From ce8c7d72380d49f951f9ee535d8ee60e1accb336 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= Date: Mon, 13 Jan 2025 14:18:59 +0000 Subject: [PATCH] fix filtering --- conf/test.config | 2 +- conf/tests/germline_small.config | 2 +- conf/tests/somatic_snv.config | 2 +- conf/tests/somatic_sv.config | 2 +- subworkflows/local/vcf_variant_filtering.nf | 17 +++--- tests/germline_small.nf.test.snap | 66 +++++++++++---------- tests/germline_sv.nf.test.snap | 44 +++++++++----- tests/somatic_snv.nf.test.snap | 16 +++-- tests/somatic_sv.nf.test.snap | 35 ++++------- 9 files changed, 98 insertions(+), 88 deletions(-) diff --git a/conf/test.config b/conf/test.config index 5c34a7a..5c09764 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,7 +23,7 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = "assets/samplesheet_small.csv" + input = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/samplesheet_small.csv" outdir = "results" // Genome references diff --git a/conf/tests/germline_small.config b/conf/tests/germline_small.config index 514688c..871751a 100644 --- a/conf/tests/germline_small.config +++ b/conf/tests/germline_small.config @@ -34,7 +34,7 @@ params { variant_type = "small" method = 'happy,rtgtools' preprocess = "normalization,deduplication,prepy" - include_expression = 'FILTER="."' + include_expression = '(ILEN >= -5 && ILEN <= 5)' // truth information truth_id = "HG002" diff --git a/conf/tests/somatic_snv.config b/conf/tests/somatic_snv.config index ec4c8c6..83a92f2 100644 --- a/conf/tests/somatic_snv.config +++ b/conf/tests/somatic_snv.config @@ -33,6 +33,6 @@ params { truth_id = "SEQC2" truth_vcf = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/sSNV_truth_set_v1.0.chr21.vcf.gz" regions_bed = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/high-confidence_sSNV_in_HC_regions_v1.2.chr21.vcf.gz" - rename_chr = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt" + rename_chr = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt" } diff --git a/conf/tests/somatic_sv.config b/conf/tests/somatic_sv.config index 7fdfe7e..00e2151 100644 --- a/conf/tests/somatic_sv.config +++ b/conf/tests/somatic_sv.config @@ -32,6 +32,6 @@ params { truth_id = "SEQC2" truth_vcf = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/13059_2022_2816_MOESM4_ESM.vcf.gz" - rename_chr = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt" + rename_chr = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt" } diff --git a/subworkflows/local/vcf_variant_filtering.nf b/subworkflows/local/vcf_variant_filtering.nf index 7f4271f..6dba51d 100644 --- a/subworkflows/local/vcf_variant_filtering.nf +++ b/subworkflows/local/vcf_variant_filtering.nf @@ -16,14 +16,7 @@ workflow VCF_VARIANT_FILTERING { versions = Channel.empty() - // unzip vcf file, required for survivor filter - TABIX_BGZIP( - vcf_ch.map{ meta, vcf, index -> tuple(meta, vcf)} - ) - versions = versions.mix(TABIX_BGZIP.out.versions.first()) - vcf_ch = TABIX_BGZIP.out.output - - if(params.exclude_expression != null & params.include_expression != null){ + if(params.exclude_expression != null | params.include_expression != null){ // filter vcf files using bcftools expressions BCFTOOLS_FILTER( @@ -32,6 +25,14 @@ workflow VCF_VARIANT_FILTERING { versions = versions.mix(BCFTOOLS_FILTER.out.versions.first()) vcf_ch = BCFTOOLS_FILTER.out.vcf } + else{ + // unzip vcf file, required for survivor filter + TABIX_BGZIP( + vcf_ch.map{ meta, vcf, index -> tuple(meta, vcf)} + ) + versions = versions.mix(TABIX_BGZIP.out.versions.first()) + vcf_ch = TABIX_BGZIP.out.output + } if(params.min_sv_size > 0 | params.max_sv_size != -1 | params.min_allele_freq != -1 | params.min_num_reads != -1){ diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap index 554f702..fabe72f 100644 --- a/tests/germline_small.nf.test.snap +++ b/tests/germline_small.nf.test.snap @@ -6,6 +6,9 @@ "BCFTOOLS_DEDUP": { "bcftools": 1.18 }, + "BCFTOOLS_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_MERGE": { "bcftools": 1.2 }, @@ -45,9 +48,6 @@ "RTGTOOLS_VCFEVAL": { "rtg-tools": "3.12.1" }, - "TABIX_BGZIP": { - "tabix": "1.19.1" - }, "TABIX_TABIX": { "tabix": "1.19.1" }, @@ -162,6 +162,7 @@ "small/test1/benchmarks/rtgtools/test1.HG002.strelka.tp.vcf.gz.tbi", "small/test1/benchmarks/rtgtools/test1.HG002.strelka.weighted_roc.tsv.gz", "small/test1/preprocess", + "small/test1/preprocess/HG002.strelka.variants.chr21.rh.norm.filter.vcf", "small/test1/preprocess/test1.HG002.strelka.prepy.vcf.gz", "small/test1/preprocess/test1.dedup.sort.vcf.gz", "small/test1/stats", @@ -196,6 +197,7 @@ "small/test2/benchmarks/rtgtools/test2.HG002.bcftools.tp.vcf.gz.tbi", "small/test2/benchmarks/rtgtools/test2.HG002.bcftools.weighted_roc.tsv.gz", "small/test2/preprocess", + "small/test2/preprocess/HG002.bcftools.chr21.rh.norm.filter.vcf", "small/test2/preprocess/test2.HG002.bcftools.prepy.vcf.gz", "small/test2/preprocess/test2.dedup.sort.vcf.gz", "small/test2/stats", @@ -228,10 +230,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T10:55:37.880792825" + "timestamp": "2025-01-13T13:40:17.22451061" }, "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": { "content": [ @@ -240,6 +242,9 @@ "BCFTOOLS_DEDUP": { "bcftools": 1.18 }, + "BCFTOOLS_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_MERGE": { "bcftools": 1.2 }, @@ -279,9 +284,6 @@ "RTGTOOLS_VCFEVAL": { "rtg-tools": "3.12.1" }, - "TABIX_BGZIP": { - "tabix": "1.19.1" - }, "TABIX_TABIX": { "tabix": "1.19.1" }, @@ -491,6 +493,7 @@ "small/test1/benchmarks/rtgtools/test1.HG002.strelka.tp.vcf.gz.tbi", "small/test1/benchmarks/rtgtools/test1.HG002.strelka.weighted_roc.tsv.gz", "small/test1/preprocess", + "small/test1/preprocess/HG002.strelka.variants.chr21.rh.norm.filter.vcf", "small/test1/preprocess/test1.HG002.strelka.prepy.vcf.gz", "small/test1/preprocess/test1.dedup.sort.vcf.gz", "small/test1/stats", @@ -525,6 +528,7 @@ "small/test2/benchmarks/rtgtools/test2.HG002.bcftools.tp.vcf.gz.tbi", "small/test2/benchmarks/rtgtools/test2.HG002.bcftools.weighted_roc.tsv.gz", "small/test2/preprocess", + "small/test2/preprocess/HG002.bcftools.chr21.rh.norm.filter.vcf", "small/test2/preprocess/test2.HG002.bcftools.prepy.vcf.gz", "small/test2/preprocess/test2.dedup.sort.vcf.gz", "small/test2/stats", @@ -549,32 +553,32 @@ "suffixdata0:md5,f2876dd730673cd49c4de191001f634e", "suffixpointer0:md5,468281ffb10d7dd934289af762a03781", "HG002.bcftools_stats.txt:md5,b215fc0030c53bc8887e28b23b97efb6", - "test1.HG002.strelka.extended.csv:md5,098dc352d1beeab27e72f97e64fc182e", - "test1.HG002.strelka.roc.Locations.INDEL.PASS.csv.gz:md5,bd1f1a1e138f75511de7aae157fa2fa4", - "test1.HG002.strelka.roc.Locations.INDEL.csv.gz:md5,8912022beb3c5b234d29300b764b56bc", - "test1.HG002.strelka.roc.Locations.SNP.PASS.csv.gz:md5,63279f14076a5a9919a4d30b0fbb7746", - "test1.HG002.strelka.roc.Locations.SNP.csv.gz:md5,77aedefc4516566b136acfba82bed147", - "test1.HG002.strelka.roc.all.csv.gz:md5,ccefcf1ff7ef04c9d97b8afbbcfb3c51", - "test1.HG002.strelka.summary.csv:md5,c14117d825b861657b38c058644896f9", - "test1.HG002.strelka.phasing.txt:md5,5ab9ffbd7c18a5512851086b6e7ecf59", - "test1.HG002.strelka.summary.txt:md5,e045d6a048bdec24cb55f9dd1b55ffe7", - "test1.strelka.bcftools_stats.txt:md5,f9f8cf5c1be9c88754888ef8cbfb06f4", - "test2.HG002.bcftools.extended.csv:md5,14392c3b5a1c060d63414cfc10e670b6", - "test2.HG002.bcftools.roc.Locations.INDEL.PASS.csv.gz:md5,507b54e5b6d1f956f557b39a7dc38ff4", - "test2.HG002.bcftools.roc.Locations.INDEL.csv.gz:md5,4694d6169ce0819d36768045a7ef43d0", - "test2.HG002.bcftools.roc.Locations.SNP.PASS.csv.gz:md5,83d1fa126072c16b0471fb8877c5c818", - "test2.HG002.bcftools.roc.Locations.SNP.csv.gz:md5,10045ce81f85c51e142a7ff30d7579bb", - "test2.HG002.bcftools.roc.all.csv.gz:md5,b176e3c9910ecf3209353682553c1a06", - "test2.HG002.bcftools.summary.csv:md5,3815ea18e8fc11f198a5821dee79a3c7", + "test1.HG002.strelka.extended.csv:md5,4362260b357ac0221414095f4c5a8981", + "test1.HG002.strelka.roc.Locations.INDEL.PASS.csv.gz:md5,a5ba4044a89ae80fb0ddf95147b5ae4c", + "test1.HG002.strelka.roc.Locations.INDEL.csv.gz:md5,52edef7d20ac8a7e03771037f5c93fe4", + "test1.HG002.strelka.roc.Locations.SNP.PASS.csv.gz:md5,f71e697d7ebaf1d670e5dc2c0e0106d3", + "test1.HG002.strelka.roc.Locations.SNP.csv.gz:md5,c388d5a15ba2ae8dff709b030f1b4828", + "test1.HG002.strelka.roc.all.csv.gz:md5,59ebbe78bf428b5c2c78c8ff92f54545", + "test1.HG002.strelka.summary.csv:md5,60af846379cf4fe078fbed6b9d1e8178", + "test1.HG002.strelka.phasing.txt:md5,838e67ae5b9cd9e218095596c03fbee3", + "test1.HG002.strelka.summary.txt:md5,e79779d3faebe02bae943ddc17c4cf91", + "test1.strelka.bcftools_stats.txt:md5,492f42090004470e7e0ea7abc5f89bdf", + "test2.HG002.bcftools.extended.csv:md5,2f8ef20f46c821333ba970e3034a6ccd", + "test2.HG002.bcftools.roc.Locations.INDEL.PASS.csv.gz:md5,cdf3fdb7c5b4c54d9896e37a99dbf4f9", + "test2.HG002.bcftools.roc.Locations.INDEL.csv.gz:md5,9b16abcfe483356020c550e1292554ed", + "test2.HG002.bcftools.roc.Locations.SNP.PASS.csv.gz:md5,f71e697d7ebaf1d670e5dc2c0e0106d3", + "test2.HG002.bcftools.roc.Locations.SNP.csv.gz:md5,c388d5a15ba2ae8dff709b030f1b4828", + "test2.HG002.bcftools.roc.all.csv.gz:md5,e772fefec84f9a6e60c6979bac14cedc", + "test2.HG002.bcftools.summary.csv:md5,05722d23f523141fdce842a18f1d8aa2", "test2.HG002.bcftools.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6", - "test2.HG002.bcftools.summary.txt:md5,b9a0c74a8b5af4f2c1c0623b61d7cbe3", - "test2.bcftools.bcftools_stats.txt:md5,57aff2f0a6f830e920869b987502a343" + "test2.HG002.bcftools.summary.txt:md5,a7bbcdf86cd3f1f7815ea9bc25b57b61", + "test2.bcftools.bcftools_stats.txt:md5,440fd66ee557b215bbacd05953215f7a" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T10:53:32.971378431" + "timestamp": "2025-01-13T14:00:31.553072869" } } \ No newline at end of file diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap index 9af6025..84d6427 100644 --- a/tests/germline_sv.nf.test.snap +++ b/tests/germline_sv.nf.test.snap @@ -6,6 +6,9 @@ "BCFTOOLS_DEDUP": { "bcftools": 1.18 }, + "BCFTOOLS_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_NORM": { "bcftools": 1.18 }, @@ -264,6 +267,7 @@ "structural/test1/preprocess/manta.HG002.chr21.norm.vcf.gz", "structural/test1/preprocess/test1.dedup.sort.vcf.gz", "structural/test1/preprocess/test1.manta.svync.vcf.gz", + "structural/test1/preprocess/test1.norm.filter.filter.vcf", "structural/test1/preprocess/test1.norm.filter.vcf", "structural/test1/stats", "structural/test1/stats/bcftools", @@ -296,6 +300,7 @@ "structural/test2/preprocess/Ashkenazim_HG002.filtered.sv.chr21.norm.sort.vcf.gz", "structural/test2/preprocess/Ashkenazim_HG002.filtered.sv.chr21.norm.vcf.gz", "structural/test2/preprocess/test2.dedup.sort.vcf.gz", + "structural/test2/preprocess/test2.norm.filter.filter.vcf", "structural/test2/preprocess/test2.norm.filter.vcf", "structural/test2/stats", "structural/test2/stats/bcftools", @@ -329,6 +334,7 @@ "structural/test3/preprocess/HG002_DRAGEN_SV_hg19.chr21.norm.vcf.gz", "structural/test3/preprocess/test3.dedup.sort.vcf.gz", "structural/test3/preprocess/test3.dragen.svync.vcf.gz", + "structural/test3/preprocess/test3.norm.filter.filter.vcf", "structural/test3/preprocess/test3.norm.filter.vcf", "structural/test3/stats", "structural/test3/stats/bcftools", @@ -339,25 +345,25 @@ [ "HG002.bcftools_stats.txt:md5,8294f172a72ca7219a32db9c27e2524c", "HG002_mqc.stats:md5,68681df47b35e3193be03610f5c6e3d6", - "test1.HG002.manta.distances:md5,33dcbe29f7129dc30c184b564803ec63", - "test1.HG002.manta.report:md5,91b0fbfd6fcdf45b85290f92c5a470fb", - "test1.manta.bcftools_stats.txt:md5,0e4cf1707b245c026fe6a0af6e8f8c0a", - "test1.manta_mqc.stats:md5,6f25a9372095052218110390e8e75c54", + "test1.HG002.manta.distances:md5,346f18a5cbeece98716951c8fc2aaea4", + "test1.HG002.manta.report:md5,4a53712a9d15fa6dfe6ddd5848ca691c", + "test1.manta.bcftools_stats.txt:md5,7d65792aa3a84de09675facf62135c93", + "test1.manta_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b", "test2.HG002.merged.distances:md5,346f18a5cbeece98716951c8fc2aaea4", - "test2.HG002.merged.report:md5,6466d73155f88084efc69cad3628eb8c", - "test2.merged.bcftools_stats.txt:md5,576f9bc7e06bc2bbfccceb9da161a467", - "test2.merged_mqc.stats:md5,36d80468e13b583d0761b434d095312d", + "test2.HG002.merged.report:md5,4a53712a9d15fa6dfe6ddd5848ca691c", + "test2.merged.bcftools_stats.txt:md5,1445742129b0ee67d8706af3dcf0ab2d", + "test2.merged_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b", "test3.HG002.dragen.distances:md5,346f18a5cbeece98716951c8fc2aaea4", - "test3.HG002.dragen.report:md5,b295d4867b7a96f0ca0bb5e8bb45eb68", - "test3.dragen.bcftools_stats.txt:md5,0683a5d3c47a5a6a43ad2b6a0387672e", - "test3.dragen_mqc.stats:md5,5c59cceb2e7d909d91074bb8e5804abc" + "test3.HG002.dragen.report:md5,4a53712a9d15fa6dfe6ddd5848ca691c", + "test3.dragen.bcftools_stats.txt:md5,5d2b48ac5f194f5a2cf01b9623a28cce", + "test3.dragen_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T10:42:14.227940401" + "timestamp": "2025-01-13T13:53:07.620717905" }, "-stub": { "content": [ @@ -366,6 +372,9 @@ "BCFTOOLS_DEDUP": { "bcftools": 1.18 }, + "BCFTOOLS_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_NORM": { "bcftools": 1.18 }, @@ -563,6 +572,7 @@ "structural/test1/preprocess/manta.HG002.chr21.norm.vcf.gz", "structural/test1/preprocess/test1.dedup.sort.vcf.gz", "structural/test1/preprocess/test1.manta.svync.vcf.gz", + "structural/test1/preprocess/test1.norm.filter.filter.vcf", "structural/test1/preprocess/test1.norm.filter.vcf", "structural/test1/stats", "structural/test1/stats/bcftools", @@ -595,6 +605,7 @@ "structural/test2/preprocess/Ashkenazim_HG002.filtered.sv.chr21.norm.sort.vcf.gz", "structural/test2/preprocess/Ashkenazim_HG002.filtered.sv.chr21.norm.vcf.gz", "structural/test2/preprocess/test2.dedup.sort.vcf.gz", + "structural/test2/preprocess/test2.norm.filter.filter.vcf", "structural/test2/preprocess/test2.norm.filter.vcf", "structural/test2/stats", "structural/test2/stats/bcftools", @@ -628,6 +639,7 @@ "structural/test3/preprocess/HG002_DRAGEN_SV_hg19.chr21.norm.vcf.gz", "structural/test3/preprocess/test3.dedup.sort.vcf.gz", "structural/test3/preprocess/test3.dragen.svync.vcf.gz", + "structural/test3/preprocess/test3.norm.filter.filter.vcf", "structural/test3/preprocess/test3.norm.filter.vcf", "structural/test3/stats", "structural/test3/stats/bcftools", @@ -653,9 +665,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T10:44:36.4725572" + "timestamp": "2025-01-13T13:55:36.985456265" } } \ No newline at end of file diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap index 5f03580..45b7e8c 100644 --- a/tests/somatic_snv.nf.test.snap +++ b/tests/somatic_snv.nf.test.snap @@ -3,6 +3,9 @@ "content": [ 38, { + "BCFTOOLS_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_REHEADER": { "bcftools": 1.18 }, @@ -33,9 +36,6 @@ "PLOTS": { "r-base": "4.3.1" }, - "TABIX_BGZIP": { - "tabix": "1.19.1" - }, "TABIX_BGZIPTABIX": { "tabix": "1.19.1" }, @@ -90,6 +90,8 @@ "snv/test1/benchmarks/sompy/test1.SEQC2.freebayes.features.csv", "snv/test1/benchmarks/sompy/test1.SEQC2.freebayes.metrics.json", "snv/test1/benchmarks/sompy/test1.SEQC2.freebayes.stats.csv", + "snv/test1/preprocess", + "snv/test1/preprocess/test1.filter.vcf", "snv/test1/stats", "snv/test1/stats/bcftools", "snv/test1/stats/bcftools/test1.freebayes.bcftools_stats.txt", @@ -101,6 +103,7 @@ "snv/test2/benchmarks/sompy/test2.SEQC2.manta.stats.csv", "snv/test2/preprocess", "snv/test2/preprocess/HCC1395T_vs_HCC1395N.manta.somatic_sv.sort.vcf.gz", + "snv/test2/preprocess/test2.filter.vcf", "snv/test2/stats", "snv/test2/stats/bcftools", "snv/test2/stats/bcftools/test2.manta.bcftools_stats.txt", @@ -112,6 +115,7 @@ "snv/test3/benchmarks/sompy/test3.SEQC2.strelka.stats.csv", "snv/test3/preprocess", "snv/test3/preprocess/HCC1395T_vs_HCC1395N.strelka.somatic_snvs.sort.vcf.gz", + "snv/test3/preprocess/test3.filter.vcf", "snv/test3/stats", "snv/test3/stats/bcftools", "snv/test3/stats/bcftools/test3.strelka.bcftools_stats.txt" @@ -124,9 +128,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T13:54:36.607079161" + "timestamp": "2025-01-13T14:15:33.922876808" } } \ No newline at end of file diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap index b2ccd3d..f5cf4b6 100644 --- a/tests/somatic_sv.nf.test.snap +++ b/tests/somatic_sv.nf.test.snap @@ -3,6 +3,9 @@ "content": [ 69, { + "BCFTOOLS_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_REHEADER": { "bcftools": 1.18 }, @@ -71,10 +74,6 @@ "structural/multiqc", "structural/multiqc/multiqc_data", "structural/multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", - "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", - "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", - "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", - "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", "structural/multiqc/multiqc_data/multiqc.log", "structural/multiqc/multiqc_data/multiqc_bcftools_stats.txt", "structural/multiqc/multiqc_data/multiqc_citations.txt", @@ -86,28 +85,16 @@ "structural/multiqc/multiqc_plots", "structural/multiqc/multiqc_plots/pdf", "structural/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", - "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", - "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", - "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", - "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", "structural/multiqc/multiqc_plots/pdf/general_stats_table.pdf", "structural/multiqc/multiqc_plots/pdf/survivor-cnt.pdf", "structural/multiqc/multiqc_plots/pdf/survivor-pct.pdf", "structural/multiqc/multiqc_plots/png", "structural/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", - "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", - "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", - "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", - "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", "structural/multiqc/multiqc_plots/png/general_stats_table.png", "structural/multiqc/multiqc_plots/png/survivor-cnt.png", "structural/multiqc/multiqc_plots/png/survivor-pct.png", "structural/multiqc/multiqc_plots/svg", "structural/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", - "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", - "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", - "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", - "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", "structural/multiqc/multiqc_plots/svg/general_stats_table.svg", "structural/multiqc/multiqc_plots/svg/survivor-cnt.svg", "structural/multiqc/multiqc_plots/svg/survivor-pct.svg", @@ -166,6 +153,7 @@ "structural/test1/benchmarks/truvari/test1.SEQC2.tiddit.tp-comp.vcf.gz.tbi", "structural/test1/preprocess", "structural/test1/preprocess/HCC1395T_vs_HCC1395N.tiddit_sv_merge.sort.vcf.gz", + "structural/test1/preprocess/test1.filter.filter.vcf", "structural/test1/preprocess/test1.filter.vcf", "structural/test1/stats", "structural/test1/stats/bcftools", @@ -186,6 +174,7 @@ "structural/test2/benchmarks/truvari/test2.SEQC2.manta.tp-comp.vcf.gz.tbi", "structural/test2/preprocess", "structural/test2/preprocess/HCC1395T_vs_HCC1395N.manta.somatic_sv.sort.vcf.gz", + "structural/test2/preprocess/test2.filter.filter.vcf", "structural/test2/preprocess/test2.filter.vcf", "structural/test2/stats", "structural/test2/stats/bcftools", @@ -196,16 +185,16 @@ [ "SEQC2.bcftools_stats.txt:md5,a60de9c4d2f3db87d8ae404b73859bfa", "SEQC2_mqc.stats:md5,a1327ec0cd3131f9e16cccf0024f61a1", - "test1.tiddit.bcftools_stats.txt:md5,56b036b7bd2d7368620713613dd0cae2", - "test1.tiddit_mqc.stats:md5,0eb749429a6072f6bf63d377e37514d1", - "test2.manta.bcftools_stats.txt:md5,1c4cc5ab438537308e7f08a6c202118c", - "test2.manta_mqc.stats:md5,73bc60cd2754202ddca8be6552e85ffa" + "test1.tiddit.bcftools_stats.txt:md5,aace5a23af8b02f56bcaf03722f9bb50", + "test1.tiddit_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b", + "test2.manta.bcftools_stats.txt:md5,1e700076bd303ee079b23658485eb7d4", + "test2.manta_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T11:06:49.710866299" + "timestamp": "2025-01-13T14:18:00.311055864" } } \ No newline at end of file