Merge branch 'release/0.2.0'

Author: rhshah

.gitignore

@@ -1,3 +1,6 @@
+# Mac
+.DS_Store
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.gitmodules

@@ -1,3 +1,4 @@
 [submodule "command_line_tools"]
 	path = command_line_tools
-	url = https://github.com/mskcc/cwl-commandlinetools.git
+	url = https://github.com/msk-access/cwl-commandlinetools.git
+	branch = 0.6.1

abra_fx-cwl.cwl

@@ -0,0 +1,162 @@
+class: Workflow
+cwlVersion: v1.0
+id: abra_fx_cwl
+label: abra_fx.cwl
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: input_bam
+    type:
+      - File
+      - type: array
+        items: File
+    secondaryFiles:
+      - ^.bai
+    'sbg:x': 0
+    'sbg:y': 853.5625
+  - id: reference_fasta
+    type: File
+    secondaryFiles:
+      - .fai
+      - ^.dict
+    'sbg:x': 0
+    'sbg:y': 320.125
+  - id: bam_index
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1280.34375
+  - id: option_bedgraph
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 426.8203125
+  - id: window_size
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 0
+  - id: soft_clip_contig
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 106.6953125
+  - id: scoring_gap_alignments
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 213.4296875
+  - id: no_sort
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 533.515625
+  - id: maximum_mixmatch_rate
+    type: float?
+    'sbg:x': 0
+    'sbg:y': 640.171875
+  - id: maximum_average_depth
+    type: int?
+    'sbg:x': 0
+    'sbg:y': 746.8671875
+  - id: ignore_bad_assembly
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 960.2578125
+  - id: contig_anchor
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 1066.9921875
+  - id: consensus_sequence
+    type: boolean?
+    'sbg:x': 0
+    'sbg:y': 1173.6875
+  - id: number_of_threads
+    type: int?
+    label: abra_number_of_threads
+    'sbg:x': 535.44482421875
+    'sbg:y': 314.0636291503906
+outputs:
+  - id: abra_fx_bam
+    outputSource:
+      - picard_fix_mate_information_1_97/bam
+    type: File
+    secondaryFiles:
+      - ^.bai
+    'sbg:x': 1346.0264892578125
+    'sbg:y': 640.171875
+  - id: output_file
+    outputSource:
+      - bedtools_merge/output_file
+    type: File?
+    label: indel_realign_targets
+    'sbg:x': 676.9483642578125
+    'sbg:y': 502.8046875
+steps:
+  - id: bedtools_genomecov
+    in:
+      - id: input
+        source: input_bam
+      - id: option_bedgraph
+        source: option_bedgraph
+    out:
+      - id: output_file
+    run: >-
+      command_line_tools/bedtools_genomecov_v2.28.0_cv2/bedtools_genomecov_v2.28.0_cv2.cwl
+    label: bedtools_genomecov
+    'sbg:x': 257.390625
+    'sbg:y': 633.1328125
+  - id: bedtools_merge
+    in:
+      - id: input
+        source: bedtools_genomecov/output_file
+    out:
+      - id: output_file
+    run: >-
+      command_line_tools/bedtools_merge_v2.28.0_cv2/bedtools_merge_v2.28.0_cv2.cwl
+    label: bedtools_merge
+    'sbg:x': 503.6046142578125
+    'sbg:y': 640.1328125
+  - id: abra2_2_18
+    in:
+      - id: number_of_threads
+        source: number_of_threads
+      - id: input_bam
+        source:
+          - input_bam
+      - id: reference_fasta
+        source: reference_fasta
+      - id: targets
+        source: bedtools_merge/output_file
+      - 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: ignore_bad_assembly
+        source: ignore_bad_assembly
+      - id: bam_index
+        source: bam_index
+      - id: no_sort
+        source: no_sort
+    out:
+      - id: realigned_bam
+    run: command_line_tools/abra2_2.17/abra2_2.17.cwl
+    label: abra2_2.17
+    'sbg:x': 787.517578125
+    'sbg:y': 767.3450317382812
+  - id: picard_fix_mate_information_1_97
+    in:
+      - id: input
+        source: abra2_2_18/realigned_bam
+    out:
+      - id: bam
+    run: >-
+      command_line_tools/picard_fix_mate_information_1.96/picard_fix_mate_information_1.96.cwl
+    label: picard_fix_mate_information_1.96
+    'sbg:x': 1150.2608642578125
+    'sbg:y': 640.171875
+requirements: []

abra_fx.cwl

@@ -10,68 +10,83 @@ inputs:
     secondaryFiles:
       - .fai
       - ^.dict
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
     'sbg:x': 0
-    'sbg:y': 106.5390625
+    'sbg:y': 107
   - id: reads
     type: 'File[]'
     'sbg:x': 0
-    'sbg:y': 213.0390625
+    'sbg:y': 214
   - id: P
     type: boolean?
     'sbg:x': 0
-    'sbg:y': 959.9453125
+    'sbg:y': 963
   - id: M
     type: boolean?
     'sbg:x': 0
-    'sbg:y': 1066.4453125
+    'sbg:y': 1177
   - id: read_group_identifier
     type: string
     'sbg:x': 0
-    'sbg:y': 853.328125
+    'sbg:y': 856
   - id: sort_order
     type: string?
     'sbg:x': 0
     'sbg:y': 0
   - id: create_bam_index
     type: boolean?
-    'sbg:x': 479.32232666015625
-    'sbg:y': 854.1065063476562
+    'sbg:x': 319.171875
+    'sbg:y': 560.5
   - id: read_group_sequnecing_center
     type: string
     'sbg:x': 0
-    'sbg:y': 319.65625
+    'sbg:y': 321
   - id: read_group_sequencing_platform
     type: string
     'sbg:x': 0
-    'sbg:y': 426.390625
+    'sbg:y': 428
   - id: read_group_sample_name
     type: string
     'sbg:x': 0
-    'sbg:y': 533.125
+    'sbg:y': 535
   - id: read_group_platform_unit
     type: string
     'sbg:x': 0
-    'sbg:y': 639.859375
+    'sbg:y': 642
   - id: read_group_library
     type: int
     'sbg:x': 0
-    'sbg:y': 746.59375
+    'sbg:y': 749
+  - id: output_file_name
+    type: string?
+    'sbg:x': 319.171875
+    'sbg:y': 453.5
+  - id: output
+    type: string?
+    'sbg:x': 0
+    'sbg:y': 1070
 outputs:
   - id: bam
     outputSource:
       - picard_add_or_replace_read_groups_1_96/bam
     type: File
     secondaryFiles:
       - ^.bai
-    'sbg:x': 908.6610107421875
-    'sbg:y': 533.2421875
+    'sbg:x': 922.9844970703125
+    'sbg:y': 588.5
 steps:
   - id: bwa_mem_0_7_5a
     in:
       - id: M
         source: M
       - id: P
         source: P
+      - id: output
+        source: output
       - id: reads
         source:
           - reads
@@ -81,12 +96,14 @@ steps:
       - id: sam
     run: command_line_tools/bwa_mem_0.7.5a/bwa_mem_0.7.5a.cwl
     label: bwa-mem
-    'sbg:x': 292.4254455566406
-    'sbg:y': 725.329833984375
+    'sbg:x': 319.171875
+    'sbg:y': 695.5
   - id: picard_add_or_replace_read_groups_1_96
     in:
       - id: input
         source: bwa_mem_0_7_5a/sam
+      - id: output_file_name
+        source: output_file_name
       - id: sort_order
         source: sort_order
       - id: read_group_identifier
@@ -108,6 +125,6 @@ steps:
     run: >-
       command_line_tools/picard_add_or_replace_read_groups_1.96/picard_add_or_replace_read_groups_1.96.cwl
     label: picard_add_or_replace_read_groups_1.96
-    'sbg:x': 715.1737670898438
-    'sbg:y': 346.0451965332031
+    'sbg:x': 520.293212890625
+    'sbg:y': 525.5
 requirements: []