From a86bd74ee1423a6f0205490e6c484f50d14a5105 Mon Sep 17 00:00:00 2001
From: Ronak Shah <shahr2@mskcc.org>
Date: Thu, 6 Jul 2023 16:29:47 -0400
Subject: [PATCH] Update qc_generator

---
 cwl-commandlinetools                 |   2 +-
 cwl_subworkflows                     |   2 +-
 qc_generator/nucleo_qc_generator.cwl | 203 ++++++++++++++-------------
 3 files changed, 108 insertions(+), 99 deletions(-)

diff --git a/cwl-commandlinetools b/cwl-commandlinetools
index c8e3cad..14b230b 160000
--- a/cwl-commandlinetools
+++ b/cwl-commandlinetools
@@ -1 +1 @@
-Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd
+Subproject commit 14b230bdf44a69ac5b4ec0b312876f4d16e8defc
diff --git a/cwl_subworkflows b/cwl_subworkflows
index 18a44c5..3e06132 160000
--- a/cwl_subworkflows
+++ b/cwl_subworkflows
@@ -1 +1 @@
-Subproject commit 18a44c56e67d0202f565fbf9ac2ec07600e663e7
+Subproject commit 3e06132261bfeeb449fd91eb5e7afe1274ebba9d
diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl
index 6d013ef..0578561 100644
--- a/qc_generator/nucleo_qc_generator.cwl
+++ b/qc_generator/nucleo_qc_generator.cwl
@@ -12,27 +12,27 @@ inputs:
       - ^.fasta.fai
       - ^.dict
     'sbg:x': 0
-    'sbg:y': 1068.28125
+    'sbg:y': 1067.125
   - id: duplex_bam
     type: File
     label: duplex_bam
     secondaryFiles:
       - ^.bai
     'sbg:x': 0
-    'sbg:y': 2243.390625
+    'sbg:y': 2561.34375
   - id: collapsed_bam
     type: File
     label: collapsed_bam
     secondaryFiles:
       - ^.bai
     'sbg:x': 0
-    'sbg:y': 2563.875
+    'sbg:y': 2881.5
   - id: group_reads_by_umi_bam
     type: File
     label: group_reads_by_umi_bam
     doc: Input BAM file generated by GroupReadByUmi.
     'sbg:x': 0
-    'sbg:y': 2029.734375
+    'sbg:y': 2134.4140625
   - id: uncollapsed_bam_base_recal
     type: File
     label: uncollapsed_bam_base_recal
@@ -40,17 +40,17 @@ inputs:
     secondaryFiles:
       - ^.bai
     'sbg:x': 0
-    'sbg:y': 106.828125
+    'sbg:y': 106.703125
   - id: target_intervals
     type: File
     label: target_intervals
     'sbg:x': 0
-    'sbg:y': 213.65625
+    'sbg:y': 213.4296875
   - id: bait_intervals
     type: File
     label: bait_intervals
     'sbg:x': 0
-    'sbg:y': 2884.359375
+    'sbg:y': 3308.359375
   - id: noise_sites_bed
     type: File
     label: noise_sites_bed
@@ -58,87 +58,87 @@ inputs:
       Path to BED file containing regions over which to calculate noise
       [required]
     'sbg:x': 0
-    'sbg:y': 1175.109375
+    'sbg:y': 1280.53125
   - id: sample_sex
     type: string?
     doc: Expected sample sex (i.e. M or F).
     'sbg:x': 0
-    'sbg:y': 854.625
+    'sbg:y': 853.671875
   - id: sample_name
     type: string?
     doc: >-
       Sample name. If not specified, sample name is automatically figured out
       from the BAM file.
-    'sbg:x': 361.90625
-    'sbg:y': 686.9375
+    'sbg:x': 386.90625
+    'sbg:y': 1020.75
   - id: sample_group
     type: string
     doc: The sample group (e.g. the sample patient ID).
     'sbg:x': 0
-    'sbg:y': 961.453125
+    'sbg:y': 960.3984375
   - id: simplex_bam
     type: File
     label: simplex_bam
     secondaryFiles:
       - ^.bai
     'sbg:x': 0
-    'sbg:y': 320.484375
+    'sbg:y': 320.15625
   - id: biometrics_plot
     type: boolean?
     label: biometrics_plot
     doc: Also output plots of the data.
     'sbg:x': 0
-    'sbg:y': 2670.703125
+    'sbg:y': 2988.203125
   - id: biometrics_json
     type: boolean?
     label: biometrics_json
     doc: Also output data in JSON format.
     'sbg:x': 0
-    'sbg:y': 2777.53125
+    'sbg:y': 3094.9296875
   - id: biometrics_bed_file
     type: File?
-    'sbg:x': -423.2972106933594
-    'sbg:y': 2095.491455078125
+    'sbg:x': 0
+    'sbg:y': 3201.65625
   - id: collapsed_biometrics_minor_threshold
     type: float?
     label: collapsed_biometrics_minor_threshold
     doc: Minor contamination threshold for bad sample.
     'sbg:x': 0
-    'sbg:y': 2350.21875
+    'sbg:y': 2668.046875
   - id: collapsed_biometrics_coverage_threshold
     type: int?
     label: collapsed_biometrics_coverage_threshold
     doc: Samples with Y chromosome above this value will be considered male.
     'sbg:x': 0
-    'sbg:y': 2457.046875
+    'sbg:y': 2774.7734375
   - id: sequence_qc_min_basq
     type: int?
     'sbg:x': 0
-    'sbg:y': 747.796875
+    'sbg:y': 746.96875
   - id: sequence_qc_min_mapq
     type: int?
     'sbg:x': 0
-    'sbg:y': 640.96875
+    'sbg:y': 640.265625
   - id: sequence_qc_threshold
     type: float?
     'sbg:x': 0
-    'sbg:y': 534.140625
+    'sbg:y': 533.5625
   - id: sequence_qc_truncate
     type: int?
     'sbg:x': 0
-    'sbg:y': 427.3125
+    'sbg:y': 426.859375
   - id: hsmetrics_minimum_mapping_quality
     type: int?
     'sbg:x': 0
-    'sbg:y': 1602.421875
+    'sbg:y': 1707.4609375
   - id: hsmetrics_minimum_base_quality
     type: int?
     'sbg:x': 0
-    'sbg:y': 1709.25
+    'sbg:y': 1814.2109375
   - id: hsmetrics_coverage_cap
     type: int?
     'sbg:x': 0
-    'sbg:y': 1816.078125
+    'sbg:y': 1920.9609375
   - id: vcf_file
     type: File
     'sbg:x': 0
@@ -146,158 +146,164 @@ inputs:
   - id: hotspots_maf
     type: File
     'sbg:x': 0
-    'sbg:y': 1922.90625
+    'sbg:y': 2027.6875
   - id: mosdepth_bed
     type: File?
-    'sbg:x': -359.3104248046875
-    'sbg:y': 1495
+    'sbg:x': 0
+    'sbg:y': 1600.734375
   - id: mosdepth_flag
     type: int?
     'sbg:x': 0
-    'sbg:y': 1388.765625
+    'sbg:y': 1494.0078125
   - id: mosdepth_minimum_mapping_quality
     type: int?
     'sbg:x': 0
-    'sbg:y': 1281.9375
+    'sbg:y': 1387.2578125
   - id: athena_transcript_file
     type: File?
     'sbg:x': 0
-    'sbg:y': 3098.015625
+    'sbg:y': 3521.765625
   - id: athena_build
     type: File?
     'sbg:x': 386.90625
-    'sbg:y': 2556.5625
+    'sbg:y': 2821.171875
   - id: athena_flagstat
     type: File?
     'sbg:x': 386.90625
-    'sbg:y': 2342.90625
+    'sbg:y': 2500.9921875
   - id: athena_thresholds
     type: 'int[]?'
     'sbg:x': 0
-    'sbg:y': 3204.84375
+    'sbg:y': 3628.46875
   - id: athena_threshold
     type: int?
     'sbg:x': 0
-    'sbg:y': 3311.671875
+    'sbg:y': 3735.171875
   - id: athena_limit
     type: int?
     'sbg:x': 386.90625
-    'sbg:y': 2236.078125
+    'sbg:y': 2394.265625
   - id: athena_summary
     type: boolean?
     'sbg:x': 0
-    'sbg:y': 3418.5
+    'sbg:y': 3841.8984375
   - id: athena_vcf
     type: File?
     'sbg:x': 0
-    'sbg:y': 2991.1875
+    'sbg:y': 3415.0625
   - id: athena_cores
     type: int?
     'sbg:x': 386.90625
-    'sbg:y': 2449.734375
+    'sbg:y': 2714.46875
   - id: output
     type: 'string[]?'
     'sbg:exposed': true
   - id: omaf
     type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1173.828125
   - id: generic_counting
     type: boolean?
+    'sbg:x': 0
+    'sbg:y': 2241.1640625
   - id: fragment_count
     type: int
-    'sbg:x': 300.2456970214844
-    'sbg:y': 0
+    'sbg:x': 0
+    'sbg:y': 2347.9140625
   - id: filter_duplicate
     type: int
-    'sbg:x': 170.50595092773438
-    'sbg:y': -103.53236389160156
+    'sbg:x': 0
+    'sbg:y': 2454.640625
 outputs:
   - id: uncollapsed_bam_stats_dir
     outputSource:
       - uncollapsed_bam_stats/directory
     type: Directory
     label: uncollapsed_bam_stats_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1281.9375
+    'sbg:x': 1614.439697265625
+    'sbg:y': 1440.7734375
   - id: gatk_mean_quality_by_cycle_recal_dir
     outputSource:
       - gatk_mean_quality_by_cycle_recal/directory
     type: Directory
     label: gatk_mean_quality_by_cycle_recal_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1495.59375
+    'sbg:x': 1614.439697265625
+    'sbg:y': 1654.203125
   - id: collapsed_bam_biometrics_dir
     outputSource:
       - collapsed_bam_biometrics/directory
     type: Directory
     label: collapsed_bam_biometrics_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 2136.5625
+    'sbg:x': 1614.439697265625
+    'sbg:y': 2294.4453125
   - id: biometrics_extract_files_dir
     outputSource:
       - biometrics_extract_files/directory
     type: Directory
     label: biometrics_extract_files_dir
-    'sbg:x': 1658.52490234375
-    'sbg:y': 2355.774658203125
+    'sbg:x': 1614.439697265625
+    'sbg:y': 2401.1484375
   - id: collapsed_bam_duplex_metrics_dir
     outputSource:
       - collapsed_bam_duplex_metrics/directory
     type: Directory
     label: collapsed_bam_duplex_metrics_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 2029.734375
+    'sbg:x': 1614.439697265625
+    'sbg:y': 2187.7421875
   - id: collapsed_bam_stats_dir
     outputSource:
       - collapsed_bam_stats/directory
     type: Directory
     label: collapsed_bam_stats_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1922.90625
+    'sbg:x': 1614.439697265625
+    'sbg:y': 2081.0390625
   - id: simplex_bam_stats_dir
     outputSource:
       - simplex_bam_stats/directory
     type: Directory
     label: simplex_bam_stats_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1388.765625
+    'sbg:x': 1614.439697265625
+    'sbg:y': 1547.4765625
   - id: duplex_bam_sequence_qc_dir
     outputSource:
       - duplex_bam_sequence_qc/directory
     type: Directory
     label: duplex_bam_sequence_qc_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1709.25
+    'sbg:x': 1614.439697265625
+    'sbg:y': 1867.6328125
   - id: duplex_bam_stats_dir
     outputSource:
       - duplex_bam_stats/directory
     type: Directory
     label: duplex_bam_stats_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1602.421875
+    'sbg:x': 1614.439697265625
+    'sbg:y': 1760.9296875
   - id: duplex_bam_biometrics_dir
     outputSource:
       - duplex_bam_biometrics/directory
     type: Directory
     label: duplex_bam_biometrics_dir
-    'sbg:x': 1625.7747802734375
-    'sbg:y': 1816.078125
+    'sbg:x': 1614.439697265625
+    'sbg:y': 1974.3359375
   - id: duplex_biometrics_extract_pickle
     outputSource:
       - qc_duplex_bam/duplex_biometrics_extract_pickle
     type: File
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1216.3515625
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1428.5
   - id: collapsed_biometrics_extract_pickle
     outputSource:
       - qc_collapsed_bam/collapsed_biometrics_extract_pickle
     type: File
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1792.4921875
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1897.3125
   - id: athena_coverage_report_dir
     outputSource:
       - athena_coverage_report/directory
     type: Directory
     label: athena_coverage_report_dir
+    'sbg:x': 1276.111572265625
+    'sbg:y': 2761.5546875
 steps:
   - id: qc_collapsed_bam
     in:
@@ -317,8 +323,6 @@ steps:
         source: biometrics_json
       - id: plot
         source: biometrics_plot
-      - id: bed_file
-        source: biometrics_bed_file
       - id: minor_threshold
         source: collapsed_biometrics_minor_threshold
       - id: coverage_threshold
@@ -339,6 +343,8 @@ steps:
         source: sample_group
       - id: maf
         source: hotspots_maf
+      - id: bed_file
+        source: biometrics_bed_file
       - id: omaf
         source: omaf
       - id: filter_duplicate
@@ -376,7 +382,7 @@ steps:
     run: ../cwl_subworkflows/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl
     label: qc_collapsed_bam
     'sbg:x': 386.90625
-    'sbg:y': 1975.25
+    'sbg:y': 2133.5625
   - id: qc_uncollapsed_bam
     in:
       - id: reference
@@ -406,7 +412,7 @@ steps:
     run: ../cwl_subworkflows/qc_uncollapsed_bam/qc_uncollapsed_bam_v2.0.cwl
     label: qc_uncollapsed_bam
     'sbg:x': 386.90625
-    'sbg:y': 1017.765625
+    'sbg:y': 1176.453125
   - id: qc_duplex_bam
     in:
       - id: reference
@@ -492,7 +498,7 @@ steps:
     run: ../cwl_subworkflows/qc_duplex_bam/qc_duplex_bam_v2.0.cwl
     label: qc_duplex_bam
     'sbg:x': 386.90625
-    'sbg:y': 1539.421875
+    'sbg:y': 1697.859375
   - id: athena_report
     in:
       - id: transcript_file
@@ -511,7 +517,8 @@ steps:
       - id: sample_name
         source: sample_name
       - id: output
-        source: output
+        source:
+          - output
       - id: limit
         source: athena_limit
       - id: summary
@@ -529,8 +536,8 @@ steps:
       - id: coverage_report_single
     run: ../cwl_subworkflows/athena_report/athena_report.cwl
     label: athena_report
-    'sbg:x': 1382.922119140625
-    'sbg:y': 2798.76611328125
+    'sbg:x': 1276.111572265625
+    'sbg:y': 2570.828125
   - id: simplex_bam_stats
     in:
       - id: files
@@ -549,8 +556,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: simplex_bam_stats
-    'sbg:x': 1283.092529296875
-    'sbg:y': 981.6953125
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1194.046875
   - id: uncollapsed_bam_stats
     in:
       - id: files
@@ -569,8 +576,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: uncollapsed_bam_stats
-    'sbg:x': 1283.092529296875
-    'sbg:y': 860.8671875
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1073.34375
   - id: gatk_mean_quality_by_cycle_recal
     in:
       - id: files
@@ -586,8 +593,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: gatk_mean_quality_by_cycle_recal
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1102.5234375
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1314.7734375
   - id: collapsed_bam_stats
     in:
       - id: files
@@ -607,8 +614,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: collapsed_bam_stats
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1906.3203125
+    'sbg:x': 1276.111572265625
+    'sbg:y': 2011.015625
   - id: collapsed_bam_duplex_metrics
     in:
       - id: files
@@ -628,8 +635,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: collapsed_bam_duplex_metrics
-    'sbg:x': 1283.092529296875
-    'sbg:y': 2133.9765625
+    'sbg:x': 1276.111572265625
+    'sbg:y': 2131.71875
   - id: collapsed_bam_biometrics
     in:
       - id: files
@@ -654,8 +661,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: collapsed_bam_biometrics
-    'sbg:x': 1283.092529296875
-    'sbg:y': 2254.8046875
+    'sbg:x': 1276.111572265625
+    'sbg:y': 2252.421875
   - id: biometrics_extract_files
     in:
       - id: files
@@ -670,8 +677,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: biometrics_extract_files
-    'sbg:x': 1290.449951171875
-    'sbg:y': 2410.44970703125
+    'sbg:x': 1276.111572265625
+    'sbg:y': 2373.125
   - id: duplex_bam_sequence_qc
     in:
       - id: files
@@ -691,8 +698,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: duplex_bam_sequence_qc
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1451.0078125
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1662.90625
   - id: duplex_bam_stats
     in:
       - id: files
@@ -716,8 +723,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: duplex_bam_stats
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1330.1796875
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1542.203125
   - id: athena_coverage_report
     in:
       - id: files
@@ -731,6 +738,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: athena_coverage_report
+    'sbg:x': 386.90625
+    'sbg:y': 2607.7421875
   - id: duplex_bam_biometrics
     in:
       - id: files
@@ -747,8 +756,8 @@ steps:
       - id: directory
     run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl
     label: duplex_bam_biometrics
-    'sbg:x': 1283.092529296875
-    'sbg:y': 1678.6640625
+    'sbg:x': 1276.111572265625
+    'sbg:y': 1783.609375
   - id: qc_simplex_bam
     in:
       - id: reference
@@ -775,7 +784,7 @@ steps:
     run: ../cwl_subworkflows/qc_simplex_bam/qc_simplex_bam_v2.0.cwl
     label: qc_simplex_bam
     'sbg:x': 386.90625
-    'sbg:y': 1215.59375
+    'sbg:y': 1374.15625
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement