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Merge pull request #443 from genomic-medicine-sweden/develop
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chore: dev to master
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@Smeds
Smeds authored Apr 26, 2024
2 parents e4df9bb + a077d64 commit f95bb41
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Showing 21 changed files with 13,682 additions and 114 deletions.
13 changes: 12 additions & 1 deletion .tests/integration/config/config.yaml
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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"
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25 changes: 25 additions & 0 deletions .tests/integration/reference/chromosome_arm_size.tsv
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@@ -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
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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
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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
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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
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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
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results/dna/HD827_T/qc/HD827_T.coverage_and_mutations.tsv 8a0e25a13c1c24b1fcb31c6ed0fa30b2
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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
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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
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results/dna/NA12878_T/additional_files/qc/NA12878_T.contamination.table e2ab7189dcf7c8cfb1f0ac24ac8766dc
Expand All @@ -95,23 +95,23 @@ results/dna/NA12878_T/additional_files/vcf/vardict_NA12878_T.vcf.gz d4b82ab064af
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