add module for stecfinder (nf-core#2702)

* add module for stecfinder

* make prettier

* Update modules/nf-core/stecfinder/main.nf

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

modules/nf-core/stecfinder/main.nf

@@ -0,0 +1,34 @@
+process STECFINDER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::stecfinder=1.1.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/stecfinder:1.1.0--pyhdfd78af_0':
+        'biocontainers/stecfinder:1.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(seqs)
+
+    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}"
+    """
+    stecfinder \\
+        -i $seqs \\
+        $args \\
+        -t $task.cpus > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stecfinder: \$(echo \$(stecfinder --version 2>&1) | sed 's/^.*STECFinder version: //;' )
+    END_VERSIONS
+    """
+}

modules/nf-core/stecfinder/meta.yml

@@ -0,0 +1,44 @@
+name: "stecfinder"
+description: Serotype STEC samples from paired-end reads or assemblies
+keywords:
+  - serotype
+  - Escherichia coli
+  - fastq
+  - fasta
+tools:
+  - "stecfinder":
+      description: "Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies"
+      homepage: "https://github.com/LanLab/STECFinder"
+      documentation: "https://github.com/LanLab/STECFinder"
+      tool_dev_url: "https://github.com/LanLab/STECFinder"
+      doi: "10.3389/fcimb.2021.772574"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - seqs:
+      type: file
+      description: Illumina paired-end reads or an assembly
+      pattern: "*.{fastq.gz,fasta.gz,fna.gz}"
+
+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 report of results
+      pattern: "*.tsv"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -3732,6 +3732,10 @@ star/starsolo:
   - modules/nf-core/star/starsolo/**
   - tests/modules/nf-core/star/starsolo/**
 
+stecfinder:
+  - modules/nf-core/stecfinder/**
+  - tests/modules/nf-core/stecfinder/**
+
 stitch:
   - modules/nf-core/stitch/**
   - tests/modules/nf-core/stitch/**

tests/modules/nf-core/stecfinder/main.nf

@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STECFINDER } from '../../../../modules/nf-core/stecfinder/main.nf'
+include { STECFINDER as STECFINDER_READS } from '../../../../modules/nf-core/stecfinder/main.nf'
+
+workflow test_stecfinder_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    STECFINDER ( input )
+}
+
+workflow test_stecfinder_reads {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+    ]
+
+    STECFINDER_READS ( input )
+}

tests/modules/nf-core/stecfinder/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: STECFINDER_READS {
+        ext.args = '-r'
+    }
+
+}

tests/modules/nf-core/stecfinder/test.yml

@@ -0,0 +1,17 @@
+- name: stecfinder test_stecfinder_fasta
+  command: nextflow run ./tests/modules/nf-core/stecfinder -entry test_stecfinder_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stecfinder/nextflow.config
+  tags:
+    - stecfinder
+  files:
+    - path: output/stecfinder/test.tsv
+      md5sum: c17e1e69728b48c06c47a7d10086f1da
+    - path: output/stecfinder/versions.yml
+
+- name: stecfinder test_stecfinder_reads
+  command: nextflow run ./tests/modules/nf-core/stecfinder -entry test_stecfinder_reads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stecfinder/nextflow.config
+  tags:
+    - stecfinder
+  files:
+    - path: output/stecfinder/test.tsv
+      md5sum: f0a5c4e3509bc8bd03f09aa21c31c526
+    - path: output/stecfinder/versions.yml