Merge remote-tracking branch 'upstream/master'

software/bismark/report/main.nf

@@ -22,17 +22,13 @@ process BISMARK_REPORT {
     tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
 
     output:
-    tuple val(meta), path("*{html,txt}"), emit: report
+    tuple val(meta), path("*report.{html,txt}"), emit: report
     path  "*.version.txt"                      , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
-    bismark2report \\
+    bismark2report $options.args
-        --alignment_report $align_report \\
-        --dedup_report $dedup_report \\
-        --splitting_report $splitting_report \\
-        --mbias_report $mbias
 
     echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
     """

software/bismark/summary/main.nf

@@ -25,7 +25,7 @@ process BISMARK_SUMMARY {
     path(mbias)
 
     output:
-    path("*{html,txt}")  , emit: summary
+    path  "*report.{html,txt}", emit: summary
     path  "*.version.txt"     , emit: version
 
     script:

software/bwameth/align/main.nf

@@ -13,9 +13,9 @@ process BWAMETH_ALIGN {
 
     conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
+        container "https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1"
     } else {
-        container "quay.io/biocontainers/bwameth:0.20--py35_0"
+        container "quay.io/biocontainers/bwameth:0.2.2--py_1"
     }
 
     input:

software/bwameth/index/main.nf

@@ -13,9 +13,9 @@ process BWAMETH_INDEX {
 
     conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
+        container "https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1"
     } else {
-        container "quay.io/biocontainers/bwameth:0.20--py35_0"
+        container "quay.io/biocontainers/bwameth:0.2.2--py_1"
     }
 
     input:

software/gubbins/functions.nf

@@ -0,0 +1,60 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.args3         = args.args3 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gubbins/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GUBBINS {
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconda::gubbins=2.4.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
+    } else {
+        container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
+    }
+
+    input:
+    path alignment
+
+    output:
+    path "*.fasta"                          , emit: fasta
+    path "*.gff"                            , emit: gff
+    path "*.vcf"                            , emit: vcf
+    path "*.csv"                            , emit: stats
+    path "*.phylip"                         , emit: phylip
+    path "*.recombination_predictions.embl" , emit: embl_predicted
+    path "*.branch_base_reconstruction.embl", emit: embl_branch
+    path "*.final_tree.tre"                 , emit: tree
+    path "*.node_labelled.final_tree.tre"   , emit: tree_labelled
+    path "*.version.txt"                    , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    run_gubbins.py \\
+        --threads $task.cpus \\
+        $options.args \\
+        $alignment
+    echo \$(run_gubbins.py --version 2>&1) > ${software}.version.txt
+    """
+}

software/gubbins/meta.yml

@@ -0,0 +1,61 @@
+name: gubbins
+description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies
+            loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the
+            putative point mutations outside of these regions.
+keywords:
+  - recombination
+  - alignment
+tools:
+  - gubbins:
+      description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
+      homepage: https://sanger-pathogens.github.io/gubbins/
+      documentation: https://sanger-pathogens.github.io/gubbins/
+input:
+  - alignment:
+      type: file
+      description: fasta alignment file
+      pattern: "*.{fasta,fas,fa,aln}"
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - fasta:
+      type: file
+      description: Filtered variant alignment in fasta format
+      pattern: "*.{fasta}"
+  - embl_predicted:
+      type: file
+      description: Recombination predictions in embl format
+      pattern: "*.{recombination_predictions.embl}"
+  - gff:
+      type: file
+      description: Recombination predictions in gff format
+      pattern: "*.{gff}"
+  - embl_branch:
+      type: file
+      description: Branch base reconstruction
+      pattern: "*.{branch_base_reconstruction.embl}"
+  - vcf:
+      type: file
+      description: SNP distribution
+      pattern: "*.{vcf}"
+  - stats:
+      type: file
+      description: Per branch statistics
+      pattern: "*.{csv}"
+  - phylip:
+      type: file
+      description: Filtered variant alignment in phylip format
+      pattern: "*.{phylip}"
+  - tree:
+      type: file
+      description: Recombination removed RAxML phylogenetic tree
+      pattern: "*.{final_tree.tre}"
+  - tree_labelled:
+      type: file
+      description: Recombination removed RAxML phylogenetic tree (nodes labelled)
+      pattern: "*.{node_labelled.final_tree.tre}"
+authors:
+  - "@avantonder"
+

software/methyldackel/extract/main.nf

@@ -35,6 +35,6 @@ process METHYLDACKEL_EXTRACT {
         $fasta \\
         $bam
 
-    echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
+    echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
     """
 }

software/methyldackel/mbias/main.nf

@@ -24,7 +24,7 @@ process METHYLDACKEL_MBIAS {
     path fai
 
     output:
-    tuple val(meta), path("*.txt"), emit: txt
+    tuple val(meta), path("*.mbias.txt"), emit: txt
     path  "*.version.txt"               , emit: version
 
     script:
@@ -37,8 +37,8 @@ process METHYLDACKEL_MBIAS {
         $bam \\
         $prefix \\
         --txt \\
-        > ${prefix}.txt
+        > ${prefix}.mbias.txt
 
-    echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
+    echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
     """
 }

software/pangolin/main.nf

@@ -11,11 +11,11 @@ process PANGOLIN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::pangolin=2.3.2' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=2.3.8' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.2--py_0'
+        container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.8--py_0'
     } else {
-        container 'quay.io/biocontainers/pangolin:2.3.2--py_0'
+        container 'quay.io/biocontainers/pangolin:2.3.8--py_0'
     }
 
     input:

software/rsem/preparereference/main.nf

@@ -19,11 +19,12 @@ process RSEM_PREPAREREFERENCE {
     }
 
     input:
-    path fasta
+    path fasta, stageAs: "rsem/*"
     path gtf
 
     output:
     path "rsem"                , emit: index
+    path "rsem/*transcripts.fa", emit: transcript_fasta
     path "*.version.txt"       , emit: version
 
     script:
@@ -33,7 +34,6 @@ process RSEM_PREPAREREFERENCE {
         args.removeIf { it.contains('--star') }
         def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
         """
-        mkdir rsem
         STAR \\
             --runMode genomeGenerate \\
             --genomeDir rsem/ \\
@@ -54,7 +54,6 @@ process RSEM_PREPAREREFERENCE {
         """
     } else {
         """
-        mkdir rsem
         rsem-prepare-reference \\
             --gtf $gtf \\
             --num-threads $task.cpus \\

software/spades/main.nf

@@ -11,17 +11,16 @@ process SPADES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::spades=3.15.0" : null)
+    conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
+        container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
     } else {
-        container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
+        container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
     }
 
     input:
     tuple val(meta), path(reads)
     path  hmm
-    val   coronaspades
 
     output:
     tuple val(meta), path('*.scaffolds.fa')    , optional:true, emit: scaffolds
@@ -37,9 +36,8 @@ process SPADES {
     def prefix      = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
-    def command     = coronaspades ? "coronaspades.py" : "spades.py"
     """
-    $command \\
+    spades.py \\
         $options.args \\
         --threads $task.cpus \\
         $custom_hmms \\

software/spades/meta.yml

@@ -29,11 +29,6 @@ input:
       type: file
       description:
         File or directory with amino acid HMMs for Spades HMM-guided mode.
-  - coronaspades:
-      type: boolean
-      description: |
-        Run coronaspades instead of default spades mode. coronaSPAdes is a special
-        mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
 output:
   - meta:
       type: map

software/subread/featurecounts/meta.yml

@@ -0,0 +1,52 @@
+name: subread_featurecounts
+description: Count reads that map to genomic features
+keywords:
+    - counts
+    - fasta
+    - genome
+    - reference
+
+tools:
+  - featurecounts:
+      description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
+      homepage: http://bioinf.wehi.edu.au/featureCounts/
+      documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
+      doi: "10.1093/bioinformatics/btt656"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/SAM file containing read alignments
+      pattern: "*.{bam}"
+  - annotation:
+      type: file
+      description: Genomic features annotation in GTF or SAF
+      pattern: "*.{gtf,saf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+  - counts:
+      type: file
+      description: Counts of reads mapping to features
+      pattern: "*featureCounts.txt"
+  - summary:
+      type: file
+      description: Summary log file
+      pattern: "*.featureCounts.txt.summary"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@ntoda03"

software/tabix/bgzip/main.nf

@@ -30,6 +30,7 @@ process TABIX_BGZIP {
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bgzip -c $options.args $input > ${prefix}.${input.getExtension()}.gz
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+
+    echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
     """
 }

tests/config/pytest_software.yml

@@ -246,6 +246,10 @@ gffread:
   - software/gffread/**
   - tests/software/gffread/**
 
+gubbins:
+  - software/gubbins/**
+  - tests/software/gubbins/**
+
 gunzip:
   - software/gunzip/**
   - tests/software/gunzip/**
@@ -466,6 +470,10 @@ stringtie:
   - software/stringtie/**
   - tests/software/stringtie/**
 
+subread_featurecounts:
+  - software/subread/featurecounts/**
+  - tests/software/subread/featurecounts/**
+
 tabix_bgzip:
   - software/tabix/bgzip/**
   - tests/software/tabix/bgzip/**

tests/config/test_data.config

@@ -9,6 +9,7 @@ params {
                 genome_fasta_fai                          = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
                 genome_dict                               = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
                 genome_gff3                               = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
+                genome_gff3_gz                            = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
                 genome_gtf                                = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
                 genome_sizes                              = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
                 transcriptome_fasta                       = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
@@ -24,6 +25,8 @@ params {
                 kraken2_tar_gz                            = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
                 
                 test_wig_gz                               = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
+
+                test_fas                                  = "${test_data_dir}/genomics/sarscov2/genome/alignment/test.fas"
             }
             'illumina' {
                 test_single_end_bam                       = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"

tests/software/blast/blastn/main.nf

@@ -6,7 +6,7 @@ include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.
 include { BLAST_BLASTN      } from '../../../../software/blast/blastn/main.nf'      addParams( options: [:] )
 
 workflow test_blast_blastn {
-    input = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
 
     BLAST_MAKEBLASTDB ( input )
     BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )

tests/software/blast/blastn/test.yml

@@ -5,18 +5,18 @@
     - blast_blastn
   files:
     - path: ./output/blast/test.blastn.txt
-    - path: ./output/blast/blast_db/test_genome.fasta.nsq
+    - path: ./output/blast/blast_db/genome.fasta.nsq
       md5sum: 982cbc7d9e38743b9b1037588862b9da
-    - path: ./output/blast/blast_db/test_genome.fasta.nin
+    - path: ./output/blast/blast_db/genome.fasta.nin
-    - path: ./output/blast/blast_db/test_genome.fasta
+    - path: ./output/blast/blast_db/genome.fasta
       md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: ./output/blast/blast_db/test_genome.fasta.nhr
+    - path: ./output/blast/blast_db/genome.fasta.nhr
       md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
-    - path: ./output/blast/blast_db/test_genome.fasta.ndb
+    - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 5134241fd6e34d01a6ab0f2d0986e8ed
+      md5sum: 45f2daf9769957ff80868dd3d80d30a3
-    - path: ./output/blast/blast_db/test_genome.fasta.not
+    - path: ./output/blast/blast_db/genome.fasta.not
       md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
-    - path: ./output/blast/blast_db/test_genome.fasta.nto
+    - path: ./output/blast/blast_db/genome.fasta.nto
       md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: ./output/blast/blast_db/test_genome.fasta.ntf
+    - path: ./output/blast/blast_db/genome.fasta.ntf
       md5sum: 1f6027d443e67a98ad0edc2d39971b0c

tests/software/blast/makeblastdb/main.nf

@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
 
 workflow test_blast_makeblastdb {
-    input =  [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+    input =  [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
 
     BLAST_MAKEBLASTDB ( input )
 }

tests/software/blast/makeblastdb/test.yml

@@ -4,18 +4,18 @@
     - blast
     - blast_makeblastdb
   files:
-    - path: ./output/blast/blast_db/test_genome.fasta.nsq
+    - path: ./output/blast/blast_db/genome.fasta.nsq
       md5sum: 982cbc7d9e38743b9b1037588862b9da
-    - path: ./output/blast/blast_db/test_genome.fasta.nin
+    - path: ./output/blast/blast_db/genome.fasta.nin
-    - path: ./output/blast/blast_db/test_genome.fasta
+    - path: ./output/blast/blast_db/genome.fasta
       md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: ./output/blast/blast_db/test_genome.fasta.nhr
+    - path: ./output/blast/blast_db/genome.fasta.nhr
       md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
-    - path: ./output/blast/blast_db/test_genome.fasta.ndb
+    - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 5134241fd6e34d01a6ab0f2d0986e8ed
+      md5sum: 45f2daf9769957ff80868dd3d80d30a3
-    - path: ./output/blast/blast_db/test_genome.fasta.not
+    - path: ./output/blast/blast_db/genome.fasta.not
       md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
-    - path: ./output/blast/blast_db/test_genome.fasta.nto
+    - path: ./output/blast/blast_db/genome.fasta.nto
       md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: ./output/blast/blast_db/test_genome.fasta.ntf
+    - path: ./output/blast/blast_db/genome.fasta.ntf
       md5sum: 1f6027d443e67a98ad0edc2d39971b0c

tests/software/flash/main.nf

@@ -6,8 +6,8 @@ include { FLASH } from '../../../software/flash/main.nf' addParams( options: [ar
 
 workflow test_flash {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
             ]
 
     FLASH ( input )

tests/software/gubbins/main.nf

@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUBBINS } from '../../../software/gubbins/main.nf' addParams( options: [:] )
+
+workflow test_gubbins { 
+    input = file(params.test_data['sarscov2']['genome']['test_fas'], checkIfExists: true)
+
+    GUBBINS ( input )
+}

tests/software/gubbins/test.yml

@@ -0,0 +1,23 @@
+- name: gubbins
+  command: nextflow run ./tests/software/gubbins -entry test_gubbins -c tests/config/nextflow.config
+  tags:
+    - gubbins
+  files:
+    - path: output/gubbins/test.filtered_polymorphic_sites.fasta
+      md5sum: c9dff2294307eb2200a6e19efce47796
+    - path: output/gubbins/test.recombination_predictions.embl
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/gubbins/test.recombination_predictions.gff
+      md5sum: a2ca9c119674f4d121a8f78e4078fe05
+    - path: output/gubbins/test.branch_base_reconstruction.embl
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/gubbins/test.summary_of_snp_distribution.vcf
+      md5sum: afee50e92fb919a5df487fbda0b9dbb5
+    - path: output/gubbins/test.per_branch_statistics.csv
+      md5sum: 0f364b5e0b01a6be9b6a4407658ab25f
+    - path: output/gubbins/test.filtered_polymorphic_sites.phylip
+      md5sum: 85db9d0896cfec34a73641496b7498bb
+    - path: output/gubbins/test.final_tree.tre
+      md5sum: dce7164a0c69bb3d642a419907364aa3
+    - path: output/gubbins/test.node_labelled.final_tree.tre
+      md5sum: beef5ce05aca4598bb3f42caf126e045

tests/software/methyldackel/extract/main.nf

@@ -6,10 +6,10 @@ include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract
 
 workflow test_methyldackel_extract {
     input = [ [ id:'test', single_end:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) ]
+              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
     METHYLDACKEL_EXTRACT ( input, fasta, fai )
 }

tests/software/methyldackel/mbias/main.nf

@@ -6,11 +6,10 @@ include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/mai
 
 workflow test_methyldackel_mbias {
     input = [ [ id:'test', single_end:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam", checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai", checkIfExists: true) 
+              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    fai   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
 
     METHYLDACKEL_MBIAS ( input, fasta, fai )
 }

tests/software/methyldackel/mbias/test.yml

@@ -4,5 +4,5 @@
     - methyldackel
     - methyldackel_mbias
   files:
-    - path: output/methyldackel/test.txt
+    - path: output/methyldackel/test.mbias.txt
       md5sum: 357bb944dc2cdffcc47fa0d34376e016

tests/software/mosdepth/main.nf

@@ -6,8 +6,8 @@ include { MOSDEPTH } from '../../../software/mosdepth/main.nf' addParams( option
 
 workflow test_mosdepth {
     input  = [ [ id:'test', single_end:true ],
-               [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ],
+               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-               [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) ] 
+               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] 
              ]
     dummy  = file("dummy_file.txt")
     window = 100

tests/software/optitype/main.nf

@@ -2,11 +2,11 @@
 
 nextflow.enable.dsl = 2
 
-include { OPTITYPE } from ''../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
+include { OPTITYPE } from '../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
 
 workflow test_optitype {
     input = [ [ id:'test', seq_type:'dna' ], // meta map
-              file("${launchDir}/tests/data/genomics/homo_sapiens/illumina/bam/example_pe.bam", checkIfExists: true) 
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true) 
             ]
             
     OPTITYPE ( input )

tests/software/pangolin/main.nf

@@ -6,7 +6,7 @@ include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams( option
 
 workflow test_pangolin {
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] ]
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]
 
     PANGOLIN ( input )
 }

tests/software/pangolin/test.yml

@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 1d513775cec0901ebee1359c91035d3a
+      md5sum: c8b1720f98c9e032908f61bbc05a0fe2

tests/software/qualimap/bamqc/main.nf

@@ -6,7 +6,7 @@ include { QUALIMAP_BAMQC } from '../../../../software/qualimap/bamqc/main.nf' ad
 
 workflow test_qualimap_bamqc {
     input   = [ [ id:'test', single_end:false ], // meta map
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) 
+                [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
               ]
     gff     = file("dummy_file.txt")
     use_gff = false

tests/software/quast/main.nf

@@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
 include { QUAST }   from '../../../software/quast/main.nf'   addParams(options: [:])
 
 workflow test_quast_ref {
-    fasta     = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff       = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+    gff       = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-    consensus = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
+    consensus = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
     use_fasta = true
     use_gtf   = true
 
@@ -17,7 +17,7 @@ workflow test_quast_ref {
 workflow test_quast_noref {
     fasta     = file('fasta_dummy')
     gff       = file('gff_dummy')
-    consensus = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    consensus = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     use_fasta = false
     use_gtf   = false
 

tests/software/quast/test.yml

@@ -6,32 +6,32 @@
   files:
     - path: ./output/quast/report.tsv
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 73ae4f7cbe0da640819214cb013a79ef
+      md5sum: 5dee51af1e7f916200d0a80f0c66be60
     - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 117ed0d235b8e74b8f7ae8ed7b78c449
+      md5sum: 336ec8d7b403fe1e0519e3a39eadd691
     - path: ./output/quast/quast/icarus.html
     - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 475bf9987c421b72fe1675b54ae0bcbe
+      md5sum: 0e1b2eff1e8fd91a0bf80165d8f31ae5
     - path: ./output/quast/quast/report.tex
-      md5sum: e4c1d12bfe94d5a10e2264397bb90f83
+      md5sum: a9aac7d2ac2263df7e4599e4431c7393
     - path: ./output/quast/quast/report.txt
-      md5sum: 6295e6d462b1db45b1bb9f3f508275ad
+      md5sum: 2da78350f20819f2625bd467800700ad
     - path: ./output/quast/quast/report.tsv
-      md5sum: b70404d2b4d4e905afcfe3d149a5bd15
+      md5sum: 38fb41afadc09ffcbef62e42fea49f5e
     - path: ./output/quast/quast/report.html
     - path: ./output/quast/quast/report.pdf
     - path: ./output/quast/quast/quast.log
-    - path: ./output/quast/quast/genome_stats/test_transcriptome_genomic_features_any.txt
+    - path: ./output/quast/quast/genome_stats/transcriptome_genomic_features_any.txt
       md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
     - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
     - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
     - path: ./output/quast/quast/genome_stats/genome_info.txt
-      md5sum: a4bb1f2792c175fc8d7fbf37f219e552
+      md5sum: d0193b322079565dc78608291e9c44d1
-    - path: ./output/quast/quast/genome_stats/test_transcriptome_gaps.txt
+    - path: ./output/quast/quast/genome_stats/transcriptome_gaps.txt
       md5sum: c52381f09ea40b6141be5232494727b6
     - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
     - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
-    - path: ./output/quast/quast/basic_stats/test_transcriptome_GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/transcriptome_GC_content_plot.pdf
     - path: ./output/quast/quast/basic_stats/gc.icarus.txt
       md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
     - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
@@ -39,45 +39,45 @@
     - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
     - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
     - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.mis_contigs.info
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.mis_contigs.info
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.unaligned.info
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
       md5sum: a8505cf206bf53ca369f7e3073fee587
     - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
-      md5sum: 4895cb02a010f1db85fc4992ac3c63b1
+      md5sum: d778f337899736cc62ed837b739b375c
     - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
-      md5sum: d5c9dd22ce8f382649f74ba1f61d8a84
+      md5sum: 8b9a6d675a41bab6bf344dde2a20a939
-    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stdout
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
-    - path: ./output/quast/quast/contigs_reports/all_alignments_test_transcriptome.tsv
+    - path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
       md5sum: c247152eb82b361106492642fd796e2c
     - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
-      md5sum: 0df52940978f10c0fc9ed5f6770f170e
+      md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
-    - path: ./output/quast/quast/contigs_reports/test_transcriptome.mis_contigs.fa
+    - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
-      md5sum: d83abdf60e7ef02354a783dff4262d7d
+      md5sum: fdb440c653e2f0306286798cacceaadb
     - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
-      md5sum: f2adf811a611abdcb9f10bd7801e61e1
+      md5sum: 81d9597314356363a6b4e0d67027345a
     - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
-      md5sum: dd6e08408ea9a6830d47d5c21b84d587
+      md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3
     - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
     - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
-      md5sum: e77d87bafe0e2c881805f8dfcc5f2351
+      md5sum: a32a09a0df811d1a75fbfe124081d1ca
-    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stderr
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stderr
     - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
     - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
-      md5sum: 6f9bd38e646b0a754b153e0dfe2c57b0
+      md5sum: e8e3bcb86da2cbd8eded980de80fa45c
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords.filtered
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
       md5sum: ec9191d0acb5d5bce56b4842551a8598
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
       md5sum: dda3fc0addc41ecc0d5183dee6f95886
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.used_snps.gz
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.used_snps.gz
       md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.sf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.unaligned
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords_tmp
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords_tmp
       md5sum: ce66eaeb99fdc11e4d50efadc1816e04
     - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
     - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
@@ -89,26 +89,26 @@
     - quast_no_reference
   files:
     - path: ./output/quast/report.tsv
-      md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
+      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 5496230d4bc3846616d7e08d52ffc081
+      md5sum: 8784d7c7349498e1507e09fbf554625d
     - path: ./output/quast/quast/transposed_report.tex
-      md5sum: cf6a3b50575b510a7c42f5e745dd8674
+      md5sum: 4c2a9dd0c1d3cbb80a2ac2577b5d363b
     - path: ./output/quast/quast/icarus.html
-      md5sum: ba0ddcdbcd743191d282e3986cb68735
+      md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
     - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 4b128bbf595b07dd2e2d5230bf575d29
+      md5sum: f0b5f65b2050af83b6d170d384c7616b
     - path: ./output/quast/quast/report.tex
-      md5sum: ac22b93fad7cdb6a812e5f670e815647
+      md5sum: 3da038cc5a02ef83e225c5277b87970b
     - path: ./output/quast/quast/report.txt
-      md5sum: 283160faa1d8cd32064c49e3c6d738d5
+      md5sum: bd2faaef244f02aa072d544c0d6d6e71
     - path: ./output/quast/quast/report.tsv
-      md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
+      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
     - path: ./output/quast/quast/report.html
     - path: ./output/quast/quast/report.pdf
     - path: ./output/quast/quast/quast.log
     - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
     - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
-    - path: ./output/quast/quast/basic_stats/test_genome_GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/genome_GC_content_plot.pdf
     - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
     - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html

tests/software/spades/main.nf

@@ -2,43 +2,20 @@
 
 nextflow.enable.dsl = 2
 
-include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )
+include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: ['args': '--rnaviral'] )
 
 workflow test_spades_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    coronaspades = false
+    SPADES ( input, [] )
-
-    SPADES ( input, [], coronaspades )
 }
 
 workflow test_spades_paired_end {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    coronaspades = false
 
-    SPADES ( input, [], coronaspades )
+    SPADES ( input, [] )
 }
-
-workflow test_coronospades_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] 
-            ]
-    coronaspades = true
-
-    SPADES ( input, [], coronaspades )
-}
-
-workflow test_coronospades_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] 
-            ]
-    coronaspades = true
-
-    SPADES ( input, [], coronaspades )
-}
-

tests/software/spades/test.yml

@@ -5,13 +5,12 @@
     - spades_single_end
   files:
     - path: output/spades/test.assembly.gfa
-      md5sum: f15ad4a198324de37c6010dafb3fe781
+      md5sum: b2616d2beba83ab7d361b54778d1e759
     - path: output/spades/test.contigs.fa
-      md5sum: bc21771042b465c26dfc85beedc33d58
+      md5sum: 2690fefde046bc904e90df09a065257a
     - path: output/spades/test.scaffolds.fa
-      md5sum: bc21771042b465c26dfc85beedc33d58
+      md5sum: 2690fefde046bc904e90df09a065257a
     - path: output/spades/test.spades.log
-    - path: output/spades/warnings.log
 
 - name: spades paired end
   command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
@@ -20,39 +19,7 @@
     - spades_paired_end
   files:
       - path: output/spades/test.assembly.gfa
-        md5sum: 5da5b04c6fce549c77a209034a9c1e72
+        md5sum: faf76135ee390606b899c0197dc38e04
       - path: output/spades/test.contigs.fa
-        md5sum: 403b612d52edf390f662ab601873f09f
+        md5sum: 6148e25b33890c80f176f90f2dd88989
-      - path: output/spades/test.scaffolds.fa
-        md5sum: 49a9cbb29cee4d088e05e62eb4bc77c4
       - path: output/spades/test.spades.log
-      - path: output/spades/warnings.log
-
-- name: coronaspades single end
-  command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
-  tags:
-    - spades
-    - coronaspades_single_end
-  files:
-      - path: output/spades/test.assembly.gfa
-        md5sum: 46531ec9b845c1a1cb469627688fecb7
-      - path: output/spades/test.contigs.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.scaffolds.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.spades.log
-
-- name: coronaspades paired end
-  command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
-  tags:
-    - spades
-    - coronaspades_paired_end
-  files:
-      - path: output/spades/test.assembly.gfa
-        md5sum: 46531ec9b845c1a1cb469627688fecb7
-      - path: output/spades/test.contigs.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.scaffolds.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.spades.log
-

tests/software/subread/featurecounts/main.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SUBREAD_FEATURECOUNTS } from '../../../../software/subread/featurecounts/main.nf' addParams( options: [args:'-t CDS'] )
+
+workflow test_subread_featurecounts_forward {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
+
+workflow test_subread_featurecounts_reverse {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
+
+workflow test_subread_featurecounts_unstranded {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}

tests/software/subread/featurecounts/test.yml

@@ -0,0 +1,35 @@
+- name: subread featurecounts test_subread_featurecounts_forward
+  command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_forward -c tests/config/nextflow.config
+  tags:
+    - subread
+    - subread_featurecounts_forward
+    - subread_featurecounts
+  files:
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: d78617192451a57f6ef249ddcaf13720
+    - path: output/subread/test.featureCounts.txt
+      md5sum: b0a1f7563afe49007f422d4c9ca5ee6c
+
+- name: subread featurecounts test_subread_featurecounts_reverse
+  command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
+  tags:
+    - subread
+    - subread_featurecounts
+    - subread_featurecounts_reverse
+  files:
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 4217004d0b55f870f77092364f59e44d
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 412840a8880cd29674b3d5404d3de19b
+
+- name: subread featurecounts test_subread_featurecounts_unstranded
+  command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
+  tags:
+    - subread
+    - subread_featurecounts
+    - subread_featurecounts_unstranded
+  files:
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: ee585faeb1edfcd2188a5e486a0e98a9
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 6b684e11a1e54bec7e1ee5e3f651d7fd

tests/software/tabix/bgzip/main.nf

@@ -6,7 +6,7 @@ include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParam
 
 workflow test_tabix_bgzip {
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
             ]
 
     TABIX_BGZIP ( input )

tests/software/tabix/tabix/main.nf

@@ -8,7 +8,7 @@ include { TABIX_TABIX as TABIX_VCF } from '../../../../software/tabix/tabix/main
 
 workflow test_tabix_tabix_bed {
     input = [ [ id:'B.bed' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ] 
             ]
 
     TABIX_BED ( input )
@@ -16,7 +16,7 @@ workflow test_tabix_tabix_bed {
 
 workflow test_tabix_tabix_gff {
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ] 
             ]
 
     TABIX_GFF ( input )
@@ -24,7 +24,7 @@ workflow test_tabix_tabix_gff {
 
 workflow test_tabix_tabix_vcf {
     input = [ [ id:'test.vcf' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] 
             ]
 
     TABIX_VCF ( input )

tests/software/tabix/tabix/test.yml

@@ -14,8 +14,8 @@
     - tabix_tabix
     - gff
   files:
-    - path: ./output/tabix/test_genome.gff3.gz.tbi
+    - path: ./output/tabix/genome.gff3.gz.tbi
-      md5sum: 30de27e3f44662272cfe6b3093126ea6
+      md5sum: 4059fe4762568194cf293fc6df7b358b
 - name: tabix tabix vcf
   command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
   tags:

tests/software/tiddit/sv/main.nf

@@ -6,17 +6,17 @@ include { TIDDIT_SV } from '../../../../software/tiddit/sv/main.nf' addParams( o
 
 workflow test_tiddit_sv {
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
     TIDDIT_SV ( input, fasta, fai )
 }
 
 workflow test_tiddit_sv_no_ref {
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
             ]
 
     TIDDIT_SV ( input, [], [] )

tests/software/unicycler/main.nf

@@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
 
 workflow test_unicycler_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] 
             ]
 
     UNICYCLER ( input )
@@ -14,8 +14,8 @@ workflow test_unicycler_single_end {
 
 workflow test_unicycler_paired_end {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
             ]
 
     UNICYCLER ( input )