From 05bb4e148bcc0c02c3d8d3fced6818e5298a1a3d Mon Sep 17 00:00:00 2001
From: Jason Walker <jason.walker@wustl.edu>
Date: Mon, 9 Dec 2019 15:14:33 -0600
Subject: [PATCH] first pass at saving all BAMs/CRAMs that might be needed

---
 .../pipelines/alignment_umi_molecular.cwl     | 48 ++++++++++++++++---
 .../subworkflows/molecular_alignment.cwl      | 37 ++++++++++++--
 definitions/subworkflows/molecular_qc.cwl     | 16 +++++--
 3 files changed, 85 insertions(+), 16 deletions(-)

diff --git a/definitions/pipelines/alignment_umi_molecular.cwl b/definitions/pipelines/alignment_umi_molecular.cwl
index 4707011a4..89e553d46 100644
--- a/definitions/pipelines/alignment_umi_molecular.cwl
+++ b/definitions/pipelines/alignment_umi_molecular.cwl
@@ -29,10 +29,18 @@ inputs:
     target_intervals:
        type: File?
 outputs:
-    aligned_cram:
+    umi_aligned_cram:
         type: File
         secondaryFiles: [.crai, ^.crai]
-        outputSource: index_cram/indexed_cram
+        outputSource: umi_index_cram/indexed_cram
+    grouped_aligned_cram:
+        type: File
+        secondaryFiles: [.crai, ^.crai]
+        outputSource: grouped_index_cram/indexed_cram
+    consensus_aligned_cram:
+        type: File
+        secondaryFiles: [.crai, ^.crai]
+        outputSource: consensus_index_cram/indexed_cram
     adapter_histogram:
         type: File[]
         outputSource: alignment_workflow/adapter_histogram
@@ -62,17 +70,43 @@ steps:
             reference: reference
             target_intervals: target_intervals
         out:
-            [aligned_bam, adapter_histogram, duplex_seq_metrics]
-    bam_to_cram:
+            [umi_aligned_bam, grouped_aligned_bam, consensus_aligned_bam,  adapter_histogram, duplex_seq_metrics]
+    umi_bam_to_cram:
+        run: ../tools/bam_to_cram.cwl
+        in:
+            bam: alignment_workflow/umi_aligned_bam
+            reference: reference
+        out:
+            [cram]
+    umi_index_cram:
+        run: ../tools/index_cram.cwl
+        in: 
+            cram: umi_bam_to_cram/cram
+        out:
+            [indexed_cram]
+    grouped_bam_to_cram:
+        run: ../tools/bam_to_cram.cwl
+        in:
+            bam: alignment_workflow/grouped_aligned_bam
+            reference: reference
+        out:
+            [cram]
+    grouped_index_cram:
+        run: ../tools/index_cram.cwl
+        in:
+            cram: grouped_bam_to_cram/cram
+        out:
+            [indexed_cram]
+    consensus_bam_to_cram:
         run: ../tools/bam_to_cram.cwl
         in:
-            bam: alignment_workflow/aligned_bam
+            bam: alignment_workflow/consensus_aligned_bam
             reference: reference
         out:
             [cram]
-    index_cram:
+    consensus_index_cram:
          run: ../tools/index_cram.cwl
          in:
-            cram: bam_to_cram/cram
+            cram: consensus_bam_to_cram/cram
          out:
             [indexed_cram]
diff --git a/definitions/subworkflows/molecular_alignment.cwl b/definitions/subworkflows/molecular_alignment.cwl
index 1266d7747..172c5d7a8 100644
--- a/definitions/subworkflows/molecular_alignment.cwl
+++ b/definitions/subworkflows/molecular_alignment.cwl
@@ -36,10 +36,18 @@ inputs:
        type: float
        default: 0.5
 outputs:
-    aligned_bam:
+    umi_aligned_bam:
         type: File
         secondaryFiles: [.bai, ^.bai]
-        outputSource: index_bam/indexed_bam
+        outputSource: umi_index_bam/indexed_bam
+    grouped_aligned_bam:
+        type: File
+        secondaryFiles: [.bai, ^.bai]
+        outputSource: grouped_index_bam/indexed_bam
+    consensus_aligned_bam:
+        type: File
+        secondaryFiles: [.bai, ^.bai]
+        outputSource: consensus_index_bam/indexed_bam
     adapter_histogram:
         type: File[]
         outputSource: align/adapter_metrics
@@ -68,6 +76,13 @@ steps:
             bam: merge/merged_bam
         out:
             [grouped_bam]
+    grouped_clip_overlap:
+        run: ../tools/clip_overlap.cwl
+        in:
+            bam: group_reads_by_umi/grouped_bam
+            reference: reference
+        out:
+            [clipped_bam]
     call_molecular_consensus:
         run: ../tools/call_molecular_consensus.cwl
         in:
@@ -93,7 +108,7 @@ steps:
             max_no_call_fraction: max_no_call_fraction
         out:
             [filtered_bam]
-    clip_overlap:
+    consensus_clip_overlap:
         run: ../tools/clip_overlap.cwl
         in:
             bam: filter_consensus/filtered_bam
@@ -108,9 +123,21 @@ steps:
             description: sample_name
        out:
             [duplex_seq_metrics]
-    index_bam:
+    umi_index_bam:
+        run: ../tools/index_bam.cwl
+        in:
+            bam: merge/merged_bam
+        out:
+            [indexed_bam]
+    grouped_index_bam:
+        run: ../tools/index_bam.cwl
+        in:
+            bam: grouped_clip_overlap/clipped_bam
+        out:
+            [indexed_bam]
+    consensus_index_bam:
         run: ../tools/index_bam.cwl
         in:
-            bam: clip_overlap/clipped_bam
+            bam: consensus_clip_overlap/clipped_bam
         out:
             [indexed_bam]
diff --git a/definitions/subworkflows/molecular_qc.cwl b/definitions/subworkflows/molecular_qc.cwl
index 397f185ed..51d936894 100644
--- a/definitions/subworkflows/molecular_qc.cwl
+++ b/definitions/subworkflows/molecular_qc.cwl
@@ -38,10 +38,18 @@ inputs:
     summary_intervals:
         type: ../types/labelled_file.yml#labelled_file[]
 outputs:
-    aligned_bam:
+    umi_aligned_bam:
         type: File
         secondaryFiles: [.bai, ^.bai]
-        outputSource: alignment/aligned_bam
+        outputSource: alignment/umi_aligned_bam
+    grouped_aligned_bam:
+        type: File
+        secondaryFiles: [.bai, ^.bai]
+        outputSource: alignment/grouped_aligned_bam
+    consensus_aligned_bam:
+        type: File
+        secondaryFiles: [.bai, ^.bai]
+        outputSource: alignment/consensus_aligned_bam
     adapter_histogram:
         type: File[]
         outputSource: alignment/adapter_histogram
@@ -94,11 +102,11 @@ steps:
             reference: reference
             target_intervals: target_intervals
         out:
-            [aligned_bam, adapter_histogram, duplex_seq_metrics]
+            [umi_aligned_bam, grouped_aligned_bam, consensus_aligned_bam, adapter_histogram, duplex_seq_metrics]
     qc:
         run: qc_exome.cwl
         in:
-            bam: alignment/aligned_bam
+            bam: alignment/umi_aligned_bam
             reference: reference
             bait_intervals: bait_intervals
             target_intervals: target_intervals