALOPNAME] --opOncoKbMafName
+       OPONCOKBMAFNAME --oncoKbApiToken ONCOKBAPITOKEN
+       [--oncoKbAnnotateHotspots] --input_complexity_bed INPUT_COMPLEXITY_BED
+       --input_DUST_bed INPUT_DUST_BED
+       [--output_DUST_filename OUTPUT_DUST_FILENAME]
+       [--column_name_DUST COLUMN_NAME_DUST]
+       [--output_complexity_filename OUTPUT_COMPLEXITY_FILENAME]
+       [--column_name_complexity COLUMN_NAME_COMPLEXITY]
        [job_order]
 
 positional arguments:
@@ -27,10 +36,19 @@ optional arguments:
   --vardict_input_vcf VARDICT_INPUT_VCF
   --input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF
   --min_hom_vaf MIN_HOM_VAF
-  --output_mafName OUTPUT_MAFNAME
+  --output_vcf2mafName OUTPUT_VCF2MAFNAME
   --retain_info RETAIN_INFO
   --tumor_id TUMOR_ID
   --snpsift_countOpName SNPSIFT_COUNTOPNAME
   --snpsift_prevalOpName SNPSIFT_PREVALOPNAME
+  --opOncoKbMafName OPONCOKBMAFNAME
+  --oncoKbApiToken ONCOKBAPITOKEN
+  --oncoKbAnnotateHotspots
+  --input_complexity_bed INPUT_COMPLEXITY_BED
+  --input_DUST_bed INPUT_DUST_BED
+  --output_DUST_filename OUTPUT_DUST_FILENAME
+  --column_name_DUST COLUMN_NAME_DUST
+  --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME
+  --column_name_complexity COLUMN_NAME_COMPLEXITY
 ```
 
diff --git a/variant_annotation/example_inputs.yaml b/variant_annotation/example_inputs.yaml
@@ -11,7 +11,18 @@ input_cosmicprevalenceDB_vcf:
     /work/cch/production/resources/cosmic/versions/v96/CosmicCodingMuts_GRCh37_processed.vcf.gz
 snpsift_countOpName: tumorId_cosmic.vcf
 snpsift_prevalOpName: tumorId_preval.vcf
-output_mafName: tumorId_annotated.maf
+opOncoKbMafName: tumorId_annotated.maf
 retain_info: CNT,TUMOR_TYPE
 tumor_id: tumorId
 min_hom_vaf: 0
+column_name_mappability: mappability
+column_name_complexity: complexity
+input_mappability_bed:
+  class: File
+  path: /path/to/mappability_algo/bedfile.bed
+input_complexity_bed:
+  class: File
+  path: /path/to/complexity/bedfile.bed
+output_mappability_filename: mappability.maf
+output_complexity_filename: complexity.maf
+output_vcf2mafName: vcf2maf.maf