Fixing vcftools and bismark tests (#383)

* fixed vcftools

* fixed genomepreparation, methylationextractor

* fixed deduplicate

tests/software/bismark/align/main.nf

@@ -11,9 +11,9 @@ include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark
  */
 workflow test_bismark_align_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BISMARK_GENOMEPREPARATION ( fasta )
     BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index )
@@ -24,10 +24,10 @@ workflow test_bismark_align_single_end {
  */
 workflow test_bismark_align_paired_end {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], 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)
 
     BISMARK_GENOMEPREPARATION ( fasta )
     BISMARK_ALIGN_PE ( input, BISMARK_GENOMEPREPARATION.out.index )

tests/software/bismark/deduplicate/main.nf

@@ -6,7 +6,7 @@ include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/m
 
 workflow test_bismark_deduplicate {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ]
             ]
 
     BISMARK_DEDUPLICATE ( input )

tests/software/bismark/genomepreparation/main.nf

@@ -5,7 +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)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BISMARK_GENOMEPREPARATION ( fasta )
 }

tests/software/bismark/genomepreparation/test.yml

@@ -4,7 +4,7 @@
     - bismark
     - bismark_genomepreparation
   files:
-    - path: ./output/bismark/BismarkIndex/test_genome.fasta
+    - path: ./output/bismark/BismarkIndex/genome.fasta
       md5sum: 6e9fe4042a72f2345f644f239272b7e6
     - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
       md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa

tests/software/bismark/methylationextractor/main.nf

@@ -7,9 +7,9 @@ include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/meth
 
 workflow test_bismark_methylationextractor {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BISMARK_GENOMEPREPARATION ( fasta )
     BISMARK_METHYLATIONEXTRACTOR ( input, BISMARK_GENOMEPREPARATION.out.index )

tests/software/bismark/report/main.nf

@@ -10,10 +10,10 @@ include { BISMARK_REPORT               } from '../../../../software/bismark/repo
 
 workflow test_bismark_report {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], 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)
 
     BISMARK_GENOMEPREPARATION ( fasta )
     BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )

tests/software/vcftools/main.nf

@@ -7,7 +7,7 @@ include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../software/vcftools/main.
 
 workflow test_vcftools_vcf_base {
     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)
             ]
 
     VCFTOOLS_BASE ( input, [], [] )
@@ -15,7 +15,7 @@ workflow test_vcftools_vcf_base {
 
 workflow test_vcftools_vcfgz_base {
     input = [ [ id:'test' ], // 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)
             ]
 
     VCFTOOLS_BASE ( input, [], [] )
@@ -23,18 +23,18 @@ workflow test_vcftools_vcfgz_base {
 
 workflow test_vcftools_vcf_optional {
     input = [ [ id:'test' ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) 
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
             ]
-    bed   = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
 
     VCFTOOLS_OPTIONAL ( input, bed, [] )
 }
 
 workflow test_vcftools_vcfgz_optional {
     input = [ [ id:'test' ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) 
+              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
             ]
-    bed   = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
 
     VCFTOOLS_OPTIONAL ( input, bed, [] )
 }