Merge pull request #196 from msk-access/PV_vardict

Author: rhshah

.gitignore

@@ -107,3 +107,4 @@ ENV/
 #vscode
 .vscode/*
 
+pv_vardict/pv_maf_processing.cwl

command_line_tools

@@ -6,27 +6,39 @@
 
 - [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/)
+- [maf_annotated_by_bed](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/)
+- [maf_annotated_by_tsv](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/)
 
 #### Usage
 
 ```bash
 usage: variant_annotation.cwl
-       [-h] --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
+        [-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_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]
+       [--oncoKbAnnotateHotspots] --input_mappability_bed
+       INPUT_MAPPABILITY_BED --input_complexity_bed INPUT_COMPLEXITY_BED
+       --output_mappability_filename OUTPUT_MAPPABILITY_FILENAME
+       [--column_name_mappability COLUMN_NAME_MAPPABILITY]
+       --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME
        [--column_name_complexity COLUMN_NAME_COMPLEXITY]
+       --input_hotspot_tsv_file INPUT_HOTSPOT_TSV_FILE
+       [--output_column_name_hotpsot OUTPUT_COLUMN_NAME_HOTPSOT]
+       [--output_hotspot_maf_name OUTPUT_HOTSPOT_MAF_NAME]
+       --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE
+       [--output_47kchpd_maf_name OUTPUT_47KCHPD_MAF_NAME]
+       [--output_column_name_47kchpd OUTPUT_COLUMN_NAME_47KCHPD]
+       --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE
+       [--output_maf_name_panmyeloid OUTPUT_MAF_NAME_PANMYELOID]
+       [--output_column_name_panmyeloid OUTPUT_COLUMN_NAME_PANMYELOID]
        [job_order]
 
+variant_annotation
+
 positional arguments:
   job_order             Job input json file
 
@@ -44,11 +56,48 @@ optional arguments:
   --opOncoKbMafName OPONCOKBMAFNAME
   --oncoKbApiToken ONCOKBAPITOKEN
   --oncoKbAnnotateHotspots
+  --input_mappability_bed INPUT_MAPPABILITY_BED
   --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_mappability_filename OUTPUT_MAPPABILITY_FILENAME
+  --column_name_mappability COLUMN_NAME_MAPPABILITY
   --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME
   --column_name_complexity COLUMN_NAME_COMPLEXITY
+  --input_hotspot_tsv_file INPUT_HOTSPOT_TSV_FILE
+  --output_column_name_hotpsot OUTPUT_COLUMN_NAME_HOTPSOT
+  --output_hotspot_maf_name OUTPUT_HOTSPOT_MAF_NAME
+  --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE
+  --output_47kchpd_maf_name OUTPUT_47KCHPD_MAF_NAME
+  --output_column_name_47kchpd OUTPUT_COLUMN_NAME_47KCHPD
+  --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE
+  --output_maf_name_panmyeloid OUTPUT_MAF_NAME_PANMYELOID
+  --output_column_name_panmyeloid OUTPUT_COLUMN_NAME_PANMYELOID
+```
+
+## Chipvar_postprocessing
+
+### Tools used
+
+- [maf_filter_cmoch](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_filter_cmoch/)
+- [maf_tag_cmoch](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_tag_cmoch/)
+
+#### Usage
+
+```
+usage: chipvar_processing.cwl
+[-h] --input_variant_annotated_maf INPUT_VARIANT_ANNOTATED_MAF
+       [--output_maf_name_filter OUTPUT_MAF_NAME_FILTER]
+       [--output_maf_name_tag OUTPUT_MAF_NAME_TAG]
+       [job_order]
+
+chipvar_processing
+
+positional arguments:
+  job_order             Job input json file
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --input_variant_annotated_maf INPUT_VARIANT_ANNOTATED_MAF
+  --output_maf_name_filter OUTPUT_MAF_NAME_FILTER
+  --output_maf_name_tag OUTPUT_MAF_NAME_TAG
 ```
 

variant_annotation/README.md

@@ -0,0 +1,60 @@
+class: Workflow
+cwlVersion: v1.0
+id: chipvar_processing
+label: chipvar_processing
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: output_maf_name_filter
+    type: string?
+    'sbg:x': -453
+    'sbg:y': -272.5
+  - id: output_maf_name_tag
+    type: string?
+    'sbg:x': -911
+    'sbg:y': -200
+  - id: input_variant_annotated_maf
+    type: File
+    'sbg:x': -1012.5234375
+    'sbg:y': 20
+outputs:
+  - id: output_maf_cmoch_filtered
+    outputSource:
+      - pv_maf_filter/output
+    type: File?
+    'sbg:x': -183
+    'sbg:y': 111
+  - id: output_maf_cmoch_tag
+    outputSource:
+      - pv_maf_tag/output
+    type: File?
+    'sbg:x': -559
+    'sbg:y': 104
+steps:
+  - id: pv_maf_filter
+    in:
+      - id: input_maf
+        source: pv_maf_tag/output
+      - id: output_maf_name
+        source: output_maf_name_filter
+    out:
+      - id: output
+    run: >-
+      ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_filter_cmoch/maf_filter_cmoch.cwl
+    label: pv_maf_filter
+    'sbg:x': -303
+    'sbg:y': -116
+  - id: pv_maf_tag
+    in:
+      - id: input_maf
+        source: input_variant_annotated_maf
+      - id: output_maf_name
+        source: output_maf_name_tag
+    out:
+      - id: output
+    run: >-
+      ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_tag_cmoch/maf_tag_cmoch.cwl
+    label: pv_maf_tag
+    'sbg:x': -777
+    'sbg:y': -80
+requirements: []