allow fastq.gz and fq.gz as file input, add meta.yml and test

modules/sortmerna/main.nf

@@ -33,7 +33,7 @@ process SORTMERNA {
             --other non_rRNA_reads \\
             $args
 
-        mv non_rRNA_reads.fq.gz ${prefix}.fastq.gz
+        mv non_rRNA_reads.f*q.gz ${prefix}.fastq.gz
         mv rRNA_reads.log ${prefix}.sortmerna.log
 
         cat <<-END_VERSIONS > versions.yml
@@ -55,8 +55,8 @@ process SORTMERNA {
             --out2 \\
             $args
 
-        mv non_rRNA_reads_fwd.fq.gz ${prefix}_1.fastq.gz
-        mv non_rRNA_reads_rev.fq.gz ${prefix}_2.fastq.gz
+        mv non_rRNA_reads_fwd.f*q.gz ${prefix}_1.fastq.gz
+        mv non_rRNA_reads_rev.f*q.gz ${prefix}_2.fastq.gz
         mv rRNA_reads.log ${prefix}.sortmerna.log
 
         cat <<-END_VERSIONS > versions.yml

modules/sortmerna/meta.yml

@@ -0,0 +1,50 @@
+name: sortmerna
+description: Local sequence alignment tool for filtering, mapping and clustering.
+keywords:
+  - filtering
+  - mapping
+  - clustering
+  - rRNA
+  - ribosomal RNA
+tools:
+  - SortMeRNA:
+      description: The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.
+      homepage: https://hpc.nih.gov/apps/sortmeRNA.html
+      documentation: https://github.com/biocore/sortmerna/wiki/
+      licence: ['GPL-3.0-or-later']
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - fastas:
+      type: file
+      description: |
+        Path to reference file(s)
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: The filtered fastq reads
+      pattern: "*fastq.gz"
+  - log:
+      type: file
+      description: SortMeRNA log file
+      pattern: "*sortmerna.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@mashehu"

tests/config/pytest_modules.yml

@@ -1397,6 +1397,10 @@ snpsites:
   - modules/snpsites/**
   - tests/modules/snpsites/**
 
+sortmerna:
+  - modules/sortmerna/**
+  - tests/modules/sortmerna/**
+
 spades:
   - modules/spades/**
   - tests/modules/spades/**

tests/modules/sortmerna/main.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SORTMERNA } from '../../../modules/sortmerna/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_sortmerna_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    SORTMERNA ( input, fasta )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_sortmerna_paired_end {
+    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) ]
+            ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    SORTMERNA ( input, fasta )
+}
+

tests/modules/sortmerna/nextflow.config

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

tests/modules/sortmerna/test.yml

@@ -0,0 +1,9 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml sortmerna
+- name: sortmerna
+  command: nextflow run ./tests/modules/sortmerna -entry test_sortmerna -c ./tests/config/nextflow.config -c ./tests/modules/sortmerna/nextflow.config
+  tags:
+    - sortmerna
+  files:
+    - path: output/sortmerna/test.bam
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc