VecScreen (nf-core#4304)

* vecscreen module * VecScreen module edit * VecScreen module edit * VecScreen module edit * VecScreen module update * VecScreen module update * VecScreen module minor edit * VecScreen module edit * VecScreen module edit * VecScreen module edit * VecScreen module update: switched to using new BioContainers image * Changes to the VecScreen module as requested by mahesh-panchal * Removing a line from modules/nf-core/ncbitools/vecscreen/main.nf, suggested by mahesh-panchal Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Added the missing final end-of-line * Added the missing final end-of-line * Edited the VecScreen module and its test workflow to make it compatible with the recent change in the BLAST_MAKEBLASTDB module (which now requires a meta in its input) * The convention is to skip the md5sum of `versions.yml` * Fix for Docker * Making this an array --------- Co-authored-by: Mahesh Binzer-Panchal <[email protected]> Co-authored-by: Matthieu Muffato <[email protected]>
WackerO · Nov 14, 2023 · 1e4ac4a · 1e4ac4a
1 parent bba7e36
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -259,6 +259,8 @@ jobs:
             tags: mitohifi/findmitoreference
           - profile: "conda"
             tags: nanoplot
+          - profile: "conda"
+            tags: ncbitools/vecscreen
           - profile: "conda"
             tags: parabricks/applybqsr
           - profile: "conda"

diff --git a/modules/nf-core/ncbitools/vecscreen/main.nf b/modules/nf-core/ncbitools/vecscreen/main.nf
@@ -0,0 +1,46 @@
+process NCBITOOLS_VECSCREEN {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "docker.io/biocontainers/ncbi-tools-bin:6.1.20170106-6-deb_cv2"
+
+    input:
+    tuple val(meta), path(fasta_file)
+    tuple val(adapters_database_meta), path(adapters_database_directory)
+
+    output:
+    tuple val(meta), path("${meta.id}.vecscreen.out")    , emit: vecscreen_output
+    path "versions.yml"                                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "The VecScreen module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // WARN: VecScreen doesn't output a version number and doesn't appear to have a Github repository. 1.0 is arbitrarily used here as the version number
+    """
+    DB=`find -L ${adapters_database_directory} -maxdepth 1 -name "*.nin" | sed 's/\\.nin\$//'`
+    vecscreen -d \$DB ${args} -i ${fasta_file} -o ${prefix}.vecscreen.out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vecscreen: 1.0
+    END_VERSIONS
+    """
+
+    stub:
+    // WARN: VecScreen doesn't output a version number and doesn't appear to have a Github repository. 1.0 is arbitrarily used here as the version number
+    """
+    touch ${prefix}.vecscreen.out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vecscreen: 1.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/ncbitools/vecscreen/meta.yml b/modules/nf-core/ncbitools/vecscreen/meta.yml
@@ -0,0 +1,50 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "NCBITOOLS_VECSCREEN"
+description: NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose
+keywords:
+  - assembly
+  - genomics
+  - quality control
+  - contamination
+  - vector
+  - NCBI
+tools:
+  - "ncbitools":
+      description: |
+        "NCBI libraries for biology applications (text-based utilities)"
+      homepage: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/"
+      documentation: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/interpretation/"
+      tool_dev_url: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/"
+      licence: ["The Open Database License"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', taxid:'6973' ]
+  - fasta_file:
+      type: file
+      description: FASTA file that will be screened for contaminants
+  - adapters_database_file:
+      type: file
+      description: Path to a nucleotide BLAST database file with vector sequences
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', taxid:'9606' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vecscreen_output:
+      type: file
+      description: VecScreen report file. This can be in different formats depending on the value of the optional -f  parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0
+      pattern: "*.vecscreen.out"
+
+authors:
+  - "@eeaunin"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -2474,6 +2474,10 @@ ncbigenomedownload:
   - modules/nf-core/ncbigenomedownload/**
   - tests/modules/nf-core/ncbigenomedownload/**
 
+ncbitools/vecscreen:
+  - modules/nf-core/ncbitools/vecscreen/**
+  - tests/modules/nf-core/ncbitools/vecscreen/**
+
 nextclade/datasetget:
   - modules/nf-core/nextclade/datasetget/**
   - tests/modules/nf-core/nextclade/datasetget/**

diff --git a/tests/modules/nf-core/ncbitools/vecscreen/main.nf b/tests/modules/nf-core/ncbitools/vecscreen/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BLAST_MAKEBLASTDB   } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf'
+include { NCBITOOLS_VECSCREEN } from '../../../../../modules/nf-core/ncbitools/vecscreen/main.nf'
+
+workflow test_ncbitools_vecscreen {
+    input = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+    BLAST_MAKEBLASTDB   (  [[id:'test'], input] )
+    NCBITOOLS_VECSCREEN (  [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db)
+}
diff --git a/tests/modules/nf-core/ncbitools/vecscreen/nextflow.config b/tests/modules/nf-core/ncbitools/vecscreen/nextflow.config
@@ -0,0 +1,17 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: BLAST_MAKEBLASTDB {
+        ext.args = '-dbtype nucl -blastdb_version 4'
+    }
+    withName: NCBITOOLS_VECSCREEN {
+        ext.args = '-f3'
+    }
+}
+
+// The BioContainer runs things as the user `biodocker`, which has no write
+// access to the directory and can't even touch `.command.trace`.
+// Setting `userEmulation` to true fixes things, but only if actually loaded !
+// There has to be an explicit `-c ./tests/modules/nf-core/ncbitools/vecscreen/nextflow.config`
+// in the test.yml
+docker.userEmulation = true
+
diff --git a/tests/modules/nf-core/ncbitools/vecscreen/test.yml b/tests/modules/nf-core/ncbitools/vecscreen/test.yml
@@ -0,0 +1,9 @@
+- name: "ncbitools vecscreen"
+  command: nextflow run ./tests/modules/nf-core/ncbitools/vecscreen -entry test_ncbitools_vecscreen -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ncbitools/vecscreen/nextflow.config
+  tags:
+    - "ncbitools"
+    - "ncbitools/vecscreen"
+  files:
+    - path: "output/ncbitools/test.vecscreen.out"
+      md5sum: b1e5bff88cbc6195bf730e13dc7f5873
+    - path: "output/ncbitools/versions.yml"