Re-organise all test data (#354)

* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint

software/flash/functions.nf

@@ -1,3 +1,4 @@
+
 /*
  * -----------------------------------------------------
  *  Utility functions used in nf-core DSL2 module files
@@ -31,7 +32,7 @@ def initOptions(Map args) {
  */
 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
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 

software/strelka/germline/functions.nf

@@ -1,3 +1,4 @@
+
 /*
  * -----------------------------------------------------
  *  Utility functions used in nf-core DSL2 module files
@@ -31,7 +32,7 @@ def initOptions(Map args) {
  */
 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
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 

software/strelka/germline/main.nf

@@ -20,35 +20,36 @@ process STRELKA_GERMLINE {
 
     input:
     tuple val(meta), path(bam), path(bai)
-    path fasta
+    path  fasta
-    path fai
+    path  fai
-    path target_bed
+    path  target_bed
 
     output:
-    tuple val(meta), path("*_variants.vcf.gz"), emit: vcf
+    tuple val(meta), path("*_variants.vcf.gz")    , emit: vcf
     tuple val(meta), path("*_variants.vcf.gz.tbi"), emit: vcf_tbi
-    tuple val(meta), path("*_genome.vcf.gz"), emit: genome_vcf
+    tuple val(meta), path("*_genome.vcf.gz")      , emit: genome_vcf
-    tuple val(meta), path("*_genome.vcf.gz.tbi"), emit: genome_vcf_tbi
+    tuple val(meta), path("*_genome.vcf.gz.tbi")  , emit: genome_vcf_tbi
-    path "*.version.txt", emit: version 
+    path  "*.version.txt"                         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def ioptions = initOptions(options)
     def prefix   = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
-    
+    def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
-    options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
     """
-    configureStrelkaGermlineWorkflow.py \
+    configureStrelkaGermlineWorkflow.py \\
-        --bam ${bam} \
+        --bam $bam \\
-        --referenceFasta ${fasta} \
+        --referenceFasta $fasta \\
-        ${options_strelka} \
+        $options_strelka \\
-        ${options.args} \
+        $options.args \\
         --runDir strelka
-    python strelka/runWorkflow.py -m local -j ${task.cpus}
+
+    python strelka/runWorkflow.py -m local -j $task.cpus
     mv strelka/results/variants/genome.*.vcf.gz     ${prefix}_genome.vcf.gz
     mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}_genome.vcf.gz.tbi
     mv strelka/results/variants/variants.vcf.gz     ${prefix}_variants.vcf.gz
     mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}_variants.vcf.gz.tbi
+
     echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1
     """
 }

software/strelka/germline/meta.yml

@@ -44,17 +44,17 @@ output:
       description: gzipped germline variant file
       pattern: "*.{vcf.gz}"
   - vcf_tbi:
-     type: file
+      type: file
-     description: index file for the vcf file
+      description: index file for the vcf file
-     pattern: "*.vcf.gz.tbi"
+      pattern: "*.vcf.gz.tbi"
   - genome_vcf:
-     type: file
+      type: file
-     description: variant records and compressed non-variant blocks
+      description: variant records and compressed non-variant blocks
-     pattern: "*_genome.vcf.gz"
+      pattern: "*_genome.vcf.gz"
   - genome_vcf_tbi:
-     type: file
+      type: file
-     description: index file for the genome_vcf file
+      description: index file for the genome_vcf file
-     pattern: "*_genome.vcf.gz.tbi"
+      pattern: "*_genome.vcf.gz.tbi"
   - version:
       type: file
       description: File containing software version

tests/data/generic/fasta/NC_010473.fa.fai

@@ -1 +0,0 @@
-gi|170079663|ref|NC_010473.1|	4686137	89	70	71

tests/data/generic/sizes/test.sizes

@@ -1 +0,0 @@
-chr7	159138663

tests/software/adapterremoval/main.nf

@@ -5,30 +5,27 @@ nextflow.enable.dsl = 2
 include { ADAPTERREMOVAL } from '../../../software/adapterremoval/main.nf' addParams( options: [:] )
 
 workflow test_adapterremoval_single_end {
-    
-    def input = []
     input = [ [ id:'test', single_end:true, collapse:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+            ]
 
     ADAPTERREMOVAL ( input )
 }
 
 workflow test_adapterremoval_paired_end {
-    
-    def input = []
     input = [ [ id:'test', single_end:false, collapse:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+            ]
 
     ADAPTERREMOVAL ( input )
 }
 
 workflow test_adapterremoval_paired_end_collapse {
-    
-    def input = []
     input = [ [ id:'test', single_end:false, collapse:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+            ]
 
     ADAPTERREMOVAL ( input )
 }

tests/software/allelecounter/main.nf

@@ -4,11 +4,11 @@ nextflow.enable.dsl = 2
 include { ALLELECOUNTER } from '../../../software/allelecounter/main.nf' addParams( options: [:] )
 
 workflow test_allelecounter {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)]
+              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
-    positions = [ file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+            ]
+    positions = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ]
+
     ALLELECOUNTER ( input, positions )
 }

tests/software/bandage/image/main.nf

@@ -5,10 +5,10 @@ nextflow.enable.dsl = 2
 include { BANDAGE_IMAGE } from '../../../../software/bandage/image/main.nf' addParams( options: [:] )
 
 workflow test_bandage_image {
-
-    def input = []
     input = [ [ id:'B-3106' ], // meta map
-              [ file("${launchDir}/tests/data/generic/gfa/B-3106.gfa", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/generic/gfa/B-3106.gfa", checkIfExists: true) ]
+              //[ file("${launchDir}/tests/data/genomics/sarscov2/genome/gfa/test.gfa", checkIfExists: true) ]
+            ]
 
     BANDAGE_IMAGE ( input )
 }

tests/software/bcftools/consensus/main.nf

@@ -5,11 +5,11 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
 
 workflow test_bcftools_consensus {
-    def input = []
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ],
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) ],
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi", checkIfExists: true) ],
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true) ],
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+            ]
 
     BCFTOOLS_CONSENSUS ( input )
 }

tests/software/bcftools/filter/main.nf

@@ -6,9 +6,9 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
 
 workflow test_bcftools_filter {
-    def input = []
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) ]
+            ]
 
     BCFTOOLS_FILTER ( input )
 }

tests/software/bcftools/isec/main.nf

@@ -5,13 +5,12 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
 
 workflow test_bcftools_isec {
-    def input = []
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz", checkIfExists: true)],
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz", checkIfExists: true)],
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi", checkIfExists: true)]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi", checkIfExists: true)]
-                ]
+            ]
 
     BCFTOOLS_ISEC ( input )
 }

tests/software/bcftools/merge/main.nf

@@ -6,12 +6,12 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] )
 
 workflow test_bcftools_merge {
-    def input = []
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/vcf/test3.vcf.gz", checkIfExists: true) ],
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz", checkIfExists: true) ],
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi", checkIfExists: true) ]]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi", checkIfExists: true) ]
+            ]
 
     BCFTOOLS_MERGE ( input )
 }

tests/software/bcftools/mpileup/main.nf

@@ -6,10 +6,9 @@ include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf
                                                                                                        'args3': '--no-version' ] )
 
 workflow test_bcftools_mpileup {
-    def input = []
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true) ]]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ]]
-    fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
+    fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
 
     BCFTOOLS_MPILEUP ( input, fasta )
 }

tests/software/bcftools/stats/main.nf

@@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' addParams( options: [:] )
 
 workflow test_bcftools_stats {
-    def input = []
     input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) ]
+            ]
 
     BCFTOOLS_STATS ( input )
 }

tests/software/bedtools/complement/main.nf

@@ -5,9 +5,10 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_COMPLEMENT } from '../../../../software/bedtools/complement/main.nf' addParams( options: [suffix: '_out'] )
 
 workflow test_bedtools_complement {
-    def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+            ]
+    sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
 
-    BEDTOOLS_COMPLEMENT ( input, file("${launchDir}/tests/data/genomics/sarscov2/general/test.genome.sizes", checkIfExists: true) )
+    BEDTOOLS_COMPLEMENT ( input, sizes )
 }

tests/software/bedtools/genomecov/main.nf

@@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/main.nf' addParams( options: [suffix: '_out'] )
 
 workflow test_bedtools_genomecov {
-    def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.bam", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true)
+            ]
 
     BEDTOOLS_GENOMECOV ( input )
 }

tests/software/bedtools/getfasta/main.nf

@@ -5,8 +5,8 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_GETFASTA } from '../../../../software/bedtools/getfasta/main.nf' addParams( options: [:] )
 
 workflow test_bedtools_getfasta {
-    def bed   = [ file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+    bed   = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ]
-    def fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
+    fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
 
     BEDTOOLS_GETFASTA ( bed, fasta )
 }

tests/software/bedtools/intersect/main.nf

@@ -5,10 +5,10 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_INTERSECT } from '../../../../software/bedtools/intersect/main.nf' addParams( options: [suffix: '_out'] )
 
 workflow test_bedtools_intersect {
-    def input = []
+    input = [ [ id:'test' ],
-    input = [ [ id:'test',],
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test2.bed", checkIfExists: true)
-              file("${launchDir}/tests/data/genomics/sarscov2/bed/test2.bed", checkIfExists: true) ]
+            ]
 
     BEDTOOLS_INTERSECT ( input )
 }

tests/software/bedtools/maskfasta/main.nf

@@ -5,9 +5,10 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_MASKFASTA } from '../../../../software/bedtools/maskfasta/main.nf' addParams( options: [:] )
 
 workflow test_bedtools_maskfasta {
-    def bed  =  [ [ id:'test'],
+    bed   = [ [ id:'test'],
-                  file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
-    def fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
+            ]
+    fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
 
-    BEDTOOLS_MASKFASTA( bed, fasta )
+    BEDTOOLS_MASKFASTA ( bed, fasta )
 }

tests/software/bedtools/merge/main.nf

@@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_MERGE } from '../../../../software/bedtools/merge/main.nf' addParams( options: [suffix: '_out'] )
 
 workflow test_bedtools_merge {
-    def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+            ]
 
     BEDTOOLS_MERGE ( input )
 }

tests/software/bedtools/slop/main.nf

@@ -5,10 +5,11 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addParams( options: [args: '-l 15 -r 30', suffix: '_out'] )
 
 workflow test_bedtools_slop {
-    def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+            ]
+    sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
 
-    BEDTOOLS_SLOP ( input, file("${launchDir}/tests/data/genomics/sarscov2/general/test.genome.sizes", checkIfExists: true) )
+    BEDTOOLS_SLOP ( input, sizes )
 }
 

tests/software/bedtools/sort/main.nf

@@ -5,9 +5,9 @@ nextflow.enable.dsl = 2
 include { BEDTOOLS_SORT } from '../../../../software/bedtools/sort/main.nf' addParams( options: [suffix: '_out'] )
 
 workflow test_bedtools_sort {
-    def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+              file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+            ]
 
     BEDTOOLS_SORT ( input )
 }

tests/software/bismark/align/main.nf

@@ -2,41 +2,33 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION         } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:]                               )
-include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../software/bismark/align/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../software/bismark/align/main.nf'             addParams( options: [ publish_dir:'test_single_end' ] )
-include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark/align/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
+include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark/align/main.nf'             addParams( options: [ publish_dir:'test_paired_end' ] )
 
 /*
  * Test with single-end data
  */
 workflow test_bismark_align_single_end {
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-
+    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_ALIGN_SE (
-        input,
-        BISMARK_GENOMEPREPARATION.out.index
-    )
 }
 
 /*
  * Test with paired-end data
  */
 workflow test_bismark_align_paired_end {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-
+    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_ALIGN_PE ( input, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_ALIGN_PE (
-        input,
-        BISMARK_GENOMEPREPARATION.out.index
-    )
 }

tests/software/bismark/deduplicate/main.nf

@@ -5,10 +5,9 @@ nextflow.enable.dsl = 2
 include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
 
 workflow test_bismark_deduplicate {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam", checkIfExists: true) ]
+            ]
 
     BISMARK_DEDUPLICATE ( input )
 }

tests/software/bismark/genomepreparation/main.nf

@@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
 include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
 
 workflow test_bismark_genomepreparation {
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( fasta )
 }

tests/software/bismark/methylationextractor/main.nf

@@ -2,19 +2,15 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf'    addParams( options: [:] )
 include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
 
 workflow test_bismark_methylationextractor {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( fasta )
-
+    BISMARK_METHYLATIONEXTRACTOR ( input, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_METHYLATIONEXTRACTOR (
-        input,
-        BISMARK_GENOMEPREPARATION.out.index
-    )
 }

tests/software/bismark/report/main.nf

@@ -2,24 +2,23 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf'    addParams( options: [:] )
-include { BISMARK_ALIGN                 } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
+include { BISMARK_ALIGN                } from '../../../../software/bismark/align/main.nf'                addParams( options: [:] )
-include { BISMARK_DEDUPLICATE           } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
+include { BISMARK_DEDUPLICATE          } from '../../../../software/bismark/deduplicate/main.nf'          addParams( options: [:] )
 include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
-include { BISMARK_REPORT                } from '../../../../software/bismark/report/main.nf' addParams( options: [:] )
+include { BISMARK_REPORT               } from '../../../../software/bismark/report/main.nf'               addParams( options: [:] )
 
 workflow test_bismark_report {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( fasta )
     BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
     BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
     BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
-
     BISMARK_REPORT (
         BISMARK_ALIGN.out.report
             .join(BISMARK_DEDUPLICATE.out.report)

tests/software/bismark/summary/main.nf

@@ -2,24 +2,23 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf'    addParams( options: [:] )
-include { BISMARK_ALIGN                 } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
+include { BISMARK_ALIGN                } from '../../../../software/bismark/align/main.nf'                addParams( options: [:] )
-include { BISMARK_DEDUPLICATE           } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
+include { BISMARK_DEDUPLICATE          } from '../../../../software/bismark/deduplicate/main.nf'          addParams( options: [:] )
 include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
-include { BISMARK_SUMMARY               } from '../../../../software/bismark/summary/main.nf' addParams( options: [:] )
+include { BISMARK_SUMMARY              } from '../../../../software/bismark/summary/main.nf'              addParams( options: [:] )
 
 workflow test_bismark_summary {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( fasta )
     BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
     BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
     BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
-
     BISMARK_SUMMARY (
         BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
         BISMARK_ALIGN.out.report.collect{ meta, report -> report },

tests/software/blast/blastn/main.nf

@@ -3,13 +3,11 @@
 nextflow.enable.dsl = 2
 
 include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
-include { BLAST_BLASTN } from '../../../../software/blast/blastn/main.nf' addParams( options: [:] )
+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) ]
 
-    def input = []
+    BLAST_MAKEBLASTDB ( input )
-    input = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
+    BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )
-
-    BLAST_MAKEBLASTDB (input)
-    BLAST_BLASTN ([ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db)
 }

tests/software/blast/makeblastdb/main.nf

@@ -5,8 +5,7 @@ nextflow.enable.dsl = 2
 include { BLAST_MAKEBLASTDB } from '../../../../software/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
 
 workflow test_blast_makeblastdb {
-    def input = []
+    input =  [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
-    input =  [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
 
-    BLAST_MAKEBLASTDB( input )
+    BLAST_MAKEBLASTDB ( input )
 }

tests/software/bowtie/align/main.nf

@@ -6,24 +6,22 @@ include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addPar
 include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addParams( options: [:] )
 
 workflow test_bowtie_align_single_end {
-
-    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
-    BOWTIE_BUILD ( fasta )
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
+    BOWTIE_BUILD ( fasta )
     BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
 }
 
 workflow test_bowtie_align_paired_end {
-
-    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
-    BOWTIE_BUILD ( fasta )
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
+    BOWTIE_BUILD ( fasta )
     BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
 }

tests/software/bowtie/build_test/main.nf

@@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
 include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] )
 
 workflow test_bowtie_build {
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
     BOWTIE_BUILD ( fasta )
 }

tests/software/bowtie2/align/main.nf

@@ -6,24 +6,22 @@ include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addP
 include { BOWTIE2_ALIGN } from '../../../../software/bowtie2/align/main.nf' addParams( options: [:] )
 
 workflow test_bowtie2_align_single_end {
-
-    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
-    BOWTIE2_BUILD ( fasta )
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
+    BOWTIE2_BUILD ( fasta )
     BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
 }
 
 workflow test_bowtie2_align_paired_end {
-
-    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
-    BOWTIE2_BUILD ( fasta )
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
+    BOWTIE2_BUILD ( fasta )
     BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
 }

tests/software/bowtie2/build_test/main.nf

@@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
 include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] )
 
 workflow test_bowtie2_build {
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
     BOWTIE2_BUILD ( fasta )
 }

tests/software/bwa/index/main.nf

@@ -5,5 +5,7 @@ nextflow.enable.dsl = 2
 include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] )
 
 workflow test_bwa_index {
-    BWA_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
+    BWA_INDEX ( fasta )
 }

tests/software/bwa/mem/main.nf

@@ -9,31 +9,25 @@ include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( optio
  * Test with single-end data
  */
 workflow test_bwa_mem_single_end {
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BWA_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWA_INDEX ( fasta )
-    BWA_MEM (
+    BWA_MEM ( input, BWA_INDEX.out.index )
-        input,
-        BWA_INDEX.out.index
-    )
 }
 
 /*
  * Test with paired-end data
  */
 workflow test_bwa_mem_paired_end {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BWA_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWA_INDEX ( fasta )
-    BWA_MEM (
+    BWA_MEM ( input, BWA_INDEX.out.index )
-        input,
-        BWA_INDEX.out.index
-    )
 }

tests/software/bwamem2/index/main.nf

@@ -5,5 +5,7 @@ nextflow.enable.dsl = 2
 include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
 
 workflow test_bwamem2_index {
-    BWAMEM2_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+
+    BWAMEM2_INDEX ( fasta )
 }

tests/software/bwamem2/mem/main.nf

@@ -3,37 +3,31 @@
 nextflow.enable.dsl = 2
 
 include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
-include { BWAMEM2_MEM } from '../../../../software/bwamem2/mem/main.nf' addParams( options: [:] )
+include { BWAMEM2_MEM   } from '../../../../software/bwamem2/mem/main.nf'   addParams( options: [:] )
 
 /*
  * Test with single-end data
  */
 workflow test_bwamem2_mem_single_end {
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] 
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BWAMEM2_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWAMEM2_INDEX ( fasta )
-    BWAMEM2_MEM (
+    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
-        input,
-        BWAMEM2_INDEX.out.index
-    )
 }
 
 /*
  * Test with paired-end data
  */
 workflow test_bwamem2_mem_paired_end {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] 
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BWAMEM2_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWAMEM2_INDEX ( fasta )
-    BWAMEM2_MEM (
+    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
-        input,
-        BWAMEM2_INDEX.out.index
-    )
 }

tests/software/bwameth/align/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] )
+include { BWAMETH_INDEX                     } from '../../../../software/bwameth/index/main.nf' addParams( options: [:]                               )
 include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
 include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
 
@@ -10,32 +10,25 @@ include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth
  * Test with single-end data
  */
 workflow test_bwameth_align_single_end {
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] 
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-
+    BWAMETH_INDEX ( fasta )
-    BWAMETH_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index )
-    BWAMETH_ALIGN_SE (
-        input,
-        BWAMETH_INDEX.out.index
-    )
 }
 
 /*
  * Test with paired-end data
  */
 workflow test_bwameth_align_paired_end {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] 
+            ]
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BWAMETH_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWAMETH_INDEX ( fasta )
-    BWAMETH_ALIGN_PE (
+    BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index )
-        input,
-        BWAMETH_INDEX.out.index
-    )
 }

tests/software/bwameth/index/main.nf

@@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
 include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] )
 
 workflow test_bwameth_index {
+    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
 
-    BWAMETH_INDEX ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BWAMETH_INDEX ( fasta )
 }

tests/software/cat/fastq/main.nf

@@ -5,23 +5,21 @@ nextflow.enable.dsl = 2
 include { CAT_FASTQ } from '../../../../software/cat/fastq/main.nf' addParams( options: [:] )
 
 workflow test_cat_fastq_single_end {
-
-    def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-                [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                  file("${launchDir}/tests/data/genomics/sarscov2/fastq/test2_1.fastq.gz", checkIfExists: true) ]]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true) ]
+            ]
 
     CAT_FASTQ ( input )
 }
 
 workflow test_cat_fastq_paired_end {
-
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-                [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
+              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                  file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true),
-                  file("${launchDir}/tests/data/genomics/sarscov2/fastq/test2_1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
-                  file("${launchDir}/tests/data/genomics/sarscov2/fastq/test2_2.fastq.gz", checkIfExists: true) ]]
+                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz", checkIfExists: true) ]
+            ]
 
     CAT_FASTQ ( input )
 }