Merge branch 'release/1.2.7'

Author: rhshah

indel_realignment/indel_realignment_staticbed.cwl

@@ -0,0 +1,189 @@
+class: Workflow
+cwlVersion: v1.0
+id: indel_realignment_staticbed
+label: indel_realignment_staticbed
+$namespaces:
+  s: 'https://schema.org/'
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: window_size
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 0
+  - id: soft_clip_contig
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 533.75
+  - id: scoring_gap_alignments
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 640.5
+  - id: reference_fasta
+    type: File
+    secondaryFiles:
+      - .fai
+    'sbg:x': 0
+    'sbg:y': 747.25
+  - id: no_sort
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1067.5
+  - id: maximum_mixmatch_rate
+    type: float?
+    'sbg:x': 0
+    'sbg:y': 1281
+  - id: maximum_average_depth
+    type: int?
+    'sbg:x': 0
+    'sbg:y': 1387.75
+  - id: input_bam
+    type: File
+    secondaryFiles:
+      - ^.bai
+    'sbg:x': 0
+    'sbg:y': 1494.5
+  - id: ignore_bad_assembly
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1601.25
+  - id: contig_anchor
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 1708
+  - id: consensus_sequence
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1814.75
+  - id: bam_index
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1921.5
+  - id: number_of_threads
+    type: int?
+    'sbg:x': 0
+    'sbg:y': 960.75
+  - id: no_edge_complex_indel
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1174.25
+  - id: output_bams
+    type:
+      - string
+      - type: array
+        items: string
+    'sbg:x': 0
+    'sbg:y': 854
+  - id: validation_stringency
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 106.75
+  - id: sort_order
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 427
+  - id: output_file_name
+    type: string?
+    'sbg:x': 257.390625
+    'sbg:y': 742
+  - id: create_bam_index
+    type: boolean?
+    'sbg:x': 257.390625
+    'sbg:y': 848.75
+  - id: temporary_directory
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 213.5
+  - id: targets
+    type: File
+    'sbg:x': 0
+    'sbg:y': 320.25
+outputs:
+  - id: indel_realignment_bam
+    outputSource:
+      - picard_fix_mate_information_4_1_8_1/picard_fix_mate_information_bam
+    type: File
+    secondaryFiles:
+      - ^.bai
+    'sbg:x': 1245.78662109375
+    'sbg:y': 960.75
+steps:
+  - id: abra2_2_22
+    in:
+      - id: number_of_threads
+        source: number_of_threads
+      - id: input_bam
+        source:
+          - input_bam
+      - id: working_directory
+        source: temporary_directory
+      - id: reference_fasta
+        source: reference_fasta
+      - id: targets
+        source: targets
+      - id: maximum_average_depth
+        source: maximum_average_depth
+      - id: soft_clip_contig
+        source: soft_clip_contig
+      - id: maximum_mixmatch_rate
+        source: maximum_mixmatch_rate
+      - id: scoring_gap_alignments
+        source: scoring_gap_alignments
+      - id: contig_anchor
+        source: contig_anchor
+      - id: window_size
+        source: window_size
+      - id: consensus_sequence
+        source: consensus_sequence
+      - id: output_bams
+        source:
+          - output_bams
+      - id: ignore_bad_assembly
+        source: ignore_bad_assembly
+      - id: bam_index
+        source: bam_index
+      - id: no_edge_complex_indel
+        source: no_edge_complex_indel
+      - id: no_sort
+        source: no_sort
+    out:
+      - id: abra_realigned_bam
+    run: ../command_line_tools/abra2_2.22/abra2_2.22.cwl
+    label: abra2_2.22
+    'sbg:x': 257.390625
+    'sbg:y': 1067.5
+  - id: picard_fix_mate_information_4_1_8_1
+    in:
+      - id: input
+        source: abra2_2_22/abra_realigned_bam
+      - id: output_file_name
+        source: output_file_name
+      - id: sort_order
+        source: sort_order
+      - id: validation_stringency
+        source: validation_stringency
+      - id: create_bam_index
+        source: create_bam_index
+      - id: temporary_directory
+        source: temporary_directory
+    out:
+      - id: picard_fix_mate_information_bam
+    run: >-
+      ../command_line_tools/picard_fix_mate_information_4.1.8.1/picard_fix_mate_information_4.1.8.1.cwl
+    label: picard_fix_mate_information_4.1.8.1
+    'sbg:x': 811.167236328125
+    'sbg:y': 925.75
+requirements: []
+$schemas:
+  - 'http://schema.org/version/latest/schemaorg-current-http.rdf'
+'s:author':
+  - class: 's:Person'
+    's:email': 'mailto:murphyc4@mskcc.org'
+    's:name': Charlie Murphy
+'s:citation': ''
+'s:codeRepository': 'https://github.com/msk-access/cwl_subworkflows/indel_realignment'
+'s:contributor':
+  - class: 's:Person'
+    's:email': 'mailto:murphyc4@mskcc.org'
+    's:name': Charlie Murphy
+'s:dateCreated': '2020-09-14'
+'s:license': 'https://spdx.org/licenses/Apache-2.0'