Merge branch 'release/1.1.0'

generate_aggregate.cwl

@@ -0,0 +1,325 @@
+class: Workflow
+cwlVersion: v1.0
+id: generate_aggregate
+label: generate_aggregate
+$namespaces:
+  s: 'https://schema.org/'
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: reference
+    type: File
+    'sbg:x': 0
+    'sbg:y': 640.21875
+  - id: target_intervals
+    type: File
+    'sbg:x': 0
+    'sbg:y': 106.7109375
+  - id: bait_intervals
+    type: File
+    'sbg:x': 0
+    'sbg:y': 1920.609375
+  - id: noise_sites_bed
+    type: File
+    'sbg:x': 0
+    'sbg:y': 853.59375
+  - id: biometrics_vcf_file
+    type: File
+    'sbg:x': 0
+    'sbg:y': 1813.921875
+  - id: collapsed_bam
+    type: 'File[]'
+    'sbg:x': 0
+    'sbg:y': 1707.234375
+  - id: duplex_bam
+    type: 'File[]'
+    'sbg:x': 0
+    'sbg:y': 1600.546875
+  - id: group_reads_by_umi_bam
+    type: 'File[]'
+    'sbg:x': 0
+    'sbg:y': 1173.6796875
+  - id: simplex_bam
+    type: 'File[]'
+    'sbg:x': 0
+    'sbg:y': 213.421875
+  - id: sample_sex
+    type: 'string[]?'
+    'sbg:x': 0
+    'sbg:y': 320.109375
+  - id: sample_group
+    type: 'string[]'
+    'sbg:x': 0
+    'sbg:y': 533.5078125
+  - id: uncollapsed_bam_base_recal
+    type: 'File[]'
+    'sbg:x': 0
+    'sbg:y': 0
+  - id: sample_name
+    type: 'string[]?'
+    'sbg:x': 0
+    'sbg:y': 426.796875
+  - id: hotspots_maf
+    type: File
+    'sbg:x': 0
+    'sbg:y': 1066.96875
+  - id: mosdepth_bed
+    type: File?
+    'sbg:x': 0
+    'sbg:y': 960.28125
+  - id: athena_transcript_file
+    type: File?
+    'sbg:x': 0
+    'sbg:y': 2133.984375
+  - id: athena_build
+    type: File?
+    'sbg:x': 0
+    'sbg:y': 2880.890625
+  - id: athena_flagstat
+    type: File?
+    'sbg:x': 0
+    'sbg:y': 2667.4921875
+  - id: athena_thresholds
+    type: 'int[]?'
+    'sbg:x': 0
+    'sbg:y': 2240.671875
+  - id: athena_threshold
+    type: int?
+    'sbg:x': 0
+    'sbg:y': 2347.359375
+  - id: athena_limit
+    type: int?
+    'sbg:x': 0
+    'sbg:y': 2560.78125
+  - id: athena_summary
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 2454.0703125
+  - id: athena_vcf
+    type: File?
+    'sbg:x': 0
+    'sbg:y': 2027.296875
+  - id: athena_cores
+    type: int?
+    'sbg:x': 0
+    'sbg:y': 2774.203125
+  - id: output
+    type: 'string[]?'
+    'sbg:exposed': true
+  - id: omaf
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 746.90625
+  - id: generic_counting
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1280.4140625
+  - id: fragment_count
+    type: int
+    'sbg:x': 0
+    'sbg:y': 1387.1484375
+  - id: filter_duplicate
+    type: int
+    'sbg:x': 0
+    'sbg:y': 1493.859375
+outputs:
+  - id: duplex_bam_biometrics_dir
+    outputSource:
+      - qc_generator/duplex_bam_biometrics_dir
+    type:
+      - Directory
+      - type: array
+        items: Directory
+    'sbg:x': 803.9111938476562
+    'sbg:y': 1306.364990234375
+  - id: collapsed_bam_biometrics_dir
+    outputSource:
+      - qc_generator/collapsed_bam_biometrics_dir
+    type:
+      - Directory
+      - type: array
+        items: Directory
+    'sbg:x': 1076
+    'sbg:y': 1603.4080810546875
+  - id: aggregate_qc_stats
+    outputSource:
+      - qc_aggregator/aggregate_qc_stats
+    type: Directory
+    'sbg:x': 1585.9033203125
+    'sbg:y': 1440.421875
+  - id: pickle_files_dir
+    outputSource:
+      - pickle_files/directory
+    type: Directory
+    label: pickle_files_dir
+    'sbg:x': 1582
+    'sbg:y': 993
+steps:
+  - id: qc_generator
+    in:
+      - id: reference
+        source: reference
+      - id: duplex_bam
+        source: duplex_bam
+      - id: collapsed_bam
+        source: collapsed_bam
+      - id: group_reads_by_umi_bam
+        source: group_reads_by_umi_bam
+      - id: uncollapsed_bam_base_recal
+        source: uncollapsed_bam_base_recal
+      - id: target_intervals
+        source: target_intervals
+      - id: bait_intervals
+        source: bait_intervals
+      - id: noise_sites_bed
+        source: noise_sites_bed
+      - id: sample_sex
+        source: sample_sex
+      - id: sample_name
+        source: sample_name
+      - id: sample_group
+        source: sample_group
+      - id: simplex_bam
+        source: simplex_bam
+      - id: vcf_file
+        source: biometrics_vcf_file
+      - id: hotspots_maf
+        source: hotspots_maf
+      - id: mosdepth_bed
+        source: mosdepth_bed
+      - id: athena_transcript_file
+        source: athena_transcript_file
+      - id: athena_build
+        source: athena_build
+      - id: athena_flagstat
+        source: athena_flagstat
+      - id: athena_thresholds
+        source:
+          - athena_thresholds
+      - id: athena_threshold
+        source: athena_threshold
+      - id: athena_limit
+        source: athena_limit
+      - id: athena_summary
+        source: athena_summary
+      - id: athena_vcf
+        source: athena_vcf
+      - id: athena_cores
+        source: athena_cores
+      - id: output
+        source: output
+      - id: omaf
+        source: omaf
+      - id: generic_counting
+        source: generic_counting
+      - id: fragment_count
+        default: 1
+        source: fragment_count
+      - id: filter_duplicate
+        default: 0
+        source: filter_duplicate
+    out:
+      - id: uncollapsed_bam_stats_dir
+      - id: gatk_mean_quality_by_cycle_recal_dir
+      - id: collapsed_bam_biometrics_dir
+      - id: collapsed_bam_duplex_metrics_dir
+      - id: collapsed_bam_stats_dir
+      - id: simplex_bam_stats_dir
+      - id: duplex_bam_sequence_qc_dir
+      - id: duplex_bam_stats_dir
+      - id: duplex_bam_biometrics_dir
+      - id: athena_coverage_report_dir
+      - id: duplex_biometrics_extract_pickle
+      - id: collapsed_biometrics_extract_pickle
+      - id: biometrics_extract_files_dir
+    run: qc_generator/nucleo_qc_generator.cwl
+    label: qc_generator
+    scatter:
+      - duplex_bam
+      - collapsed_bam
+      - group_reads_by_umi_bam
+      - uncollapsed_bam_base_recal
+      - sample_sex
+      - sample_name
+      - sample_group
+      - simplex_bam
+    scatterMethod: dotproduct
+    'sbg:x': 288.8125
+    'sbg:y': 1251.421875
+  - id: qc_aggregator
+    in:
+      - id: duplex_extraction_files
+        source:
+          - qc_generator/duplex_biometrics_extract_pickle
+      - id: simplex_bam_stats_dir
+        source:
+          - qc_generator/simplex_bam_stats_dir
+      - id: duplex_bam_sequence_qc_dir
+        source:
+          - qc_generator/duplex_bam_sequence_qc_dir
+      - id: duplex_bam_stats_dir
+        source:
+          - qc_generator/duplex_bam_stats_dir
+      - id: collapsed_bam_stats_dir
+        source:
+          - qc_generator/collapsed_bam_stats_dir
+      - id: biometrics_extract_files_dir
+        source: 
+          - qc_generator/biometrics_extract_files_dir
+      - id: collapsed_bam_duplex_metrics_dir
+        source:
+          - qc_generator/collapsed_bam_duplex_metrics_dir
+      - id: gatk_mean_quality_by_cycle_recal_dir
+        source:
+          - qc_generator/gatk_mean_quality_by_cycle_recal_dir
+      - id: uncollapsed_bam_stats_dir
+        source:
+          - qc_generator/uncollapsed_bam_stats_dir
+      - id: athena_coverage_report_dir
+        source:
+          - qc_generator/athena_coverage_report_dir
+      - id: collapsed_extraction_files
+        source:
+          - qc_generator/collapsed_biometrics_extract_pickle
+    out:
+      - id: aggregate_qc_stats
+    run: qc_aggregator/nucleo_qc_aggregator.cwl
+    label: qc_aggregator
+    'sbg:x': 1076.5557861328125
+    'sbg:y': 1270.734375
+  - id: pickle_files
+    in:
+      - id: files
+        linkMerge: merge_flattened
+        source:
+          - qc_generator/collapsed_biometrics_extract_pickle
+          - qc_generator/duplex_biometrics_extract_pickle
+      - id: output_directory_name
+        default: pickle_files
+    out:
+      - id: directory
+    run: cwl-commandlinetools/expression_tools/put_in_dir.cwl
+    label: pickle_files
+    'sbg:x': 1283.092529296875
+    'sbg:y': 981.6953125
+requirements:
+  - class: SubworkflowFeatureRequirement
+  - class: ScatterFeatureRequirement
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+  - class: MultipleInputFeatureRequirement
+$schemas:
+  - 'http://schema.org/version/latest/schemaorg-current-http.rdf'
+'s:author':
+  - class: 's:Person'
+    's:email': 'mailto:charalk@mskcc.org'
+    's:identifier': ''
+    's:name': Carmelina Charalambous
+'s:citation': ''
+'s:codeRepository': 'https://github.com/msk-access/nucleo'
+'s:contributor':
+  - class: 's:Person'
+    's:email': 'mailto:shahr2@mskcc.org'
+    's:identifier': 'https://orcid.org/0000-0001-9042-6213'
+    's:name': Ronak Shah
+'s:dateCreated': '2020-11-23'
+'s:license': 'https://spdx.org/licenses/Apache-2.0'

nucleo_aggregate_visualize.cwl

@@ -2,7 +2,8 @@ class: Workflow
 cwlVersion: v1.0
 id: aggregate_visualize
 doc: >-
-  This workflow takes output of per sample nucleo_qc.cwl and merges to generate a single report across one or multiple samples
+  This workflow takes output of per sample nucleo_qc.cwl and merges to generate
+  a single report across one or multiple samples
 label: aggregate_visualize
 $namespaces:
   s: 'https://schema.org/'
@@ -61,6 +62,16 @@ inputs:
         - 'null'
     'sbg:x': 0
     'sbg:y': 854.5
+  - id: biometrics_extract_files_dir
+    type:
+      type: array
+      items:
+        - File
+        - Directory
+        - 'null'
+    label: biometrics_extract_files_dir
+    'sbg:x': -23.278732299804688
+    'sbg:y': 1215.6552734375
   - id: collapsed_bam_duplex_metrics_dir
     type:
       type: array
@@ -85,8 +96,8 @@ inputs:
     'sbg:y': 213.625
   - id: config
     type: File?
-    'sbg:x': 360.765625
-    'sbg:y': 587.46875
+    'sbg:x': 390.9977111816406
+    'sbg:y': 758.3030395507812
   - id: duplex_bam_sequence_qc_dir
     type:
       type: array
@@ -133,6 +144,9 @@ steps:
       - id: collapsed_bam_stats_dir
         source:
           - collapsed_bam_stats_dir
+      - id: biometrics_extract_files_dir
+        source:
+          - biometrics_extract_files_dir
       - id: collapsed_bam_duplex_metrics_dir
         source:
           - collapsed_bam_duplex_metrics_dir
@@ -152,8 +166,8 @@ steps:
       - id: aggregate_qc_stats
     run: qc_aggregator/nucleo_qc_aggregator.cwl
     label: qc_aggregator
-    'sbg:x': 360.765625
-    'sbg:y': 417.65625
+    'sbg:x': 475.1567077636719
+    'sbg:y': 495.0506591796875
   - id: general_stats_parse
     in:
       - id: directory
@@ -198,4 +212,4 @@ $schemas:
     's:identifier': 'https://orcid.org/0000-0001-9042-6213'
     's:name': Ronak Shah
 's:dateCreated': '2020-11-23'
-'s:license': 'https://spdx.org/licenses/Apache-2.0'
+'s:license': 'https://spdx.org/licenses/Apache-2.0'