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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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process ANNOTSV_ANNOTSV { | ||
tag "$meta.id" | ||
label 'process_low' | ||
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||
conda "bioconda::annotsv=3.3.4" | ||
container "${ 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' }" | ||
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||
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) | ||
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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 | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
def prefix = task.ext.prefix ?: "${meta.id}" | ||
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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}" : "" | ||
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""" | ||
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 | ||
""" | ||
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stub: | ||
def args = task.ext.args ?: '' | ||
def prefix = task.ext.prefix ?: "${meta.id}" | ||
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def create_vcf = args.contains("-vcf 1") ? "touch ${prefix}.vcf" : "" | ||
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""" | ||
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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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" | ||
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||
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" | ||
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||
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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process ANNOTSV_INSTALLANNOTATIONS { | ||
tag 'AnnotSV annotations' | ||
label 'process_single' | ||
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conda "bioconda::annotsv=3.3.4" | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'https://depot.galaxyproject.org/singularity/annotsv:3.3.4--py311hdfd78af_1': | ||
'quay.io/biocontainers/annotsv:3.3.4--py311hdfd78af_1' }" | ||
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output: | ||
path "AnnotSV_annotations", emit: annotations | ||
path "versions.yml" , emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
""" | ||
INSTALL_annotations.sh | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
annotsv: \$(echo \$(AnnotSV --version | sed 's/AnnotSV //')) | ||
END_VERSIONS | ||
""" | ||
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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 |
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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']" | ||
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output: | ||
- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
- annotations: | ||
type: file | ||
description: A folder containing the annotations | ||
pattern: "AnnotSV_annotations" | ||
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authors: | ||
- "@nvnieuwk" |
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