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Use new sequence type in alignment. #741

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Merged
tmooney merged 6 commits into from
Aug 13, 2019
Merged

Use new sequence type in alignment. #741

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0ab1c2a
New type to represent sequence data.
tmooney Jul 18, 2019
69ecfe2
New tool to align sequence data regardless of filetype.
tmooney Jul 18, 2019
eece0dc
Subworkflow to perform alignment on "sequence_data".
tmooney Jul 18, 2019
6259aa5
Use new sequence type for standard DNA alignment process.
tmooney Jul 22, 2019
b2b638d
Use an adapter to circumvent issues in staging files.
tmooney Jul 23, 2019
398f7da
Move adapter under subworkflows.
tmooney Aug 1, 2019
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28 changes: 10 additions & 18 deletions definitions/pipelines/cle_aml_trio.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,28 +7,23 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_name:
type: string?
default: 'tumor'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_name:
type: string?
default: 'normal'
followup_bams:
type: File[]
followup_readgroups:
type: string[]
followup_sequence:
type: ../types/sequence_data.yml#sequence_data[]
followup_name:
type: string?
default: 'followup'
Expand Down Expand Up @@ -367,8 +362,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: normal_bams
readgroups: normal_readgroups
sequence: normal_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand All @@ -391,8 +385,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: tumor_bams
readgroups: tumor_readgroups
sequence: tumor_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand All @@ -415,8 +408,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: followup_bams
readgroups: followup_readgroups
sequence: followup_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
19 changes: 7 additions & 12 deletions definitions/pipelines/cle_somatic_exome.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,18 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_name:
type: string?
default: 'tumor'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_name:
type: string?
default: 'normal'
Expand Down Expand Up @@ -295,8 +292,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: tumor_bams
readgroups: tumor_readgroups
sequence: tumor_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand All @@ -319,8 +315,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: normal_bams
readgroups: normal_readgroups
sequence: normal_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
10 changes: 4 additions & 6 deletions definitions/pipelines/exome.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,12 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
mills:
type: File
secondaryFiles: [.tbi]
Expand Down Expand Up @@ -179,8 +178,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
sequence: sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
12 changes: 5 additions & 7 deletions definitions/pipelines/exome_alignment.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,12 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
mills:
type: File
secondaryFiles: [.tbi]
Expand Down Expand Up @@ -92,11 +91,10 @@ outputs:
outputSource: qc/verify_bam_id_depth
steps:
alignment:
run: ../subworkflows/bam_to_bqsr.cwl
run: ../subworkflows/sequence_to_bqsr.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
unaligned: sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
28 changes: 10 additions & 18 deletions definitions/pipelines/gathered_cle_aml_trio.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,28 +7,23 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_name:
type: string?
default: 'tumor'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_name:
type: string?
default: 'normal'
followup_bams:
type: File[]
followup_readgroups:
type: string[]
followup_sequence:
type: ../types/sequence_data.yml#sequence_data[]
followup_name:
type: string?
default: 'followup'
Expand Down Expand Up @@ -189,14 +184,11 @@ steps:
run: cle_aml_trio.cwl
in:
reference: reference
tumor_bams: tumor_bams
tumor_readgroups: tumor_readgroups
tumor_sequence: tumor_sequence
tumor_name: tumor_name
normal_bams: normal_bams
normal_readgroups: normal_readgroups
normal_sequence: normal_sequence
normal_name: normal_name
followup_bams: followup_bams
followup_readgroups: followup_readgroups
followup_sequence: followup_sequence
followup_name: followup_name
mills: mills
known_indels: known_indels
Expand Down
19 changes: 7 additions & 12 deletions definitions/pipelines/gathered_cle_somatic_exome.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,18 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_cram_name:
type: string?
default: 'tumor.cram'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_cram_name:
type: string?
default: 'normal.cram'
Expand Down Expand Up @@ -152,11 +149,9 @@ steps:
run: cle_somatic_exome.cwl
in:
reference: reference
tumor_bams: tumor_bams
tumor_readgroups: tumor_readgroups
tumor_sequence: tumor_sequence
tumor_cram_name: tumor_cram_name
normal_bams: normal_bams
normal_readgroups: normal_readgroups
normal_sequence: normal_sequence
normal_cram_name: normal_cram_name
mills: mills
known_indels: known_indels
Expand Down
19 changes: 7 additions & 12 deletions definitions/pipelines/gathered_somatic_exome.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,18 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_cram_name:
type: string?
default: 'tumor.cram'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_cram_name:
type: string?
default: 'normal.cram'
Expand Down Expand Up @@ -149,11 +146,9 @@ steps:
run: somatic_exome.cwl
in:
reference: reference
tumor_bams: tumor_bams
tumor_readgroups: tumor_readgroups
tumor_sequence: tumor_sequence
tumor_cram_name: tumor_cram_name
normal_bams: normal_bams
normal_readgroups: normal_readgroups
normal_sequence: normal_sequence
normal_cram_name: normal_cram_name
mills: mills
known_indels: known_indels
Expand Down
10 changes: 4 additions & 6 deletions definitions/pipelines/germline_exome.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,12 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
mills:
type: File
secondaryFiles: [.tbi]
Expand Down Expand Up @@ -153,8 +152,7 @@ steps:
run: exome_alignment.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
sequence: sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
10 changes: 4 additions & 6 deletions definitions/pipelines/germline_exome_hla_typing.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,12 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
mills:
type: File
secondaryFiles: [.tbi]
Expand Down Expand Up @@ -149,8 +148,7 @@ steps:
run: germline_exome.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
sequence: sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
10 changes: 4 additions & 6 deletions definitions/pipelines/germline_wgs.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,12 @@ requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
mills:
type: File
secondaryFiles: [.tbi]
Expand Down Expand Up @@ -263,8 +262,7 @@ steps:
run: wgs_alignment.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
sequence: sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
Expand Down
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