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chore: dev to master #443

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merged 56 commits into from
Apr 26, 2024
Merged

chore: dev to master #443

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6f41281
feat: hg38 config and reference file setup
Smeds Feb 9, 2024
d3e6ea3
minor fixes
Smeds Feb 16, 2024
608d2bc
set file version
Smeds Feb 16, 2024
d704c7f
fix checksum
Smeds Feb 16, 2024
1fddcad
Update references.hg19.yaml
Smeds Feb 21, 2024
fabe8ae
Update requirements.txt
Smeds Feb 21, 2024
738aa33
Merge branch 'develop' into update-hg38-ref-files
Smeds Mar 21, 2024
d6914f5
Merge pull request #412 from genomic-medicine-sweden/update-hg38-ref-…
Smeds Mar 21, 2024
a9dea4e
fix: add implied msi configuration from module to config
jonca79 Mar 22, 2024
1d9a027
feat: do not merge regions that are not identical
jonca79 Apr 9, 2024
7549036
fix: add "_" to regexp so that indels are reported correctly
jonca79 Apr 10, 2024
ccbe735
feat: added chromosome arm support to rule
jonca79 Apr 15, 2024
667d53f
feat: added calculation of cnv in chrom arms
jonca79 Apr 15, 2024
b1c9bfe
docs: added schema
jonca79 Apr 15, 2024
9a25cdc
feat: added warnings for baseline and polyploidy
jonca79 Apr 16, 2024
e681fee
fix: bugfix
jonca79 Apr 16, 2024
9a92bf2
feat: added more config variables
jonca79 Apr 17, 2024
8a508ad
fix: handle CNVs bridging the chromosome arms
jonca79 Apr 17, 2024
d460172
fix: variable baf bugfix
jonca79 Apr 17, 2024
b1ce417
feat: decreased chr arm fraction
jonca79 Apr 17, 2024
e577cdd
feat: added table to cnv_html_report
jonca79 Apr 18, 2024
62c832d
docs: added config schemas for new params
jonca79 Apr 18, 2024
2d4eb4c
test: added params to test config
jonca79 Apr 18, 2024
8f91b42
feat: added configuration of polyploidy and baseline limits
jonca79 Apr 18, 2024
4f62f57
test: added unit tests
jonca79 Apr 18, 2024
cee1f59
Merge pull request #442 from genomic-medicine-sweden/cnv_report_chr
Smeds Apr 19, 2024
59a7e89
Merge pull request #441 from genomic-medicine-sweden/fix_coverage_and…
Smeds Apr 19, 2024
1a3bdca
Merge pull request #440 from genomic-medicine-sweden/svdb_skip_merging
Smeds Apr 19, 2024
482c5d4
Merge pull request #439 from genomic-medicine-sweden/msi_config
Smeds Apr 19, 2024
c8264b2
feat: two new amplification genes reported
jonca79 Apr 19, 2024
c6f7b5e
feat: new amp genes for hg38
jonca79 Apr 19, 2024
46aef96
fix: spelling error
jonca79 Apr 19, 2024
5e057e7
feat: updated with new reference files
jonca79 Apr 19, 2024
0ad022c
feat: update ref files for hg38
jonca79 Apr 19, 2024
3e83b49
Merge pull request #445 from genomic-medicine-sweden/new_ref_files
jonca79 Apr 19, 2024
73a9450
Merge pull request #444 from genomic-medicine-sweden/new_amp_genes-1
Smeds Apr 19, 2024
f8d69e7
refactor: move chrom arm file
Smeds Apr 19, 2024
4dd24f2
Update config.data.hg19.yaml
Smeds Apr 19, 2024
acf3871
Update config.data.hg38.yaml
Smeds Apr 19, 2024
b39f438
Merge pull request #446 from genomic-medicine-sweden/Smeds-patch-1
jonca79 Apr 19, 2024
36b3b0a
fix: correct missing part of vep ref file path
Smeds Apr 19, 2024
510dcce
Merge pull request #447 from genomic-medicine-sweden/Smeds-patch-1
Smeds Apr 19, 2024
3a2cae4
fix: rm duplicate entries of cnv in report
jonca79 Apr 19, 2024
e8efb8c
fix: update hg38 ref files, point to correct release
Smeds Apr 19, 2024
6dc14a9
chore: pycodestyle
jonca79 Apr 19, 2024
e616490
chore: pycodestyle
jonca79 Apr 19, 2024
682d605
Merge pull request #449 from genomic-medicine-sweden/Smeds-patch-1
jonca79 Apr 19, 2024
0fe8c17
Merge pull request #448 from genomic-medicine-sweden/fix_tsv_report
jonca79 Apr 19, 2024
be98e22
fix: update config, merge_cnv_json, to use latest amp gene bed file
Smeds Apr 22, 2024
bcbadf7
Merge pull request #450 from genomic-medicine-sweden/Smeds-patch-1
jonca79 Apr 22, 2024
36bab94
feat: update test file for develop
Smeds Apr 24, 2024
c9d41dc
Merge pull request #451 from genomic-medicine-sweden/Smeds-patch-1
Smeds Apr 24, 2024
3d980c3
ci: update test file
Smeds Apr 25, 2024
14d4eee
Merge pull request #453 from genomic-medicine-sweden/Smeds-patch-2
Smeds Apr 25, 2024
66bf299
ci: update main test file
Smeds Apr 26, 2024
a077d64
Merge pull request #454 from genomic-medicine-sweden/Smeds-patch-2
Smeds Apr 26, 2024
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13 changes: 12 additions & 1 deletion .tests/integration/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ call_small_cnv_deletions:
call_small_cnv_amplifications:
regions_file: "DATA/cnv_amplification_genes.tsv"


cnvkit_batch:
normal_reference: "DATA/design.PoN.cnn"
method: "hybrid"
Expand All @@ -52,6 +51,18 @@ cnvkit_batch_hrd:
cnv_html_report:
template_dir: "../../config/reports/cnv_report_template"

cnv_tsv_report:
amp_cn_limit: 6.0
chrom_arm_size: "reference/chromosome_arm_size.tsv"
del_1p19q_cn_limit: 1.4
del_1p19q_chr_arm_fraction: 0.3
chr_arm_fraction: 0.5
del_chr_arm_cn_limit: 1.4
amp_chr_arm_cn_limit: 2.5
normal_baf_lower_limit: 0.4
normal_baf_upper_limit: 0.6
normal_cn_lower_limit: 1.7
normal_cn_upper_limit: 2.25

exon_skipping:
design_bed: "reference/Twist_RNA_Design5.annotated.bed"
Expand Down
25 changes: 25 additions & 0 deletions .tests/integration/reference/chromosome_arm_size.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
chromosome p q
chr1 125000000 124250621
chr2 93300000 149899373
chr3 91000000 107022430
chr4 50400000 140754276
chr5 48400000 132515260
chr6 61000000 110115067
chr7 59900000 99238663
chr8 45600000 100764022
chr9 49000000 92213431
chr10 40200000 95334747
chr11 53700000 81306516
chr12 35800000 98051895
chr13 17900000 97269878
chr14 17600000 89749540
chr15 19000000 83531392
chr16 36600000 53754753
chr17 24000000 57195210
chr18 17200000 60877248
chr19 26500000 32628983
chr20 27500000 35525520
chr21 13200000 34929895
chr22 14700000 36604566
chrX 60600000 94670560
chrY 12500000 46873566
12 changes: 6 additions & 6 deletions .tests/jenkins/test_input_develop.tsv
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Expand Up @@ -6,13 +6,13 @@ results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.purecn.scar
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.amplifications.tsv f397f92f69100d1f20ca65ffac830dd0
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.deletions.tsv f887194ae8134c8a1c8fd427ae533646
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.manta_tumorSV.vcf.gz 1c4f0a2b346d1355dc76fcd126222729
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 831ba945efe70a4fe5df10d632a017ce
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 63fb792a3010418b15c5971d402886ac
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv aebb2658c6c2112c29ffbd710e5a9d77
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 2b09144044b2bdf63c440082be760b26
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv ceb3be1abd7951617928cd5c3572a8a1
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 8a85c32ff5b4e0668376043e16dc0e77
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.svdb_query.vcf c5ebcc72790e0c6f5186298bf5890348
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.svdb_query.vcf c51a58f9332c9176b0f354a955fd25bc
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv aebb2658c6c2112c29ffbd710e5a9d77
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 73e862d949f8de401c23170ca6db09d4
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv 8a85c32ff5b4e0668376043e16dc0e77
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 2438c93ab15eb0e2f6595ac5c006a1f2
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.svdb_query.vcf 49498b22ca7af9176b31e194ef5eb42f
results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.alignment_summary_metrics.txt fa88f8adc1d6146cf399c6d17a37d098
results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.contamination.table a4ee6cd2e1cfe029229f5b218ac318e9
Expand All @@ -28,7 +28,7 @@ results/dna/VAL2022-2-5M_T/additional_files/vcf/vardict_VAL2022-2-5M_T.vcf.gz 22
results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.msisensor_pro.score.tsv e47f1fb00f0220a20335f972e1af8d39
results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.pathology_purecn.scarhrd_cnvkit_score.txt 55145eab2e60e588c66b233cf1479287
results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.TMB.txt e20d98b80deb3ad74605c0439abda1f2
results/dna/VAL2022-2-5M_T/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 73e862d949f8de401c23170ca6db09d4
results/dna/VAL2022-2-5M_T/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 2438c93ab15eb0e2f6595ac5c006a1f2
results/dna/VAL2022-2-5M_T/fusion/VAL2022-2-5M_T.fuseq_wes.report.csv ada3432e93dd1ff64f9254d8c83c91c5
results/dna/VAL2022-2-5M_T/qc/VAL2022-2-5M_T.coverage_and_mutations.tsv 62666e179f8e43450e4dd65a75928e34
results/dna/VAL2022-2-5M_T/vcf/VAL2022-2-5M_T.annotated.exon_only.filter.hard_filter.codon_snv.qci.vcf e9dc0afeeb5d2b738183ce465973b292
Expand Down
56 changes: 28 additions & 28 deletions .tests/jenkins/test_input_main.tsv
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Expand Up @@ -9,13 +9,13 @@ results/dna/HD827_T/additional_files/biomarker/HD827_T.purecn.scarhrd_cnvkit_sco
results/dna/HD827_T/additional_files/cnv/HD827_T.amplifications.tsv f397f92f69100d1f20ca65ffac830dd0
results/dna/HD827_T/additional_files/cnv/HD827_T.deletions.tsv e441b862e6d6d573d18fe40f1eaa7103
results/dna/HD827_T/additional_files/cnv/HD827_T.manta_tumorSV.vcf.gz e29abf2c24120cd652bdf6c50b7aab12
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology.amp_all_del_all.cnv_report.tsv 69a3436f01613d49a82dca7aa1828374
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology.amp_all_del_validated.cnv_report.tsv 18297cf54ddee1a0564edbb254620b6e
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology_purecn.amp_all_del_all.cnv_report.tsv b13e1595a1b891bb5a18ec24e51ee748
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology.amp_all_del_all.cnv_report.tsv cabe3be96550c2c8e86f8c4a1779de1f
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology.amp_all_del_validated.cnv_report.tsv 244385d39ffe68fabe5068ae30df123f
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 01660be1832c394b02e87e47e11afd9a
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology_purecn.svdb_query.vcf c4c706c4a72e5d1ecbb3b990bb01b425
results/dna/HD827_T/additional_files/cnv/HD827_T.pathology.svdb_query.vcf 2c73b0b03c88250d4b33db47b3d626e8
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.amp_all_del_all.cnv_report.tsv b13e1595a1b891bb5a18ec24e51ee748
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.amp_all_del_validated.cnv_report.tsv 8a9d642420b9e09e2fd8dcc7cb4a196a
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.amp_all_del_all.cnv_report.tsv 01660be1832c394b02e87e47e11afd9a
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.amp_all_del_validated.cnv_report.tsv 83f8461e2ac1537ed67f5fbb48cc6e09
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.svdb_query.vcf 9e1269f0072aa92eeaf969432af18ad8
results/dna/HD827_T/additional_files/qc/HD827_T.alignment_summary_metrics.txt 351f113346779003eae764ab6d16c5c4
results/dna/HD827_T/additional_files/qc/HD827_T.contamination.table 3c9511e7efab4fefd32144ff2ad19d19
Expand All @@ -31,23 +31,23 @@ results/dna/HD827_T/additional_files/vcf/vardict_HD827_T.vcf.gz 8654e74433b4550c
results/dna/HD827_T/biomarker/HD827_T.msisensor_pro.score.tsv 0f65c2525d900c36685c8a6e902e0f18
results/dna/HD827_T/biomarker/HD827_T.pathology_purecn.scarhrd_cnvkit_score.txt 01d2c284e52f514668a1cd55dfc3e972
results/dna/HD827_T/biomarker/HD827_T.TMB.txt daaee4de560681775bff827c15a8bc9b
results/dna/HD827_T/cnv/HD827_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 8a9d642420b9e09e2fd8dcc7cb4a196a
results/dna/HD827_T/cnv/HD827_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 83f8461e2ac1537ed67f5fbb48cc6e09
results/dna/HD827_T/fusion/HD827_T.fuseq_wes.report.csv ada3432e93dd1ff64f9254d8c83c91c5
results/dna/HD827_T/qc/HD827_T.coverage_and_mutations.tsv 8a0e25a13c1c24b1fcb31c6ed0fa30b2
results/dna/HD827_T/qc/HD827_T.coverage_and_mutations.tsv 8fdb084782b85b0892cf106ee1bc98fb
results/dna/HD827_T/vcf/HD827_T.annotated.exon_only.filter.hard_filter.codon_snv.qci.vcf d0afb01193e5806d935dbe0d3d3b7918
results/dna/HD827_T/vcf/HD827_T.annotated.exon_only.filter.hard_filter.codon_snv.vcf 48f5b016b07dbb62454690fea532ad5d
results/dna/HD832_T/additional_files/biomarker/HD832_T.pathology.scarhrd_cnvkit_score.txt e96427adba222271d6d24f5a915eb636
results/dna/HD832_T/additional_files/biomarker/HD832_T.purecn.scarhrd_cnvkit_score.txt 4b722d55d746bd2b1cc8699ebd97f2ce
results/dna/HD832_T/additional_files/cnv/HD832_T.amplifications.tsv f397f92f69100d1f20ca65ffac830dd0
results/dna/HD832_T/additional_files/cnv/HD832_T.deletions.tsv e441b862e6d6d573d18fe40f1eaa7103
results/dna/HD832_T/additional_files/cnv/HD832_T.manta_tumorSV.vcf.gz 7883b18b87db697f6f4eb0c51fc36ec9
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology.amp_all_del_all.cnv_report.tsv a41c7926a0311aea6247a8769dff6082
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology.amp_all_del_validated.cnv_report.tsv d66e8b1bb14bb1f4a0b882a00b352c4e
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology_purecn.amp_all_del_all.cnv_report.tsv cbe488d5aa2fc115614cce7b63d97b58
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology.amp_all_del_all.cnv_report.tsv 6ab99de198214814debbb31e468af5cc
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology.amp_all_del_validated.cnv_report.tsv 42617a2c42835ae9c90765ec1e5aa794
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology_purecn.amp_all_del_all.cnv_report.tsv eb1ad324eff1937f3e6db0c6cbb83aba
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology_purecn.svdb_query.vcf 6306860007d3a23296918f35d843f5f8
results/dna/HD832_T/additional_files/cnv/HD832_T.pathology.svdb_query.vcf ed9da0781e888e5fc248167096aa0678
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.amp_all_del_all.cnv_report.tsv cbe488d5aa2fc115614cce7b63d97b58
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.amp_all_del_validated.cnv_report.tsv f63fffa3ffab1b112ac2a4db77a2d969
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.amp_all_del_all.cnv_report.tsv eb1ad324eff1937f3e6db0c6cbb83aba
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.amp_all_del_validated.cnv_report.tsv 4ba0962054a276e1cfdb4298ef815240
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.svdb_query.vcf c9e96e55f8d252282ee43004710d731f
results/dna/HD832_T/additional_files/qc/HD832_T.alignment_summary_metrics.txt 8b2548b05cc43eaff20aeabb16aa1490
results/dna/HD832_T/additional_files/qc/HD832_T.contamination.table 18bef22a4210099ec22b2444e6ac2482
Expand All @@ -63,23 +63,23 @@ results/dna/HD832_T/additional_files/vcf/vardict_HD832_T.vcf.gz e105f2145cd7ee18
results/dna/HD832_T/biomarker/HD832_T.msisensor_pro.score.tsv ec30212327f70eea52bf123bf8a5b6d2
results/dna/HD832_T/biomarker/HD832_T.pathology_purecn.scarhrd_cnvkit_score.txt 4b722d55d746bd2b1cc8699ebd97f2ce
results/dna/HD832_T/biomarker/HD832_T.TMB.txt 71ff435292edd8cc8613cceef2abab25
results/dna/HD832_T/cnv/HD832_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv f63fffa3ffab1b112ac2a4db77a2d969
results/dna/HD832_T/cnv/HD832_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 4ba0962054a276e1cfdb4298ef815240
results/dna/HD832_T/fusion/HD832_T.fuseq_wes.report.csv ada3432e93dd1ff64f9254d8c83c91c5
results/dna/HD832_T/qc/HD832_T.coverage_and_mutations.tsv 6f2c4bb63ae1af1095dfa83ca63c4935
results/dna/HD832_T/qc/HD832_T.coverage_and_mutations.tsv f388030488f2f7de0388a2d077bcbb1e
results/dna/HD832_T/vcf/HD832_T.annotated.exon_only.filter.hard_filter.codon_snv.qci.vcf 57d25b05d0836bdb74081c5ef5288859
results/dna/HD832_T/vcf/HD832_T.annotated.exon_only.filter.hard_filter.codon_snv.vcf e7657d6abeafaa2784e81df47822f93f
results/dna/NA12878_T/additional_files/biomarker/NA12878_T.pathology.scarhrd_cnvkit_score.txt e98b73e2b3f15616a50c4f494f8493b2
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