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Updated workflow for basic UMI-aware alignment and qc #840

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Updated workflow for basic UMI-aware alignment and qc #840

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48 changes: 41 additions & 7 deletions definitions/pipelines/alignment_umi_molecular.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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]
37 changes: 32 additions & 5 deletions definitions/subworkflows/molecular_alignment.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand All @@ -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
Expand All @@ -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]
16 changes: 12 additions & 4 deletions definitions/subworkflows/molecular_qc.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down