Update test data paths. (#375)

* Updata test data paths.

* Remove quote

* Revert quast

* Fix broken test

* Update md5

tests/software/allelecounter/main.nf

@@ -5,10 +5,10 @@ include { ALLELECOUNTER } from '../../../software/allelecounter/main.nf' addPara
 
 workflow test_allelecounter {
     input = [ [ id:'test', single_end:false ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
-              file("${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'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
             ]
-    positions = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ]
+    positions = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
 
     ALLELECOUNTER ( input, positions )
 }

tests/software/cnvkit/main.nf

@@ -5,15 +5,15 @@ nextflow.enable.dsl = 2
 include { CNVKIT } from '../../../software/cnvkit/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
 
 workflow test_cnvkit {
-    tumourbam = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
-    normalbam = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam", checkIfExists: true)
+    tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
     
     input = [ [ id:'test' ], // meta map
               tumourbam, 
               normalbam 
             ]
-    fasta   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    targets = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true)
+    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
 
     CNVKIT ( input, fasta, targets )
 }

tests/software/cutadapt/main.nf

@@ -9,7 +9,7 @@ include { CUTADAPT } from '../../../software/cutadapt/main.nf'  addParams( optio
  */
 workflow test_cutadapt_single_end {
     input = [ [ id:'test', single_end:true ], // 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) ] 
             ]
 
     CUTADAPT ( input )
@@ -21,8 +21,8 @@ workflow test_cutadapt_single_end {
 
 workflow test_cutadapt_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) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
             ]
 
     CUTADAPT ( input )

tests/software/gunzip/main.nf

@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { GUNZIP } from '../../../software/gunzip/main.nf' addParams( options: [:] )
 
 workflow test_gunzip {
-    input = file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
 
     GUNZIP ( input )
 }

tests/software/ivar/consensus/main.nf

@@ -7,9 +7,9 @@ include { IVAR_CONSENSUS } from '../../../../software/ivar/consensus/main.nf' ad
 
 workflow test_ivar_consensus {
     input = [ [ id:'test'],
-                file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.bam", checkIfExists: true) 
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     
     IVAR_CONSENSUS ( input, fasta )
 }

tests/software/ivar/trim/main.nf

@@ -6,10 +6,10 @@ include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([:
 
 workflow test_ivar_trim {
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
-              file("${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'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) 
             ]
-    bed   = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+    bed_file   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
 
     IVAR_TRIM ( input, bed_file )
 }

tests/software/ivar/trim/test.yml

@@ -5,4 +5,4 @@
     - ivar_trim
   files:
     - path: output/ivar/test.bam
-      md5sum: d5cf5bda0c47c40d70193fbe6c4c828f
+      md5sum: 8705d032b28a1c3dbfe78fa762a2132f

tests/software/ivar/variants/main.nf

@@ -9,9 +9,9 @@ workflow test_ivar_variants_no_gff_no_mpileup {
     params.save_mpileup = false
 
     input = [ [ id:'test'],
-              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)
     dummy = file("dummy_file.txt")
     
     IVAR_VARIANTS ( input, fasta, dummy )
@@ -22,9 +22,9 @@ workflow test_ivar_variants_no_gff_with_mpileup {
     params.save_mpileup = true
 
     input = [ [ id:'test'],
-              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)
     dummy = file("dummy_file.txt")
 
     IVAR_VARIANTS ( input, fasta, dummy )
@@ -35,10 +35,10 @@ workflow test_ivar_variants_with_gff_with_mpileup {
     params.save_mpileup = true
     
     input = [ [ id:'test'],
-              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)
-    gff   = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gff   = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
     
     IVAR_VARIANTS ( input, fasta, gff )
 }

tests/software/prodigal/main.nf

@@ -6,7 +6,7 @@ include { PRODIGAL } from '../../../software/prodigal/main.nf' addParams( option
 
 workflow test_prodigal {
     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) 
             ]
 
     PRODIGAL ( input , "gff")

tests/software/prokka/main.nf

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