Merge remote-tracking branch 'nfcore/master' into main

modules/blast/tblastn/main.nf

@@ -12,8 +12,8 @@ process BLAST_TBLASTN {
     path  db
 
     output:
-    tuple val(meta), path('*.tblastn.txt'), emit: txt
-    path "versions.yml"                  , emit: versions
+    tuple val(meta), path('*.tblastn.txt') , emit: txt
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/blast/tblastn/meta.yml

@@ -38,3 +38,4 @@ output:
       pattern: "versions.yml"
 authors:
   - "@yumisims"
+  - "@gq2"

modules/dshbio/exportsegments/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_EXPORTSEGMENTS {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gfa)

modules/dshbio/filterbed/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

modules/dshbio/filtergff3/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)

modules/dshbio/splitbed/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

modules/dshbio/splitgff3/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)

modules/genmap/mappability/main.nf

@@ -1,5 +1,5 @@
 process GENMAP_MAPPABILITY {
-    tag '$fasta'
+    tag '$index'
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)

modules/genotyphi/parse/main.nf

@@ -0,0 +1,33 @@
+process GENOTYPHI_PARSE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1':
+        'quay.io/biocontainers/genotyphi:1.9.1--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(json)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    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}"
+    """
+    parse_typhi_mykrobe.py \\
+        --jsons $json \\
+        --prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genotyphi: \$(echo \$(genotyphi --version 2>&1) | sed 's/^.*GenoTyphi v//;' )
+    END_VERSIONS
+    """
+}

modules/genotyphi/parse/meta.yml

@@ -0,0 +1,42 @@
+name: "genotyphi_parse"
+description: Genotype Salmonella Typhi from Mykrobe results
+keywords:
+  - genotype
+  - Salmonella Typhi
+tools:
+  - "genotyphi":
+      description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)"
+      homepage: "https://github.com/katholt/genotyphi"
+      documentation: "https://github.com/katholt/genotyphi"
+      tool_dev_url: "https://github.com/katholt/genotyphi"
+      doi: "https://github.com/katholt/genotyphi"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - json:
+      type: file
+      description: JSON formatted file of Mykrobe results
+      pattern: "*.json"
+
+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 tab-delimited file of predicted genotypes
+      pattern: "*.tsv"
+
+authors:
+  - "@rpetit3"

modules/mlst/main.nf

@@ -22,6 +22,7 @@ process MLST {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mlst \\
+        $args \\
         --threads $task.cpus \\
         $fasta \\
         > ${prefix}.tsv

modules/mykrobe/predict/main.nf

@@ -0,0 +1,41 @@
+process MYKROBE_PREDICT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1':
+        'quay.io/biocontainers/mykrobe:0.11.0--py39h2add14b_1' }"
+
+    input:
+    tuple val(meta), path(seqs)
+    val species
+
+    output:
+    tuple val(meta), path("${prefix}.csv") , emit: csv
+    tuple val(meta), path("${prefix}.json"), emit: json
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mykrobe \\
+        predict \\
+        $args \\
+        --species $species \\
+        --threads $task.cpus \\
+        --sample $prefix \\
+        --format json_and_csv \\
+        --output ${prefix} \\
+        --seq $seqs
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mykrobe: \$(echo \$(mykrobe --version 2>&1) | sed 's/^.*mykrobe v//' )
+    END_VERSIONS
+    """
+}

modules/mykrobe/predict/meta.yml

@@ -0,0 +1,51 @@
+name: "mykrobe_predict"
+description: AMR predictions for supported species
+keywords:
+  - fastq
+  - bam
+  - antimicrobial resistance
+tools:
+  - "mykrobe":
+      description: "Antibiotic resistance prediction in minutes"
+      homepage: "http://www.mykrobe.com/"
+      documentation: "https://github.com/Mykrobe-tools/mykrobe/wiki"
+      tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe"
+      doi: "10.1038/ncomms10063"
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - seqs:
+      type: file
+      description: BAM or FASTQ file
+      pattern: "*.{bam,fastq.gz,fq.gz}"
+  - species:
+      type: string
+      description: Species to make AMR prediction against
+      pattern: "*"
+
+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"
+  - csv:
+      type: file
+      description: AMR predictions in CSV format
+      pattern: "*.csv"
+  - json:
+      type: file
+      description: AMR predictions in JSON format
+      pattern: "*.json"
+
+authors:
+  - "@rpetit3"

modules/samtools/ampliconclip/main.nf

@@ -31,6 +31,7 @@ process SAMTOOLS_AMPLICONCLIP {
     """
     samtools \\
         ampliconclip \\
+        --threads ${task.cpus-1} \\
         $args \\
         $rejects \\
         $stats \\

modules/samtools/depth/main.nf

@@ -23,6 +23,7 @@ process SAMTOOLS_DEPTH {
     """
     samtools \\
         depth \\
+        --threads ${task.cpus-1} \\
         $args \\
         -o ${prefix}.tsv \\
         $bam

modules/samtools/idxstats/main.nf

@@ -24,6 +24,7 @@ process SAMTOOLS_IDXSTATS {
     """
     samtools \\
         idxstats \\
+        --threads ${task.cpus-1} \\
         $bam \\
         > ${prefix}.idxstats
 

modules/seqwish/induce/main.nf

@@ -2,11 +2,11 @@ process SEQWISH_INDUCE {
     tag "$meta.id"
     label 'process_medium'
 
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? 'bioconda::seqwish=0.7.2' : null)
+    conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null)
+
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqwish:0.7.2--h2e03b76_0' :
-        'quay.io/biocontainers/seqwish:0.7.2--h2e03b76_0' }"
+        'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' :
+        'quay.io/biocontainers/seqwish:0.7.6--h5b5514e_1' }"
 
     input:
     tuple val(meta), path(paf), path(fasta)
@@ -21,18 +21,23 @@ process SEQWISH_INDUCE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '0.7.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def input = paf.join(',') // this ensures that we can actually input a
+        // comma-separated list of PAF files as required by
+        // https://github.com/nf-core/pangenome. If one wants to use this,
+        // ensure that you put a ".collect()" behind your channel.
+        // See https://github.com/nf-core/pangenome/blob/34149c6cdc19bce3a7b99f97c769d8986a8d429b/main.nf#L543
+        // for an example.
     """
     seqwish \\
         --threads $task.cpus \\
-        --paf-alns=$paf \\
+        --paf-alns=$input \\
         --seqs=$fasta \\
         --gfa=${prefix}.gfa \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        seqwish: $VERSION
+        seqwish: \$(echo \$(seqwish --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v')
     END_VERSIONS
     """
 }

modules/seqwish/induce/meta.yml

@@ -21,9 +21,9 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - paf:
-      type: file
-      description: PAF file of alignments
-      pattern: "*.{paf,paf.gz}"
+      type: list
+      description: comma-separated PAF file(s) of alignments, single entry allowed
+      pattern: "[*.{paf,paf.gz},*.{paf,paf.gz},...]"
   - fasta:
       type: file
       description: FASTA file used to generate alignments

modules/seroba/run/main.nf

@@ -0,0 +1,39 @@
+process SEROBA_RUN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1':
+        'quay.io/biocontainers/seroba:1.0.2--pyhdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}.tsv")                              , emit: tsv
+    tuple val(meta), path("${prefix}/detailed_serogroup_info.txt"), optional: true, emit: txt
+    path "versions.yml"                                                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seroba \\
+        runSerotyping \\
+        $reads \\
+        $prefix \\
+        $args
+
+    # Avoid name collisions
+    mv ${prefix}/pred.tsv ${prefix}/${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seroba: \$(seroba version)
+    END_VERSIONS
+    """
+}