From 37a2f25538fc4ca79cb2d5e5b5165d59ea30bb79 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Mon, 12 Aug 2024 09:52:25 +0200 Subject: [PATCH 1/2] Update echtvar --- CHANGELOG.md | 2 + modules/local/echtvar/anno/main.nf | 2 +- modules/local/echtvar/encode/main.nf | 2 +- .../local/snv_annotation/tests/main.nf.test | 4 +- .../snv_annotation/tests/main.nf.test.snap | 49 +++---------------- 5 files changed, 13 insertions(+), 46 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b54e6a6d..11a82b44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -52,6 +52,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#277](https://github.com/genomic-medicine-sweden/nallo/pull/277) - Allowed CNV calling as soon as SNV calling for a sample is finished - [#278](https://github.com/genomic-medicine-sweden/nallo/pull/278) - Changed the SNV ranking to run in parallel per region - [#300](https://github.com/genomic-medicine-sweden/nallo/pull/300) - Clarified and formatted nallo.nf +- [#306](https://github.com/genomic-medicine-sweden/nallo/pull/306) - Updated echtvar version ### `Removed` @@ -96,6 +97,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | htslib | 1.19.1 | 1.20 | | cadd | | 1.6.post1 | | gawk | | 5.3.0 | +| echtvar | 0.1.7 | 0.2.0 | ## v0.2.0 - [2024-06-26] diff --git a/modules/local/echtvar/anno/main.nf b/modules/local/echtvar/anno/main.nf index b9522494..c07f27a8 100644 --- a/modules/local/echtvar/anno/main.nf +++ b/modules/local/echtvar/anno/main.nf @@ -2,7 +2,7 @@ process ECHTVAR_ANNO { tag "$meta.id" label 'process_single' - container "docker.io/fellen31/echtvar:latest" + container "docker.io/fellen31/echtvar:0.2.0" input: tuple val(meta), path(vcf) diff --git a/modules/local/echtvar/encode/main.nf b/modules/local/echtvar/encode/main.nf index aedb277d..aa06e394 100644 --- a/modules/local/echtvar/encode/main.nf +++ b/modules/local/echtvar/encode/main.nf @@ -2,7 +2,7 @@ process ECHTVAR_ENCODE { tag "$meta.id" label 'process_single' - container "docker.io/fellen31/echtvar:latest" + container "docker.io/fellen31/echtvar:0.2.0" input: tuple val(meta), path(bcf) diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test b/subworkflows/local/snv_annotation/tests/main.nf.test index 7bb9ff38..0cfde2ab 100644 --- a/subworkflows/local/snv_annotation/tests/main.nf.test +++ b/subworkflows/local/snv_annotation/tests/main.nf.test @@ -102,8 +102,8 @@ nextflow_workflow { { assert snapshot( workflow.out.versions, file(workflow.out.tbi.get(0).get(1)).name, - path(workflow.out.vcf.get(0).get(1)).linesGzip[47..118], // Stable - path(workflow.out.vcf.get(0).get(1)).linesGzip[120..150] // Stable + path(workflow.out.vcf.get(0).get(1)).linesGzip[48..118], // Stable + path(workflow.out.vcf.get(0).get(1)).linesGzip[121..150] // Stable ).match() } ) } diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test.snap b/subworkflows/local/snv_annotation/tests/main.nf.test.snap index c8c3f045..f491df0c 100644 --- a/subworkflows/local/snv_annotation/tests/main.nf.test.snap +++ b/subworkflows/local/snv_annotation/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "bcf, db, vep_cache, '110', -stub": { "content": [ [ - "versions.yml:md5,797275193dd19766e99030e63c23bd5f", + "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", "versions.yml:md5,992301857689684643c42695c032a7f2", "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" @@ -30,12 +30,12 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-08-05T11:10:44.520214699" + "timestamp": "2024-08-12T10:11:15.912554747" }, "bcf, db, vep_cache, '110'": { "content": [ [ - "versions.yml:md5,797275193dd19766e99030e63c23bd5f", + "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", "versions.yml:md5,992301857689684643c42695c032a7f2", "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" @@ -112,8 +112,7 @@ "chr16\t171219\tchr16_171219_T_TTA\tT\tTTA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1656|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4455|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1670|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1885|1||HGNC|HGNC:4825,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1674|1||HGNC|HGNC:4824,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1724|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2282|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,3:4:1,0,20:..", "chr16\t171220\tchr16_171220_T_TATTA\tT\tTATTA\t9\t.\tAF=0.5;AQ=9;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1655|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4456|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1886|1||HGNC|HGNC:4825,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1673|1||HGNC|HGNC:4824,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1723|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2281|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:10:9,0,23:..", "chr16\t171534\tchr16_171534_AT_A\tAT\tA\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1341|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4771|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1355|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2201|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1359|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1409|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1967|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,5:20:20,0,40:..", - "chr16\t171881\tchr16_171881_TC_T\tTC\tT\t21\t.\tAF=0.5;AQ=21;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||994|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4798|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4822|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1008|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2548|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4816|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1012|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1062|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4866|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1620|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:21:21,0,35:..", - "chr16\t172288\tchr16_172288_AG_A\tAG\tA\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||587|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4391|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4415|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||601|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2955|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4409|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||605|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||655|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4459|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1213|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,2:3:0,0,26:.." + "chr16\t171881\tchr16_171881_TC_T\tTC\tT\t21\t.\tAF=0.5;AQ=21;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||994|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4798|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4822|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1008|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2548|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4816|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1012|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1062|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4866|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1620|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:21:21,0,35:.." ], [ "chr16\t172418\tchr16_172418_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||458|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4262|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4286|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||472|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3084|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4280|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||476|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||526|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4330|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4895|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1084|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:16:20,17,0:..", @@ -145,47 +144,13 @@ "chr16\t893361\tchr16_893361_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||4/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||5/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||6/7||||||||||-1||HGNC|HGNC:14154,C|upstream_gene_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000565198|retained_intron|||||||||||109|-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding||3/5||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||3/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||4/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||4/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,45:..", "chr16\t947473\tchr16_947473_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||2/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||2/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||2/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding||2/3||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|5_prime_UTR_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding|1/6||||172|||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||2/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||2/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||2/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||2/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:23:8,15:30:29,0,47:..", "chr16\t964119\tchr16_964119_A_G\tA\tG\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||1/10||||||||||-1||HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||1/7||||||||||-1||HGNC|HGNC:14154,G|missense_variant|MODERATE|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding|1/4||||4|4|2|Y/H|Tat/Cat|||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant&non_coding_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566609|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||1/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||1/9||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||1/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,G|downstream_gene_variant|MODIFIER||ENSG00000276931|Transcript|ENST00000620075|lncRNA|||||||||||4256|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:29:0,29:21:24,24,0:..", - "chr16\t977069\tchr16_977069_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|SOX8|ENSG00000005513|Transcript|ENST00000293894|protein_coding|||||||||||4701|1||HGNC|HGNC:11203,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000562570|lncRNA|2/2||||1914|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563837|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563863|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565069|lncRNA|3/3||||265|||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565139|lncRNA|||||||||||143|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565467|lncRNA||1/1||||||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000567961|lncRNA|||||||||||157|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000568394|lncRNA||1/2||||||||||-1||HGNC|HGNC:53928,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000655952|lncRNA|3/3||||743|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000662104|lncRNA|3/3||||322|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000669274|lncRNA|3/3||||225|||||||-1||HGNC|HGNC:53928\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,44:..", - "chr16\t1065904\tchr16_1065904_G_A\tG\tA\t36\t.\tAF=0.5;AQ=36;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t0/1:15:9,6:36:36,0,45:.." + "chr16\t977069\tchr16_977069_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|SOX8|ENSG00000005513|Transcript|ENST00000293894|protein_coding|||||||||||4701|1||HGNC|HGNC:11203,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000562570|lncRNA|2/2||||1914|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563837|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563863|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565069|lncRNA|3/3||||265|||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565139|lncRNA|||||||||||143|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565467|lncRNA||1/1||||||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000567961|lncRNA|||||||||||157|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000568394|lncRNA||1/2||||||||||-1||HGNC|HGNC:53928,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000655952|lncRNA|3/3||||743|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000662104|lncRNA|3/3||||322|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000669274|lncRNA|3/3||||225|||||||-1||HGNC|HGNC:53928\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,44:.." ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-08-09T12:31:54.375357945" - }, - "bcf, db, vep_cache, '110', -stub": { - "content": [ - [ - "versions.yml:md5,797275193dd19766e99030e63c23bd5f", - "versions.yml:md5,992301857689684643c42695c032a7f2", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" - ], - [ - [ - { - "id": "test_data.bed", - "contains_affected": false - }, - "test_data.bed.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - { - "id": "test_data.bed", - "contains_affected": false - }, - "test_data.bed.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-08-09T12:32:10.118218292" + "timestamp": "2024-08-12T10:10:59.241809478" } -} +} \ No newline at end of file From ef3c754eb4106b55466be49b16cc2e5147326f4d Mon Sep 17 00:00:00 2001 From: fellen31 Date: Mon, 12 Aug 2024 10:49:51 +0200 Subject: [PATCH 2/2] Add README and Dockerfile --- modules/local/echtvar/anno/Dockerfile | 11 +++++++++++ modules/local/echtvar/anno/README.md | 8 ++++++++ modules/local/echtvar/encode/Dockerfile | 11 +++++++++++ modules/local/echtvar/encode/README.md | 8 ++++++++ 4 files changed, 38 insertions(+) create mode 100644 modules/local/echtvar/anno/Dockerfile create mode 100644 modules/local/echtvar/anno/README.md create mode 100644 modules/local/echtvar/encode/Dockerfile create mode 100644 modules/local/echtvar/encode/README.md diff --git a/modules/local/echtvar/anno/Dockerfile b/modules/local/echtvar/anno/Dockerfile new file mode 100644 index 00000000..a0cdb370 --- /dev/null +++ b/modules/local/echtvar/anno/Dockerfile @@ -0,0 +1,11 @@ +# syntax=docker/dockerfile:1 +FROM ubuntu:22.04 + +USER root + +RUN apt-get update && apt-get install -y procps sed && rm -rf /var/lib/apt/lists/* +# install app +COPY echtvar /usr/bin/echtvar + +# final configuration +ENV FLASK_APP=echtvar diff --git a/modules/local/echtvar/anno/README.md b/modules/local/echtvar/anno/README.md new file mode 100644 index 00000000..b4b06510 --- /dev/null +++ b/modules/local/echtvar/anno/README.md @@ -0,0 +1,8 @@ +This docker was created with the following commands: + +```bash +wget https://github.com/brentp/echtvar/releases/download/v0.2.0/echtvar +chmod +x echtvar +docker build . -t fellen31/echtvar:0.2.0 +docker push fellen31/echtvar:0.2.0 +``` diff --git a/modules/local/echtvar/encode/Dockerfile b/modules/local/echtvar/encode/Dockerfile new file mode 100644 index 00000000..a0cdb370 --- /dev/null +++ b/modules/local/echtvar/encode/Dockerfile @@ -0,0 +1,11 @@ +# syntax=docker/dockerfile:1 +FROM ubuntu:22.04 + +USER root + +RUN apt-get update && apt-get install -y procps sed && rm -rf /var/lib/apt/lists/* +# install app +COPY echtvar /usr/bin/echtvar + +# final configuration +ENV FLASK_APP=echtvar diff --git a/modules/local/echtvar/encode/README.md b/modules/local/echtvar/encode/README.md new file mode 100644 index 00000000..b4b06510 --- /dev/null +++ b/modules/local/echtvar/encode/README.md @@ -0,0 +1,8 @@ +This docker was created with the following commands: + +```bash +wget https://github.com/brentp/echtvar/releases/download/v0.2.0/echtvar +chmod +x echtvar +docker build . -t fellen31/echtvar:0.2.0 +docker push fellen31/echtvar:0.2.0 +```