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* master: (97 commits) Use long form docker.io address for Ubuntu (nf-core#3358) Default registry to quay.io (nf-core#3344) Sbwf impute glimpse2 (nf-core#3349) added cellranger vdj/mkvdjref modules, with module test for vdj (nf-core#3033) Add space to fix singularity download error on shinyngs modules (nf-core#3351) Output channel modification star (nf-core#3350) fix corrected typo in output (nf-core#3337) give execution permissions to dumpsoftwareversions.py (nf-core#3347) fix meta.ymls for dumpsoftware and multiqc (nf-core#3345) Fixing failing subworkflow tests (nf-core#3343) remove imputeme module since it is evidently no longer supported (nf-core#3223) Update path for yaml-schema json (nf-core#3340) New module MetaPhlAn4 (nf-core#3298) Update ALL bcftools modules (nf-core#3339) update docker and singularity version of p7zip (nf-core#3338) update sratools/fasterqdump to handle 10X data (nf-core#3336) Make MAD plots optional in shinyngs (nf-core#3334) reset tools in CI to released version (nf-core#3335) new module wisecondorx/gender (nf-core#3333) Bump shinyngs modules (nf-core#3323) ...
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| process ANNOTSV_ANNOTSV { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
|
|
||
| conda "bioconda::annotsv=3.3.4" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/annotsv:3.3.4--py311hdfd78af_1' : | ||
| 'quay.io/biocontainers/annotsv:3.3.4--py311hdfd78af_1' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants) | ||
| tuple val(meta2), path(annotations) | ||
| tuple val(meta3), path(candidate_genes) | ||
| tuple val(meta4), path(false_positive_snv) | ||
| 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 | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
|
|
||
| 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}" : "" | ||
|
|
||
| """ | ||
| AnnotSV \\ | ||
| -annotationsDir ${annotations} \\ | ||
| ${cand_genes} \\ | ||
| ${small_variants} \\ | ||
| ${fp_snv} \\ | ||
| ${transcripts} \\ | ||
| -outputFile ${prefix}.tsv \\ | ||
| -SVinputFile ${sv_vcf} \\ | ||
| ${args} | ||
| mv *_AnnotSV/* . | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| annotsv: \$(echo \$(AnnotSV -help 2>&1 | head -n1 | sed 's/^AnnotSV //')) | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| 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 | ||
| ${create_vcf} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| annotsv: \$(echo \$(AnnotSV -help 2>&1 | head -n1 | sed 's/^AnnotSV //')) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| name: "annotsv_annotsv" | ||
| description: Annotation and Ranking of Structural Variation | ||
| keywords: | ||
| - annotation | ||
| - structural variants | ||
| - vcf | ||
| - bed | ||
| - tsv | ||
| tools: | ||
| - "annotsv": | ||
| description: "Annotation and Ranking of Structural Variation" | ||
| homepage: "https://lbgi.fr/AnnotSV/" | ||
| documentation: "https://lbgi.fr/AnnotSV/" | ||
| tool_dev_url: "https://github.com/lgmgeo/AnnotSV" | ||
| licence: "GPL-3.0" | ||
|
|
||
| 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" | ||
|
|
||
| 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" | ||
|
|
||
| authors: | ||
| - "@nvnieuwk" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| process ANNOTSV_INSTALLANNOTATIONS { | ||
| tag 'AnnotSV annotations' | ||
| label 'process_single' | ||
|
|
||
| conda "bioconda::annotsv=3.3.4" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/annotsv:3.3.4--py311hdfd78af_1': | ||
| 'quay.io/biocontainers/annotsv:3.3.4--py311hdfd78af_1' }" | ||
|
|
||
| output: | ||
| path "AnnotSV_annotations", emit: annotations | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| """ | ||
| INSTALL_annotations.sh | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| annotsv: \$(echo \$(AnnotSV --version | sed 's/AnnotSV //')) | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| mkdir AnnotSV_annotations | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| annotsv: \$(echo \$(AnnotSV --version | sed 's/AnnotSV //')) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| name: "annotsv_installannotations" | ||
| description: Install the AnnotSV annotations | ||
| keywords: | ||
| - annotation | ||
| - download | ||
| - installation | ||
| - structural variants | ||
| tools: | ||
| - "annotsv": | ||
| description: "Annotation and Ranking of Structural Variation" | ||
| homepage: "https://lbgi.fr/AnnotSV/" | ||
| documentation: "https://lbgi.fr/AnnotSV/" | ||
| tool_dev_url: "https://github.com/lgmgeo/AnnotSV" | ||
| licence: "['GPL v3']" | ||
|
|
||
| output: | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - annotations: | ||
| type: file | ||
| description: A folder containing the annotations | ||
| pattern: "AnnotSV_annotations" | ||
|
|
||
| authors: | ||
| - "@nvnieuwk" |
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