Merge branch 'release/1.3.2'

msk-access · May 17, 2023 · c8e3cad · c8e3cad
2 parents 7e71b5a + 939e29b
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diff --git a/athena/1.4.2/coverage_report_single/coverage_report_single.cwl b/athena/1.4.2/coverage_report_single/coverage_report_single.cwl
@@ -71,7 +71,7 @@ inputs:
       position: 0
       prefix: '-n'
   - id: output
-    type: string?
+    type: 'string[]?'
     inputBinding:
       position: 0
       prefix: '-o'

diff --git a/athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl b/athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl
@@ -58,7 +58,7 @@ inputs:
       (optional) Prefix for naming output file, if not given will use name from
       per base coverage file
   - id: flagstat
-    type: string?
+    type: File?
     inputBinding:
       position: 900
       prefix: '--flagstat'

diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md
@@ -57,6 +57,7 @@
   * [1.2.5](../getbasecountsmultisample/1.2.5/README.md)
 
 * [Manta](manta/README.md)
+
   * [Manta v1.5.1](manta/manta_1.5.1.md)
 
 * [Marianas](marianas/README.md)
@@ -106,16 +107,21 @@
   * [MarkDuplicates v4.1.8.1](picard-tools/picard_mark_duplicates_4.1.8.1.md)
 
 * [Postprocessing variant calls](postprocessing_variant_calls/README.md)
-  * [vardict_filter_case-control 0.1.3](postprocessing_variant_calls/vardict_filter_case-control_0.1.3.md)
-  * [vardict_filter_single-sample 0.1.3](postprocessing_variant_calls/vardict_filter_single-sample_0.1.3.md)
+
+  * [vardict_filter_case-control 0.1.5](postprocessing_variant_calls/vardict_filter_case-control_0.1.5.md)
+  * [vardict_filter_single-sample 0.1.5](postprocessing_variant_calls/vardict_filter_single-sample_0.1.5.md)
+  * [maf_annotated_by_bed_0.2.2](postprocessing_variant_calls/maf_annotated_by_bed_0.2.2.md)
 
 * [SnpSift](snpsift/README.md)
+
   * [v5.0](snpsift/snpsift_5.0.md)
 
 * [Trim Galore](trim-galore/README.md)
+
   * [v0.6.2](trim-galore/trim_galore_0.6.2.md)
 
 * [Ubuntu utilites](ubuntu-utilites/README.md)
+
   * [v18.04](ubuntu-utilites/utilities_ubuntu_18.04.md)
 
 * [VarDictJava](vardictjava/README.md)
@@ -128,4 +134,4 @@
   * [CountReads v3.1.1](waltz/waltz_count_reads_3.1.1.md)
   * [PileupMetrics v3.1.1](waltz/waltz_pileupmatrices_3.1.1.md)
 
-  
+
diff --git a/docs/postprocessing_variant_calls/maf_annotated_by_bed_0.2.2.md b/docs/postprocessing_variant_calls/maf_annotated_by_bed_0.2.2.md
@@ -0,0 +1,42 @@
+# CWL  for annotating a MAF file with a BED file
+
+## Version of tools in docker image (/container/Dockerfile)
+
+| Tool                         | Version | Location                                              |
+| ---------------------------- | ------- | ----------------------------------------------------- |
+| postprocessing_variant_calls | 0.2.2   | ghcr.io/msk-access/postprocessing_variant_calls:0.2.2 |
+
+## CWL
+
+- CWL specification 1.0
+- Use example_inputs.yaml to see the inputs to the cwl
+- Example Command using [toil](https://toil.readthedocs.io):
+
+```bash
+    > toil-cwl-runner maf_annotated_by_bed.cwl example_inputs.yaml
+```
+
+**If at MSK, using the JUNO cluster having installed toil version 3.19 and manually modifying [lsf.py](https://github.com/DataBiosphere/toil/blob/releases/3.19.0/src/toil/batchSystems/lsf.py#L170) by removing `type==X86_64 &&` you can use the following command**
+
+```bash
+#Using CWLTOOL
+> cwltool --singularity --non-strict /path/to/maf_annotated_by_bed.cwl /path/to/inputs.yaml
+
+#Using toil-cwl-runner
+> mkdir mafAnnotation_toil_log
+> toil-cwl-runner --singularity --logFile /path/to/mafAnnotation_toil_log/cwltoil.log  --jobStore /path/to/mafAnnotation_jobStore --batchSystem lsf --workDir /path/to/mafAnnotation_toil_log --outdir . --writeLogs /path/to/mafAnnotation_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/maf_annotated_by_bed.cwl /path/to/inputs.yaml > mafAnnotation_toil.stdout 2> mafAnnotation_toil.stderr &
+```
+
+### Usage
+
+```shell
+usage: maf_annotated_by_bed.cwl
+       [-h] [--memory_per_job MEMORY_PER_JOB]
+       [--memory_overhead MEMORY_OVERHEAD]
+       [--number_of_threads NUMBER_OF_THREADS]
+       --input_maf INPUT_MAF
+       --input_bed INPUT_BED
+       [--output_filename OUTPUT_FILENAME]
+       [--column_name COLUMN_NAME]
+       [job_order]
+```
diff --git a/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/README.md b/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/README.md
@@ -0,0 +1,42 @@
+# CWL  for annotating a MAF file with a BED file
+
+## Version of tools in docker image (/container/Dockerfile)
+
+| Tool                         | Version | Location                                              |
+| ---------------------------- | ------- | ----------------------------------------------------- |
+| postprocessing_variant_calls | 0.2.2   | ghcr.io/msk-access/postprocessing_variant_calls:0.2.2 |
+
+## CWL
+
+- CWL specification 1.0
+- Use example_inputs.yaml to see the inputs to the cwl
+- Example Command using [toil](https://toil.readthedocs.io):
+
+```bash
+    > toil-cwl-runner maf_annotated_by_bed.cwl example_inputs.yaml
+```
+
+**If at MSK, using the JUNO cluster having installed toil version 3.19 and manually modifying [lsf.py](https://github.com/DataBiosphere/toil/blob/releases/3.19.0/src/toil/batchSystems/lsf.py#L170) by removing `type==X86_64 &&` you can use the following command**
+
+```bash
+#Using CWLTOOL
+> cwltool --singularity --non-strict /path/to/maf_annotated_by_bed.cwl /path/to/inputs.yaml
+
+#Using toil-cwl-runner
+> mkdir mafAnnotation_toil_log
+> toil-cwl-runner --singularity --logFile /path/to/mafAnnotation_toil_log/cwltoil.log  --jobStore /path/to/mafAnnotation_jobStore --batchSystem lsf --workDir /path/to/mafAnnotation_toil_log --outdir . --writeLogs /path/to/mafAnnotation_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/maf_annotated_by_bed.cwl /path/to/inputs.yaml > mafAnnotation_toil.stdout 2> mafAnnotation_toil.stderr &
+```
+
+### Usage
+
+```shell
+usage: maf_annotated_by_bed.cwl
+       [-h] [--memory_per_job MEMORY_PER_JOB]
+       [--memory_overhead MEMORY_OVERHEAD]
+       [--number_of_threads NUMBER_OF_THREADS]
+       --input_maf INPUT_MAF
+       --input_bed INPUT_BED
+       [--output_filename OUTPUT_FILENAME]
+       [--column_name COLUMN_NAME]
+       [job_order]
+```
diff --git a/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/example_inputs.yaml b/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/example_inputs.yaml
@@ -0,0 +1,4 @@
+columnName: annotation
+inputMaf: /path/to/input/maf.maf
+input_bed: /path/to/input/bed.bed
+output_filename: annotated
diff --git a/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/maf_annotated_by_bed.cwl b/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/maf_annotated_by_bed.cwl
@@ -0,0 +1,75 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+  dct: 'http://purl.org/dc/terms/'
+  doap: 'http://usefulinc.com/ns/doap#'
+  foaf: 'http://xmlns.com/foaf/0.1/'
+  sbg: 'https://www.sevenbridges.com/'
+id: maf_annotated_by_bed
+baseCommand:
+  - pv
+inputs:
+  - id: memory_per_job
+    type: int?
+    doc: Memory per job in megabytes
+  - id: memory_overhead
+    type: int?
+    doc: Memory overhead per job in megabytes
+  - id: number_of_threads
+    type: int?
+  - id: input_maf
+    type: File
+    inputBinding:
+      position: 0
+      prefix: '-m'
+  - id: input_bed
+    type: File
+    inputBinding:
+      position: 1
+      prefix: '-b'
+  - id: output_filename
+    type: string?
+    inputBinding:
+      position: 3
+      prefix: '-o'
+  - 'sbg:toolDefaultValue': annotation
+    id: column_name
+    type: string?
+    inputBinding:
+      position: 4
+      prefix: '-c'
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: '*.maf'
+label: maf_annotated_by_bed
+arguments:
+  - maf
+  - annotate
+  - mafbybed
+requirements:
+  - class: ResourceRequirement
+    ramMin: 8000
+    coresMin: 2
+  - class: DockerRequirement
+    dockerPull: 'ghcr.io/msk-access/postprocessing_variant_calls:0.2.2'
+  - class: InlineJavascriptRequirement
+'dct:contributor':
+  - class: 'foaf:Organization'
+    'foaf:member':
+      - class: 'foaf:Person'
+        'foaf:mbox': 'mailto:shahr2@mskcc.org'
+        'foaf:name': Ronak Shah
+    'foaf:name': Memorial Sloan Kettering Cancer Center
+'dct:creator':
+  - class: 'foaf:Organization'
+    'foaf:member':
+      - class: 'foaf:Person'
+        'foaf:mbox': 'mailto:sivaprk@mskcc.org'
+        'foaf:name': Karthigayini Sivaprakasam
+    'foaf:name': Memorial Sloan Kettering Cancer Center
+'doap:release':
+  - class: 'doap:Version'
+    'doap:name': postprocessing_variant_calls
+    'doap:revision': 0.0.1