Merge branch 'master' of https://github.com/nf-core/modules

WackerO · Oct 2, 2023 · 1e233cf · 1e233cf
2 parents af21f19 + 0aca984
commit 1e233cf
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -16,6 +16,7 @@ concurrency:
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   prettier:
@@ -59,6 +60,7 @@ jobs:
         id: filter
         with:
           filters: "tests/config/pytest_modules.yml"
+          token: "${{ secrets.GITHUB_TOKEN }}"
 
   nf-core-lint:
     runs-on: ubuntu-20.04
@@ -367,6 +369,7 @@ jobs:
         id: filter
         with:
           filters: "tests/config/nftest_modules.yml"
+          token: "${{ secrets.GITHUB_TOKEN }}"
 
   nf-test:
     runs-on: ubuntu-20.04

diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf
@@ -24,7 +24,7 @@ process AMRFINDERPLUS_RUN {
     script:
     def args = task.ext.args ?: ''
     def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false
-    def is_compressed_db = fasta.getName().endsWith(".gz") ? true : false
+    def is_compressed_db = db.getName().endsWith(".gz") ? true : false
     prefix = task.ext.prefix ?: "${meta.id}"
     organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
     fasta_name = fasta.getName().replace(".gz", "")

diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf
@@ -23,14 +23,18 @@ process BAMCMP {
     prefix = task.ext.prefix ?: "${meta.id}_primary"
     prefix2 = task.ext.prefix2 ?: "${meta.id}_contaminant"
 
-    if ("$primary_aligned_bam" == "${prefix}.bam"  | "$contaminant_aligned_bam" == "${prefix}.bam"  )
+    if ("$primary_aligned_bam" == "${prefix}.bam"  | "$contaminant_aligned_bam" == "${prefix}.bam"  ) {
         error "Input and output names for the primary-genome bam file are the same, use \"task.ext.prefix\" to disambiguate!"
-    if ("$primary_aligned_bam" == "${prefix2}.bam" | "$contaminant_aligned_bam" == "${prefix2}.bam" )
+    }
+    if ("$primary_aligned_bam" == "${prefix2}.bam" | "$contaminant_aligned_bam" == "${prefix2}.bam" ) {
         error "Input and output names for the contaminant-genome bam file are the same, use \"task.ext.prefix2\" to disambiguate!"
-    if ("primary_aligned_bam"    == "contaminant_aligned_bam" )
+    }
+    if ("primary_aligned_bam"    == "contaminant_aligned_bam" ) {
         error "Input file names for the two bam files are the same, ensure they are renamed upstream."
-    if ("${prefix}.bam"    == "${prefix2}.bam" )
+    }
+    if ("${prefix}.bam"    == "${prefix2}.bam" ) {
         error "Output names for the two bam files are identical, use \"task.ext.prefix\" and \"task.ext.prefix2\" to disambiguate!"
+    }
 
     def VERSION = '2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """

diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
@@ -34,4 +34,18 @@ process BCFTOOLS_INDEX {
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--tsi") || args.contains("-t") ? "tbi" :
+                    "csi"
+    """
+    touch ${vcf}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
@@ -2,18 +2,18 @@ process BLAST_BLASTN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::blast=2.13.0"
+    conda "bioconda::blast=2.14.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
-        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0':
+        'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
 
     input:
     tuple val(meta), path(fasta)
     path  db
 
     output:
-    tuple val(meta), path('*.blastn.txt'), emit: txt
-    path "versions.yml"                  , emit: versions
+    tuple val(meta), path('*.txt'), emit: txt
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,7 +28,20 @@ process BLAST_BLASTN {
         -db \$DB \\
         -query $fasta \\
         $args \\
-        -out ${prefix}.blastn.txt
+        -out ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')

diff --git a/modules/nf-core/blast/blastn/meta.yml b/modules/nf-core/blast/blastn/meta.yml
@@ -31,11 +31,12 @@ output:
   - txt:
       type: file
       description: File containing blastn hits
-      pattern: "*.{blastn.txt}"
+      pattern: "*.txt"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@vagkaratzas"
diff --git a/modules/nf-core/blast/blastp/main.nf b/modules/nf-core/blast/blastp/main.nf
@@ -0,0 +1,57 @@
+process BLAST_BLASTP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::blast=2.14.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0':
+        'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path(db)
+
+    output:
+    tuple val(meta), path("*.csv"), emit: csv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.name.endsWith(".gz")
+    def fasta_name = fasta.name.replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    DB=`find -L ./ -name "*.phr" | sed 's/\\.phr\$//'`
+    blastp \\
+        -db \$DB \\
+        -query ${fasta_name} \\
+        -out ${prefix}.csv \\
+        -num_threads ${task.cpus} \\
+        -outfmt 10 \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blast: \$(blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blast: \$(blastp -version 2>&1 | sed 's/^.*blastp: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/blast/blastp/meta.yml b/modules/nf-core/blast/blastp/meta.yml
@@ -0,0 +1,52 @@
+---
+name: "blast_blastp"
+description: BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database
+keywords:
+  - fasta
+  - blast
+  - blastp
+  - protein
+tools:
+  - "blast":
+      description: "BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit."
+      homepage: "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
+      documentation: "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs"
+      doi: "10.1016/S0022-2836(05)80360-2"
+      licence: "['US-Government-Work']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - fasta:
+      type: file
+      description: Input fasta file containing queries sequences
+      pattern: "*.{fa,fasta}"
+
+  - db:
+      type: directory
+      description: Directory containing blast database
+      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: File containing blastp hits
+      pattern: "*.csv"
+
+authors:
+  - "@vagkaratzas"
diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf
@@ -2,17 +2,17 @@ process BLAST_MAKEBLASTDB {
     tag "$fasta"
     label 'process_medium'
 
-    conda "bioconda::blast=2.13.0"
+    conda "bioconda::blast=2.14.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
-        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0':
+        'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
 
     input:
     path fasta
 
     output:
-    path 'blast_db'     , emit: db
-    path "versions.yml" , emit: versions
+    path 'blast_db'    , emit: db
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,6 +25,28 @@ process BLAST_MAKEBLASTDB {
         $args
     mkdir blast_db
     mv ${fasta}* blast_db
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    touch ${fasta}.fasta
+    touch ${fasta}.fasta.ndb
+    touch ${fasta}.fasta.nhr
+    touch ${fasta}.fasta.nin
+    touch ${fasta}.fasta.njs
+    touch ${fasta}.fasta.not
+    touch ${fasta}.fasta.nsq
+    touch ${fasta}.fasta.ntf
+    touch ${fasta}.fasta.nto
+    mkdir blast_db
+    mv ${fasta}* blast_db
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')

diff --git a/modules/nf-core/blast/makeblastdb/meta.yml b/modules/nf-core/blast/makeblastdb/meta.yml
@@ -29,3 +29,4 @@ output:
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@vagkaratzas"
diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf
@@ -2,18 +2,18 @@ process BLAST_TBLASTN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::blast=2.13.0"
+    conda "bioconda::blast=2.14.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
-        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0':
+        'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
 
     input:
     tuple val(meta), path(fasta)
     path  db
 
     output:
-    tuple val(meta), path('*.tblastn.txt') , emit: txt
-    path "versions.yml"                    , emit: versions
+    tuple val(meta), path('*.txt'), emit: txt
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,7 +28,20 @@ process BLAST_TBLASTN {
         -db \$DB \\
         -query $fasta \\
         $args \\
-        -out ${prefix}.tblastn.txt
+        -out ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blast: \$(tblastn -version 2>&1 | sed 's/^.*tblastn: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         blast: \$(tblastn -version 2>&1 | sed 's/^.*tblastn: //; s/ .*\$//')

diff --git a/modules/nf-core/blast/tblastn/meta.yml b/modules/nf-core/blast/tblastn/meta.yml
@@ -31,11 +31,12 @@ output:
   - txt:
       type: file
       description: File containing blastn hits
-      pattern: "*.{tblastn.txt}"
+      pattern: "*.txt"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@yumisims"
   - "@gq2"
+  - "@vagkaratzas"