Merge branch 'release/1.2.0'

Author: rhshah

.github/workflows/pack_cwls.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.7, 3.8, 3.9]
     steps:
       - uses: actions/checkout@v2
         with:
@@ -25,7 +25,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install cwltool
         run: |
-          python -m pip install toil[cwl]==4.2.0
+          python -m pip install toil[cwl]==5.7.1
       - name: Run cwltool --pack for all workflows
         run: |
           echo Removing old packed workflows

.github/workflows/validate_cwls.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.7, 3.8, 3.9]
     steps:
       - uses: actions/checkout@v2
         with:
@@ -23,7 +23,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install cwltool
         run: |
-          python -m pip install toil[cwl]==4.2.0
+          python -m pip install toil[cwl]==5.7.1
       - uses: actions/checkout@v2
       - name: Validate
         run: |

alignment/alignment__packed.cwl

@@ -0,0 +1,74 @@
+### Introduction
+The sub-workflow runs all steps required to generate an [athena](https://github.com/msk-access/athena) coverage report:
+
+1. Annotate BED file.
+2. Generating Coverage statistics 
+3. Generating Coverage Report 
+
+
+## CWL athena_report.cwl
+
+- CWL specification 1.2
+- Use example_inputs.yaml to see the inputs to the cwl
+- Example Command using [toil](https://toil.readthedocs.io):
+
+```bash
+    > cwltool athena_report/athena_report.cwl athena_report/example_inputs_juno.yaml
+```
+**If at MSK, using the JUNO cluster having installed toil-msk version 3.21.1 you can use the following command**
+
+### Using toil-cwl-runner
+
+```bash
+#Using CWLTOOL
+> toil-cwl-runner --singularity athena_report/athena_report.cwl athena_report/example_inputs_juno.yaml 
+```
+
+
+### Usage: 
+
+```
+Usage: qc_collapsed_bam.cwl  [OPTIONS]
+
+  This tool runs all steps associated with generating an athena coverage report.
+
+Options:
+
+-p / --panel_bed : Input panel bed file; must have ONLY the following 4 columns chromosome, start position, end position, gene/transcript
+
+-t / --transcript_file : Transcript annotation file, contains required gene and exon information. Must have ONLY the following 6 columns:
+chromosome, start, end, gene, transcript, exon
+
+-c / --coverage_file : Per base coverage file (output from mosdepth or similar)
+
+-s / -chunk_size : (optional) nrows to split per-base coverage file for intersecting, with <16GB RAM can lead to bedtools intersect failing. Reccomended values: 16GB RAM -> 20000000; 8GB RAM -> 10000000
+
+-n / --output_name : (optional) Prefix for naming output file, if not given will use name from per base coverage file
+
+--file: annotated bed file on which to generate report from
+
+--build: text file with build number used for alignment, output from mosdepth (optional)
+
+--outfile: output file name prefix, if not given the input file name will be used as the name prefix
+
+--thresholds: threshold values to calculate coverage for as comma seperated integers (default: 10, 20, 30, 50, 100)
+
+--flagstat: flagstat file for sample, required for generating run statistics (in development)
+
+--cores: Number of CPU cores to utilise, for larger numbers of genes this will drastically reduce run time. If not given will use maximum available
+
+-s / --snps: VCF(s) of known SNPs to check coverage of (optional; i.e. HGMD, ClinVar)
+
+-t / --threshold: threshold value defining sub-optimal coverage (optional; default if not given: 20)
+
+-n / --sample_name: name for title of report (optional; gene_stats file name will be used if not given)
+
+-o / --output: name for output report (optional; sample name will be used if not given)
+
+-p / --panel: panel bed file used for initial annotation, name will be displayed in summary of report (optional)
+
+-l / --limit: number of genes at which to limit including full gene plots, large numbers of genes may take a long time to generate the plots (optional)
+
+-m / --summary: boolean flag to add clinical report summary text in summary section, includes list of all genes with transcripts (optional; default False)
+
+``` 

athena_report/README.md

@@ -0,0 +1,115 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: Workflow
+inputs:
+# input for annotate 
+    - id: transcript_file
+      type: File?
+    - id: chunk_size
+      type: int?
+    - id: output_name 
+      type: string?
+# input for stat 
+    - id: build 
+      type: File?
+    - id: flagstat
+      type: File?
+    - id: thresholds   
+      type: 'int[]?'
+# input for report 
+    - id: threshold
+      type: int?
+    - id: sample_name 
+      type: string?
+    - id: output
+      type: string?
+    - id: limit
+      type: int?
+    - id: summary 
+      type: boolean?
+    - id: snps
+      type:
+        - 'null'
+        - File
+        - type: array
+          items: File
+# shared 
+    - id: panel_bed
+      type: File?
+    - id: coverage_file
+      type: File?
+    - id: cores 
+      type: int?
+
+    
+
+
+outputs:
+  coverage_report_single:
+    type: File
+    outputSource: report/coverage_report_single
+
+steps:
+  annotate:
+    run: ../command_line_tools/athena/1.4.2/annotate_bed/annotate_bed.cwl
+    in:
+      panel_bed: panel_bed
+      transcript_file: transcript_file
+      coverage_file: coverage_file
+      chunk_size: chunk_size
+      output_name: output_name
+    when: ${
+            if (inputs.panel_bed == null || inputs.transcript_file == null || inputs.coverage_file == null){
+              return false
+              } 
+            else {
+              return true
+              }
+           } 
+    out: [annotated_bed]
+  stats:
+    run: ../command_line_tools/athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl
+    in:
+      file: annotate/annotated_bed
+      build: build 
+      flagstat: flagstat  
+      thresholds: thresholds
+      cores: cores
+    when: ${
+        if (inputs.file == null){
+          return false
+          } 
+        else {
+          return true
+          }
+        } 
+    out: [gene_stats_output, exon_stats_output]
+  report:
+    run: ../command_line_tools/athena/1.4.2/coverage_report_single/coverage_report_single.cwl
+    in:
+      raw_coverage: annotate/annotated_bed 
+      gene_stats: stats/gene_stats_output
+      exon_stats: stats/exon_stats_output 
+      per_base_coverage: coverage_file
+      panel: panel_bed
+      snps: snps
+      threshold: threshold
+      sample_name: sample_name
+      output: output
+      limit: limit
+      summary: summary
+      cores: cores
+    when: ${
+        if (inputs.raw_coverage == null || inputs.gene_stats == null || inputs.exon_stats == null){
+          return false
+          } 
+        else {
+          return true
+          }
+        } 
+    out: [coverage_report_single]
+
+requirements:
+  InlineJavascriptRequirement: {}
+  MultipleInputFeatureRequirement: {}