Added fq/lint module (#1968)

* Added fq/lint module

Additions:
 - fq/lint module, which checks paired end FASTQ files and confirms they
 are valid.

Relates to #1967

* fq/lint linting

* Correct Singularity image

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

modules/fq/lint/main.nf

@@ -0,0 +1,33 @@
+process FQ_LINT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::fq=0.9.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0':
+        'quay.io/biocontainers/fq:0.9.1--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.fq_lint.txt"), emit: lint
+    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}"
+    """
+    fq lint \\
+        $args \\
+        $fastq > ${prefix}.fq_lint.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fq: \$(echo \$(fq lint --version | sed 's/fq-lint //g'))
+    END_VERSIONS
+    """
+}

modules/fq/lint/meta.yml

@@ -0,0 +1,32 @@
+name: "fq_lint"
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "fq":
+      description: "fq is a library to generate and validate FASTQ file pairs."
+      homepage: "https://github.com/stjude-rust-labs/fq"
+      documentation: "https://github.com/stjude-rust-labs/fq"
+      tool_dev_url: "https://github.com/stjude-rust-labs/fq"
+      doi: ""
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: FASTQ file list
+      pattern: "*.fastq{,.gz}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@adamrtalbot"

tests/config/pytest_modules.yml

@@ -779,6 +779,10 @@ flye:
   - modules/flye/**
   - tests/modules/flye/**
 
+fq/lint:
+  - modules/fq/lint/**
+  - tests/modules/fq/lint/**
+
 freebayes:
   - modules/freebayes/**
   - tests/modules/freebayes/**
@@ -2223,10 +2227,6 @@ trimmomatic:
   - modules/trimmomatic/**
   - tests/modules/trimmomatic/**
 
-ucsc/bedtobigbed:
-  - modules/ucsc/bedtobigbed/**
-  - tests/modules/ucsc/bedtobigbed/**
-
 ucsc/bedclip:
   - modules/ucsc/bedclip/**
   - tests/modules/ucsc/bedclip/**
@@ -2235,6 +2235,10 @@ ucsc/bedgraphtobigwig:
   - modules/ucsc/bedgraphtobigwig/**
   - tests/modules/ucsc/bedgraphtobigwig/**
 
+ucsc/bedtobigbed:
+  - modules/ucsc/bedtobigbed/**
+  - tests/modules/ucsc/bedtobigbed/**
+
 ucsc/bigwigaverageoverbed:
   - modules/ucsc/bigwigaverageoverbed/**
   - tests/modules/ucsc/bigwigaverageoverbed/**

tests/modules/fq/lint/main.nf

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FQ_LINT } from '../../../../modules/fq/lint/main.nf'
+
+workflow test_fq_lint_success {
+
+    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)
+        ]
+    ]
+
+    FQ_LINT ( input )
+}
+
+workflow test_fq_lint_fail {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FQ_LINT ( input )
+}

tests/modules/fq/lint/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/fq/lint/test.yml

@@ -0,0 +1,18 @@
+- name: fq lint test_fq_lint_success
+  command: nextflow run ./tests/modules/fq/lint -entry test_fq_lint_success -c ./tests/config/nextflow.config  -c ./tests/modules/fq/lint/nextflow.config
+  tags:
+    - fq
+    - fq/lint
+  files:
+    - path: output/fq/test.fq_lint.txt
+      contains:
+        - "fq-lint start"
+        - "read 100 records"
+        - "fq-lint end"
+
+- name: fq lint test_fq_lint_fail
+  command: nextflow run ./tests/modules/fq/lint -entry test_fq_lint_fail -c ./tests/config/nextflow.config  -c ./tests/modules/fq/lint/nextflow.config
+  tags:
+    - fq
+    - fq/lint
+  exit_code: 1