diff --git a/modules.json b/modules.json index f21c7565..dc5a044e 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "annotsv/annotsv": { "branch": "master", - "git_sha": "a94ad45fa5b350961c374c46f79bc86cd5853353", + "git_sha": "296d216c3f6384936a6526b6fbed7e6412259fb4", "installed_by": ["modules"] }, "annotsv/installannotations": { "branch": "master", - "git_sha": "a94ad45fa5b350961c374c46f79bc86cd5853353", + "git_sha": "296d216c3f6384936a6526b6fbed7e6412259fb4", "installed_by": ["modules"] }, "bcftools/annotate": { diff --git a/modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff b/modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff deleted file mode 100644 index a9c3fe23..00000000 --- a/modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff +++ /dev/null @@ -1,45 +0,0 @@ -Changes in module 'nf-core/annotsv/annotsv' ---- modules/nf-core/annotsv/annotsv/main.nf -+++ modules/nf-core/annotsv/annotsv/main.nf -@@ -17,7 +17,7 @@ - output: - tuple val(meta), path("*.tsv") , emit: tsv - tuple val(meta), path("*.unannotated.tsv") , emit: unannotated_tsv, optional: true -- tuple val(meta), path("*.vcf") , emit: vcf, optional: true -+ tuple val(meta), path("*.vcf") , emit: vcf - path "versions.yml" , emit: versions - - when: -@@ -39,11 +39,15 @@ - ${small_variants} \\ - ${fp_snv} \\ - ${transcripts} \\ -- -outputFile ${prefix}.tsv \\ -+ -outputFile ${prefix}.raw.tsv \\ - -SVinputFile ${sv_vcf} \\ - ${args} - - mv *_AnnotSV/* . -+ awk 'BEGIN { FS=OFS="\t" } { if (NR > 1 && NF >= 8) \$1 = \$1 "_" NR; print }' ${prefix}.raw.tsv > ${prefix}.tsv -+ -+ variantconvert convert -i ${prefix}.tsv -o ${prefix}.vcf -fi annotsv -fo vcf -c /usr/local/share/python3/variantconvert/configs/GRCh38/annotsv3_from_vcf.json -+ sed -i 's/contig= versions.yml - "${task.process}": -@@ -55,12 +59,10 @@ - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - -- def create_vcf = args.contains("-vcf 1") ? "touch ${prefix}.vcf" : "" -- - """ - touch ${prefix}.tsv - touch ${prefix}.unannotated.tsv -- ${create_vcf} -+ touch ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - -************************************************************ diff --git a/modules/nf-core/annotsv/annotsv/environment.yml b/modules/nf-core/annotsv/annotsv/environment.yml index e5f4a3e4..d8f5ae51 100644 --- a/modules/nf-core/annotsv/annotsv/environment.yml +++ b/modules/nf-core/annotsv/annotsv/environment.yml @@ -1,7 +1,7 @@ -name: annotsv_annotsv +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::annotsv=3.4.2 + - bioconda::annotsv=3.4.6 diff --git a/modules/nf-core/annotsv/annotsv/main.nf b/modules/nf-core/annotsv/annotsv/main.nf index e9d47db7..63eeab67 100644 --- a/modules/nf-core/annotsv/annotsv/main.nf +++ b/modules/nf-core/annotsv/annotsv/main.nf @@ -4,8 +4,11 @@ process ANNOTSV_ANNOTSV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' : - 'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/df/df5e87ce610d595afe5f1e4017c255e53590cfa9b156c43310d637b36bfd12b3/data' : + 'community.wave.seqera.io/library/annotsv:3.4.6--c5a6da1bf4c2c8e5' }" + + // Container options are needed to allow AnnotSV to overwrite a file in a dependency directory in Singularity + containerOptions "${ workflow.containerEngine == 'singularity' ? '--writable-tmpfs' : ''}" input: tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants) @@ -15,10 +18,10 @@ process ANNOTSV_ANNOTSV { tuple val(meta5), path(gene_transcripts) output: - tuple val(meta), path("*.tsv") , emit: tsv - tuple val(meta), path("*.unannotated.tsv") , emit: unannotated_tsv, optional: true - tuple val(meta), path("*.vcf") , emit: vcf, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.tsv") , emit: tsv + tuple val(meta), path("*.unannotated.tsv"), emit: unannotated_tsv, optional: true + tuple val(meta), path("*.vcf") , emit: vcf , optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -27,10 +30,10 @@ process ANNOTSV_ANNOTSV { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def cand_genes = candidate_genes ? "-candidateGenesFile ${candidate_genes}" : "" + def cand_genes = candidate_genes ? "-candidateGenesFile ${candidate_genes}" : "" def small_variants = candidate_small_variants ? "-candidateSnvIndelFiles ${candidate_small_variants}" : "" - def fp_snv = false_positive_snv ? "-snvIndelFiles ${false_positive_snv}" : "" - def transcripts = gene_transcripts ? "-txFile ${gene_transcripts}" : "" + def fp_snv = false_positive_snv ? "-snvIndelFiles ${false_positive_snv}" : "" + def transcripts = gene_transcripts ? "-txFile ${gene_transcripts}" : "" """ AnnotSV \\ @@ -52,14 +55,12 @@ process ANNOTSV_ANNOTSV { """ stub: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def create_vcf = args.contains("-vcf 1") ? "touch ${prefix}.vcf" : "" """ - echo "$args" - touch ${prefix}.tsv touch ${prefix}.unannotated.tsv ${create_vcf} diff --git a/modules/nf-core/annotsv/annotsv/meta.yml b/modules/nf-core/annotsv/annotsv/meta.yml index f690f0aa..1ba4feaf 100644 --- a/modules/nf-core/annotsv/annotsv/meta.yml +++ b/modules/nf-core/annotsv/annotsv/meta.yml @@ -14,80 +14,118 @@ tools: tool_dev_url: "https://github.com/lgmgeo/AnnotSV" doi: 10.1093/bioinformatics/bty304 licence: ["GPL-3.0"] + identifier: biotools:AnnotSV input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sv_vcf: - type: file - description: A VCF or BED file containing the structural variants to be annotated - pattern: "*.{bed,vcf,vcf.gz}" - - sv_vcf_index: - type: file - description: OPTIONAL - The index for gzipped VCF files - pattern: "*.tbi" - - candidate_small_variants: - type: file - description: OPTIONAL - A file containing candidate small variants - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing annotations information - - annotations: - type: directory - description: | - The directory containing the annotations (URL to download this will be made available soon) - For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation) - - meta3: - type: map - description: | - Groovy Map containing candidate genes information - - candidate_genes: - type: file - description: OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated) - pattern: "*.txt" - - meta4: - type: map - description: | - Groovy Map containing candidate false positive SNV information - - false_positive_snv: - type: file - description: OPTIONAL - A VCF file containing small variant candidates - pattern: "*.{vcf,vcf.gz}" - - meta5: - type: map - description: | - Groovy Map containing candidate gene transcripts information - - gene_transcripts: - type: file - description: OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated) - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sv_vcf: + type: file + description: A VCF or BED file containing the structural variants to be annotated + pattern: "*.{bed,vcf,vcf.gz}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - edam: "http://edamontology.org/format_3016" # VCF + - sv_vcf_index: + type: file + description: OPTIONAL - The index for gzipped VCF files + pattern: "*.tbi" + ontologies: + - edam: "http://edamontology.org/format_3475" # Tabix index + - candidate_small_variants: + type: file + description: OPTIONAL - A file containing candidate small variants + pattern: "*.{vcf,vcf.gz}" + ontologies: + - edam: "http://edamontology.org/format_3016" # VCF + - - meta2: + type: map + description: | + Groovy Map containing annotations information + - annotations: + type: directory + description: | + The directory containing the annotations (URL to download this will be made available soon) + For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation) + - - meta3: + type: map + description: | + Groovy Map containing candidate genes information + - candidate_genes: + type: file + description: OPTIONAL - A file containing genes (either space-separated, tab-separated + or line-break-separated) + pattern: "*.txt" + ontologies: + - edam: "http://edamontology.org/format_2330" # Text file + - - meta4: + type: map + description: | + Groovy Map containing candidate false positive SNV information + - false_positive_snv: + type: file + description: OPTIONAL - A VCF file containing small variant candidates + pattern: "*.{vcf,vcf.gz}" + ontologies: + - edam: "http://edamontology.org/format_3016" # VCF + - - meta5: + type: map + description: | + Groovy Map containing candidate gene transcripts information + - gene_transcripts: + type: file + description: OPTIONAL - A file containing the preferred gene transcripts to + be used in priority during annotation (either space-separated or tab-separated) + pattern: "*.txt" + ontologies: + - edam: "http://edamontology.org/format_2330" # Text file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tsv: - type: file - description: A TSV file containing the annotated variants - pattern: "*.tsv" - - unannotated_tsv: - type: file - description: OPTIONAL - TSV file containing the unannotated variants - pattern: "*.unannotated.tsv" - - vcf: - type: file - description: | - OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args) - pattern: "*.vcf" + tsv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV file containing the annotated variants + pattern: "*.tsv" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + unannotated_tsv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unannotated.tsv": + type: file + description: OPTIONAL - TSV file containing the unannotated variants + pattern: "*.unannotated.tsv" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: | + OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args) + pattern: "*.vcf" + ontologies: + - edam: "http://edamontology.org/format_3016" # VCF + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/format_3750" # YAML authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap b/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap index fd46d7e7..53516807 100644 --- a/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap +++ b/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap @@ -25,7 +25,7 @@ ], "3": [ - "versions.yml:md5,a5c7d9d19db00a62006faa1bafa917ec" + "versions.yml:md5,8538f3187cc91433cef9d3db1850fbb1" ], "tsv": [ [ @@ -50,14 +50,14 @@ ], "versions": [ - "versions.yml:md5,a5c7d9d19db00a62006faa1bafa917ec" + "versions.yml:md5,8538f3187cc91433cef9d3db1850fbb1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-05-29T15:10:39.33144868" + "timestamp": "2025-07-10T16:46:10.783184639" } } \ No newline at end of file diff --git a/modules/nf-core/annotsv/annotsv/tests/tags.yml b/modules/nf-core/annotsv/annotsv/tests/tags.yml deleted file mode 100644 index 54453426..00000000 --- a/modules/nf-core/annotsv/annotsv/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -annotsv/annotsv: - - "modules/nf-core/annotsv/annotsv/**" diff --git a/modules/nf-core/annotsv/installannotations/environment.yml b/modules/nf-core/annotsv/installannotations/environment.yml index b759f91d..d8f5ae51 100644 --- a/modules/nf-core/annotsv/installannotations/environment.yml +++ b/modules/nf-core/annotsv/installannotations/environment.yml @@ -1,7 +1,7 @@ -name: annotsv_installannotations +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::annotsv=3.4.2 + - bioconda::annotsv=3.4.6 diff --git a/modules/nf-core/annotsv/installannotations/main.nf b/modules/nf-core/annotsv/installannotations/main.nf index 371e1bbf..147bbc12 100644 --- a/modules/nf-core/annotsv/installannotations/main.nf +++ b/modules/nf-core/annotsv/installannotations/main.nf @@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' : - 'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/df/df5e87ce610d595afe5f1e4017c255e53590cfa9b156c43310d637b36bfd12b3/data' : + 'community.wave.seqera.io/library/annotsv:3.4.6--c5a6da1bf4c2c8e5' }" output: path "AnnotSV_annotations", emit: annotations diff --git a/modules/nf-core/annotsv/installannotations/meta.yml b/modules/nf-core/annotsv/installannotations/meta.yml index a04c4f1d..670c7150 100644 --- a/modules/nf-core/annotsv/installannotations/meta.yml +++ b/modules/nf-core/annotsv/installannotations/meta.yml @@ -12,15 +12,22 @@ tools: documentation: "https://lbgi.fr/AnnotSV/" tool_dev_url: "https://github.com/lgmgeo/AnnotSV" licence: ["GPL v3"] + identifier: biotools:AnnotSV output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - annotations: - type: file - description: A folder containing the annotations - pattern: "AnnotSV_annotations" + annotations: + - AnnotSV_annotations: + type: file + description: A folder containing the annotations + pattern: "AnnotSV_annotations" + ontologies: + - edam: "http://edamontology.org/format_3750" # YAML + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/format_3750" # YAML authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap b/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap index bb45f1bd..bc1a43d7 100644 --- a/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap +++ b/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap @@ -8,7 +8,7 @@ ] ], "1": [ - "versions.yml:md5,d0b3dc5e0199653fd81ffd3754e65f9c" + "versions.yml:md5,a7ab4be6d37013bd8c0ca0e388c0a4ee" ], "annotations": [ [ @@ -16,14 +16,14 @@ ] ], "versions": [ - "versions.yml:md5,d0b3dc5e0199653fd81ffd3754e65f9c" + "versions.yml:md5,a7ab4be6d37013bd8c0ca0e388c0a4ee" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-05-29T15:14:54.723053976" + "timestamp": "2025-07-10T16:55:38.662275457" } } \ No newline at end of file diff --git a/modules/nf-core/annotsv/installannotations/tests/tags.yml b/modules/nf-core/annotsv/installannotations/tests/tags.yml deleted file mode 100644 index 232bec39..00000000 --- a/modules/nf-core/annotsv/installannotations/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -annotsv/installannotations: - - "modules/nf-core/annotsv/installannotations/**"