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somatic_exome cram version #973

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b067d60
beginning to modify somatic_exome pipeline for bam_readcount cram sup…
johnegarza Sep 3, 2020
82b8ee0
Merge branch 'master' into somatic_exome_cram_readcount
johnegarza Sep 3, 2020
275b5c1
Update all parts of workflow to accept cram inputs when possible
johnegarza Sep 4, 2020
b4d02c5
bugfixes
johnegarza Sep 4, 2020
1f7dc0b
Merge branch 'master' into somatic_exome_cram_readcount
johnegarza Oct 7, 2020
b16fbd5
Samtools packaged with mutect is old and can't open cram files
johnegarza Dec 4, 2020
b77344d
Use custom patched version of cnvkit that supports opening crams with…
johnegarza Dec 4, 2020
dbdbb3b
Use patched version of bam-readcount that supports crams
johnegarza Dec 4, 2020
0505632
cleanup
johnegarza Dec 4, 2020
8d98d6b
Merge branch 'master' into somatic_exome_cram_readcount
johnegarza Dec 4, 2020
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10 changes: 5 additions & 5 deletions definitions/pipelines/alignment_exome.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -50,10 +50,10 @@ inputs:
qc_minimum_base_quality:
type: int?
outputs:
bam:
cram:
type: File
outputSource: alignment/final_bam
secondaryFiles: [.bai, ^.bai]
outputSource: alignment/final_cram
secondaryFiles: [.crai, ^.crai]
mark_duplicates_metrics:
type: File
outputSource: alignment/mark_duplicates_metrics_file
Expand Down Expand Up @@ -103,11 +103,11 @@ steps:
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
final_name: final_name
out: [final_bam,mark_duplicates_metrics_file]
out: [final_cram,mark_duplicates_metrics_file]
qc:
run: ../subworkflows/qc_exome.cwl
in:
bam: alignment/final_bam
cram: alignment/final_cram
reference: reference
bait_intervals: bait_intervals
target_intervals: target_intervals
Expand Down
35 changes: 18 additions & 17 deletions definitions/pipelines/detect_variants.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,12 @@ inputs:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
tumor_cram:
type: File
secondaryFiles: [.bai,^.bai]
normal_bam:
secondaryFiles: [.crai,^.crai]
normal_cram:
type: File
secondaryFiles: [.bai,^.bai]
secondaryFiles: [.crai,^.crai]
roi_intervals:
type: File
label: "roi_intervals: regions of interest in which variants will be called"
Expand Down Expand Up @@ -201,19 +201,20 @@ steps:
run: ../subworkflows/mutect.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_cram: tumor_cram
normal_cram: normal_cram
interval_list: roi_intervals
scatter_count: scatter_count
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[unfiltered_vcf, filtered_vcf]
strelka:
run: ../subworkflows/strelka_and_post_processing.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_cram: tumor_cram
normal_cram: normal_cram
interval_list: roi_intervals
exome_mode: strelka_exome_mode
cpu_reserved: strelka_cpu_reserved
Expand All @@ -225,8 +226,8 @@ steps:
run: ../subworkflows/varscan_pre_and_post_processing.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_cram: tumor_cram
normal_cram: normal_cram
interval_list: roi_intervals
scatter_count: scatter_count
strand_filter: varscan_strand_filter
Expand All @@ -242,8 +243,8 @@ steps:
run: ../subworkflows/pindel.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_cram: tumor_cram
normal_cram: normal_cram
interval_list: roi_intervals
scatter_count: scatter_count
insert_size: pindel_insert_size
Expand All @@ -255,8 +256,8 @@ steps:
run: ../subworkflows/docm_cle.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_cram: tumor_cram
normal_cram: normal_cram
docm_vcf: docm_vcf
interval_list: roi_intervals
filter_docm_variants: filter_docm_variants
Expand Down Expand Up @@ -314,7 +315,7 @@ steps:
vcf: annotate_variants/annotated_vcf
sample: tumor_sample_name
reference_fasta: reference
bam: tumor_bam
cram: tumor_cram
min_base_quality: readcount_minimum_base_quality
min_mapping_quality: readcount_minimum_mapping_quality
out:
Expand All @@ -325,7 +326,7 @@ steps:
vcf: annotate_variants/annotated_vcf
sample: normal_sample_name
reference_fasta: reference
bam: normal_bam
cram: normal_cram
min_base_quality: readcount_minimum_base_quality
min_mapping_quality: readcount_minimum_mapping_quality
out:
Expand Down Expand Up @@ -368,7 +369,7 @@ steps:
filter_somatic_llr_tumor_purity: filter_somatic_llr_tumor_purity
filter_somatic_llr_normal_contamination_rate: filter_somatic_llr_normal_contamination_rate
filter_minimum_depth: filter_minimum_depth
tumor_bam: tumor_bam
tumor_cram: tumor_cram
do_cle_vcf_filter: cle_vcf_filter
reference: reference
normal_sample_name: normal_sample_name
Expand Down
61 changes: 16 additions & 45 deletions definitions/pipelines/somatic_exome.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -252,7 +252,7 @@ inputs:
outputs:
tumor_cram:
type: File
outputSource: tumor_index_cram/indexed_cram
outputSource: tumor_alignment_and_qc/cram
tumor_mark_duplicates_metrics:
type: File
outputSource: tumor_alignment_and_qc/mark_duplicates_metrics
Expand Down Expand Up @@ -291,7 +291,7 @@ outputs:
outputSource: tumor_alignment_and_qc/verify_bam_id_depth
normal_cram:
type: File
outputSource: normal_index_cram/indexed_cram
outputSource: normal_alignment_and_qc/cram
normal_mark_duplicates_metrics:
type: File
outputSource: normal_alignment_and_qc/mark_duplicates_metrics
Expand Down Expand Up @@ -467,11 +467,9 @@ steps:
picard_metric_accumulation_level: picard_metric_accumulation_level
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
final_name:
source: tumor_name
valueFrom: "$(self).bam"
final_name: tumor_name
out:
[bam, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
[cram, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
normal_alignment_and_qc:
run: alignment_exome.cwl
in:
Expand All @@ -489,17 +487,15 @@ steps:
picard_metric_accumulation_level: picard_metric_accumulation_level
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
final_name:
source: normal_name
valueFrom: "$(self).bam"
final_name: normal_name
out:
[bam, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
[cram, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
concordance:
run: ../tools/concordance.cwl
in:
reference: reference
bam_1: tumor_alignment_and_qc/bam
bam_2: normal_alignment_and_qc/bam
cram_1: tumor_alignment_and_qc/cram
cram_2: normal_alignment_and_qc/cram
vcf: somalier_vcf
out:
[somalier_pairs, somalier_samples]
Expand All @@ -514,8 +510,8 @@ steps:
run: detect_variants.cwl
in:
reference: reference
tumor_bam: tumor_alignment_and_qc/bam
normal_bam: normal_alignment_and_qc/bam
tumor_cram: tumor_alignment_and_qc/cram
normal_cram: normal_alignment_and_qc/cram
roi_intervals: pad_target_intervals/expanded_interval_list
strelka_exome_mode:
default: true
Expand Down Expand Up @@ -552,52 +548,27 @@ steps:
cnvkit:
run: ../tools/cnvkit_batch.cwl
in:
tumor_bam: tumor_alignment_and_qc/bam
tumor_cram: tumor_alignment_and_qc/cram
reference:
source: [normal_alignment_and_qc/bam, reference]
source: [normal_alignment_and_qc/cram, reference]
valueFrom: |
${
var normal = self[0];
var fasta = self[1];
return {'normal_bam': normal, 'fasta_file': fasta};
return {'normal_cram': normal, 'fasta_file': fasta};
}
bait_intervals: bait_intervals
out:
[intervals_antitarget, intervals_target, normal_antitarget_coverage, normal_target_coverage, reference_coverage, cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios]
manta:
run: ../tools/manta_somatic.cwl
in:
normal_bam: normal_alignment_and_qc/bam
tumor_bam: tumor_alignment_and_qc/bam
normal_bam: normal_alignment_and_qc/cram
tumor_bam: tumor_alignment_and_qc/cram
reference: reference
call_regions: manta_call_regions
non_wgs: manta_non_wgs
output_contigs: manta_output_contigs
out:
[diploid_variants, somatic_variants, all_candidates, small_candidates, tumor_only_variants]
tumor_bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: tumor_alignment_and_qc/bam
reference: reference
out:
[cram]
tumor_index_cram:
run: ../tools/index_cram.cwl
in:
cram: tumor_bam_to_cram/cram
out:
[indexed_cram]
normal_bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: normal_alignment_and_qc/bam
reference: reference
out:
[cram]
normal_index_cram:
run: ../tools/index_cram.cwl
in:
cram: normal_bam_to_cram/cram
out:
[indexed_cram]

16 changes: 8 additions & 8 deletions definitions/subworkflows/docm_cle.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@ inputs:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
tumor_cram:
type: File
secondaryFiles: [^.bai]
normal_bam:
secondaryFiles: [^.crai]
normal_cram:
type: File
secondaryFiles: [^.bai]
secondaryFiles: [^.crai]
docm_vcf:
type: File
secondaryFiles: [.tbi]
Expand All @@ -34,8 +34,8 @@ steps:
run: ../tools/docm_gatk_haplotype_caller.cwl
in:
reference: reference
bam: tumor_bam
normal_bam: normal_bam
cram: tumor_cram
normal_cram: normal_cram
docm_vcf: docm_vcf
interval_list: interval_list
out:
Expand All @@ -62,8 +62,8 @@ steps:
run: ../tools/filter_vcf_docm.cwl
in:
docm_raw_variants: decompose/decomposed_vcf
normal_bam: normal_bam
tumor_bam: tumor_bam
normal_cram: normal_cram
tumor_cram: tumor_cram
filter_docm_variants: filter_docm_variants
out:
[docm_filtered_variants]
Expand Down
6 changes: 3 additions & 3 deletions definitions/subworkflows/filter_vcf.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@ inputs:
type: float
gnomad_field_name:
type: string
tumor_bam:
tumor_cram:
type: File
secondaryFiles: [.bai]
secondaryFiles: [.crai]
do_cle_vcf_filter:
type: boolean
filter_somatic_llr_threshold:
Expand Down Expand Up @@ -67,7 +67,7 @@ steps:
run: ../tools/filter_vcf_mapq0.cwl
in:
vcf: filter_vcf_gnomADe_allele_freq/filtered_vcf
tumor_bam: tumor_bam
tumor_cram: tumor_cram
threshold: filter_mapq0_threshold
reference: reference
out:
Expand Down
13 changes: 10 additions & 3 deletions definitions/subworkflows/fp_filter.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
bam:
cram:
type: File
secondaryFiles: [.bai,^.bai]
secondaryFiles: [.crai,^.crai]
reference:
type:
- string
Expand Down Expand Up @@ -59,11 +59,18 @@ steps:
vcf: decompose_variants/decomposed_vcf
out:
[indexed_vcf]
cram_to_bam:
run: cram_to_bam_and_index.cwl
in:
cram: cram
reference: reference
out:
[bam]
fp_filter:
run: ../tools/fp_filter.cwl
in:
reference: reference
bam: bam
bam: cram_to_bam/bam
vcf: index/indexed_vcf
sample_name: sample_name
min_var_freq: min_var_freq
Expand Down
10 changes: 5 additions & 5 deletions definitions/subworkflows/hs_metrics.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ requirements:
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
bam:
cram:
type: File
secondaryFiles: [^.bai]
secondaryFiles: [^.crai]
minimum_mapping_quality:
type: int?
minimum_base_quality:
Expand Down Expand Up @@ -51,7 +51,7 @@ steps:
scatter: [bait_intervals, target_intervals, output_prefix]
scatterMethod: dotproduct
in:
bam: bam
cram: cram
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
Expand All @@ -77,7 +77,7 @@ steps:
scatter: [bait_intervals, target_intervals, output_prefix]
scatterMethod: dotproduct
in:
bam: bam
cram: cram
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
Expand All @@ -103,7 +103,7 @@ steps:
scatter: [bait_intervals, target_intervals, output_prefix]
scatterMethod: dotproduct
in:
bam: bam
cram: cram
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
Expand Down
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