From 2d43eb18c4ef32f2fe9a5f8bc0d4a1d0bdd4a042 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Mon, 10 Jun 2024 11:06:48 +0200 Subject: [PATCH 1/2] test: develop cnv md5sums --- .tests/jenkins/test_input_develop.tsv | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.tests/jenkins/test_input_develop.tsv b/.tests/jenkins/test_input_develop.tsv index 07757548..2ed2027f 100644 --- a/.tests/jenkins/test_input_develop.tsv +++ b/.tests/jenkins/test_input_develop.tsv @@ -5,15 +5,15 @@ results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.pathology.s results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.purecn.scarhrd_cnvkit_score.txt 55145eab2e60e588c66b233cf1479287 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 e441b862e6d6d573d18fe40f1eaa7103 -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 56d83a956014bee636190f90552a357b -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 3e76608f00bd7f861a29d80e9b0194de -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 74be2ae4ca682618ff57bf099ca89b57 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.svdb_query.vcf 80bee8371b5f86740b20cad6dd46f7c5 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.svdb_query.vcf 0843104254a004715141cb1cce10f1c9 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv 74be2ae4ca682618ff57bf099ca89b57 -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 9e423621153bb987efc66bf0cc25623d -results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.svdb_query.vcf df493dbcc1e174b09c90696ca61d69a5 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.manta_tumorSV.vcf.gz 05c5aead798d0a04dc762657fc377f70 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 29beb70a92981779b52d26f5b3a38434 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 1bb1a34245f59a884358fb21ff2a5f69 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 1115cf9989f5ce9725bf69f2e397fde9 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.svdb_query.vcf 346fa589b5cbddbcbb49f17bad82a2c1 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.svdb_query.vcf a51174678cfd5b11bf91f21a5c475e6f +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv 1115cf9989f5ce9725bf69f2e397fde9 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 227717b4bc1de967c6ebeff9e240a274 +results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.svdb_query.vcf bf08dd41108d0b4fe2277099be90a293 results/dna/VAL2022-2-5M_T/additional_files/fusion/VAL2022-2-5M_T.fuseq_wes.unfiltered.results.csv 8ecac127fc74039d5b9eb36e522ac4a5 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 @@ -29,7 +29,7 @@ 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 9e423621153bb987efc66bf0cc25623d +results/dna/VAL2022-2-5M_T/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 227717b4bc1de967c6ebeff9e240a274 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 From 5a168e843f464370d7508eab09f3e911f82b14e6 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Mon, 10 Jun 2024 11:08:45 +0200 Subject: [PATCH 2/2] test: develop cov_and_mut md5sums --- .tests/jenkins/test_input_develop.tsv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.tests/jenkins/test_input_develop.tsv b/.tests/jenkins/test_input_develop.tsv index 2ed2027f..7c8922dd 100644 --- a/.tests/jenkins/test_input_develop.tsv +++ b/.tests/jenkins/test_input_develop.tsv @@ -31,7 +31,8 @@ results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.pathology_purecn.scarhrd_cnv 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 227717b4bc1de967c6ebeff9e240a274 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/qc/VAL2022-2-5M_T.coverage_and_mutations.tsv 8921f53aa4902a009fb34b6e6db2a8da +results/dna/VAL2022-2-5M_T/qc/VAL2022-2-5M_T.coverage_and_mutations.ENC.tsv 5331bcd5647fac6ee1424b07b3a81651 results/dna/VAL2022-2-5M_T/vcf/VAL2022-2-5M_T.annotated.exon_only.filter.hard_filter.codon_snv.qci.vcf e9dc0afeeb5d2b738183ce465973b292 results/dna/VAL2022-2-5M_T/vcf/VAL2022-2-5M_T.annotated.exon_only.filter.hard_filter.codon_snv.vcf 7c62b3abce55f9eacce567211dbb0a1b results/rna/SeraSeq-NTRK-FFPE-2-5M_R/additional_files/fusion/SeraSeq-NTRK-FFPE-2-5M_R.arriba.fusions.tsv eedffe64014818557f8fd9ea2c21fa7c