From e1637d05d39e5a07e5c49c0afda8ed527ed1ab31 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 23 Jan 2025 17:15:43 +0100 Subject: [PATCH] fix linting --- modules.json | 170 +++++------------- .../vcf_dbsnp_vcfanno/tests/nextflow.config | 2 +- 2 files changed, 44 insertions(+), 128 deletions(-) diff --git a/modules.json b/modules.json index b1756329..ef62d8c3 100644 --- a/modules.json +++ b/modules.json @@ -8,288 +8,210 @@ "bcftools/annotate": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "f85dbddd7a335fc0f5ac331e8d22ca94123b654b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/query": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "elprep/fastatoelfasta": { "branch": "master", "git_sha": "74ac5351a11a184171489dee73652e8b69ba9d22", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "elprep/filter": { "branch": "master", "git_sha": "909c4dcdbb1e751214e2bb155e8c0a59633ed12a", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/elprep/filter/elprep-filter.diff" }, "ensemblvep/download": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff" }, "ensemblvep/vep": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "gatk4/calibratedragstrmodel": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff" }, "gatk4/genomicsdbimport": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff" }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff" }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff" }, "gawk": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mosdepth/mosdepth.diff" }, "multiqc": { "branch": "master", "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/format": { "branch": "master", "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/pedfilter": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "somalier/extract": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/tabix": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/tabix/tabix/tabix-tabix.diff" }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vardictjava": { "branch": "master", "git_sha": "f85452fcbebab5dfd77c0752236f6f86e9a03b32", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2db": { "branch": "master", "git_sha": "439f05652b54826ff23f5baa505082d5d8587dd7", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/vcf2db/vcf2db.diff" }, "vcfanno": { "branch": "master", "git_sha": "b1137e22798227331c9a9a12bd92bd6e865865c5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -298,26 +220,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/subworkflows/local/vcf_dbsnp_vcfanno/tests/nextflow.config b/subworkflows/local/vcf_dbsnp_vcfanno/tests/nextflow.config index 532b6775..f2ce3221 100644 --- a/subworkflows/local/vcf_dbsnp_vcfanno/tests/nextflow.config +++ b/subworkflows/local/vcf_dbsnp_vcfanno/tests/nextflow.config @@ -2,4 +2,4 @@ process { withName: VCFANNO { ext.prefix = { "${meta.id}.annotated" } } -} \ No newline at end of file +}