Fix 459 (#534)

* Update test data names.

Closes: #459

Thanks: @FriederikeHanssen

(`samtools` tests are already fixed by another commit)

* Fix file names in tests.

The update of test data name required changes in the test yml files.

I also updated the `bismark/summary/main.nf` file to get its data
from the `params.test_data` map.

tests/software/bismark/align/test.yml

@@ -4,9 +4,9 @@
     - bismark
     - bismark/align
   files:
-    - path: output/test_single_end/test_methylated_1_bismark_bt2.bam
-      md5sum: 7f9744cec5aa7908675e5fae79af36fc
-    - path: output/test_single_end/test_methylated_1_bismark_bt2_SE_report.txt
+    - path: output/test_single_end/test.methylated_1_bismark_bt2.bam
+      md5sum: dca4ba9ff705b70446f812e59bdb1a32
+    - path: output/test_single_end/test.methylated_1_bismark_bt2_SE_report.txt
 
 - name: Run bismark align paired-end test workflow
   command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
@@ -14,6 +14,6 @@
     - bismark
     - bismark/align
   files:
-    - path: output/test_paired_end/test_methylated_1_bismark_bt2_pe.bam
-      md5sum: b13d0d40dffd336375f80fc94acc295f
-    - path: output/test_paired_end/test_methylated_1_bismark_bt2_PE_report.txt
+    - path: output/test_paired_end/test.methylated_1_bismark_bt2_pe.bam
+      md5sum: 43943b1f30d056fcbd9ed26061ea0583
+    - path: output/test_paired_end/test.methylated_1_bismark_bt2_PE_report.txt

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(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
             ]
 
     BISMARK_DEDUPLICATE ( input )

tests/software/bismark/deduplicate/test.yml

@@ -4,6 +4,7 @@
     - bismark
     - bismark/deduplicate
   files:
-    - path: output/bismark/test_methylated_paired_end.deduplicated.bam
-    - path: output/bismark/test_methylated_paired_end.deduplication_report.txt
-      md5sum: 3876d694f10c58f47e380ba8476a356b
+    - path: output/bismark/test.paired_end.methylated.deduplicated.bam
+      md5sum: 82213a207048bcb5d8cc1cee92703a29
+    - path: output/bismark/test.paired_end.methylated.deduplication_report.txt
+      md5sum: 86aaf87bac9ccdc3cc83628f20b902dc

tests/software/bismark/methylationextractor/main.nf

@@ -7,7 +7,7 @@ include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/meth
 
 workflow test_bismark_methylationextractor {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 

tests/software/bismark/methylationextractor/test.yml

@@ -4,15 +4,13 @@
     - bismark
     - bismark/methylationextractor
   files:
-    - path: output/bismark/CHG_OB_test_methylated_paired_end.txt.gz
-    - path: output/bismark/CHG_OT_test_methylated_paired_end.txt.gz
-    - path: output/bismark/CHH_OB_test_methylated_paired_end.txt.gz
-    - path: output/bismark/CHH_OT_test_methylated_paired_end.txt.gz
-    - path: output/bismark/CpG_OB_test_methylated_paired_end.txt.gz
-    - path: output/bismark/CpG_OT_test_methylated_paired_end.txt.gz
-    - path: output/bismark/test_methylated_paired_end.bedGraph.gz
-    - path: output/bismark/test_methylated_paired_end.bismark.cov.gz
-    - path: output/bismark/test_methylated_paired_end.M-bias.txt
+    - path: output/bismark/CHG_OB_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CHG_OT_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CHH_OB_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CHH_OT_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CpG_OB_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CpG_OT_test.paired_end.methylated.txt.gz
+    - path: output/bismark/test.paired_end.methylated.M-bias.txt
       md5sum: 0b100924d46b3c35115f1206f34c4a59
-    - path: output/bismark/test_methylated_paired_end_splitting_report.txt
-      md5sum: 288d6f0110127e3a8c10391802118202
+    - path: output/bismark/test.paired_end.methylated_splitting_report.txt
+      md5sum: f28a9dd8de8c42b8900b190b8f79647a

tests/software/bismark/report/test.yml

@@ -4,5 +4,5 @@
     - bismark
     - bismark/report
   files:
-    - path: output/bismark/test_methylated_1_bismark_bt2_PE_report.txt
-    - path: output/bismark/test_methylated_1_bismark_bt2_PE_report.html
+    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.html
+    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt

tests/software/bismark/summary/main.nf

@@ -10,10 +10,10 @@ include { BISMARK_SUMMARY              } from '../../../../software/bismark/summ
 
 workflow test_bismark_summary {
     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/bismark/summary/test.yml

@@ -6,4 +6,4 @@
   files:
     - path: output/bismark/bismark_summary_report.html
     - path: output/bismark/bismark_summary_report.txt
-      md5sum: 06fc717e81b3f8f0d6e279d572f407f6
+      md5sum: fdfadd5399c4e7b2108da100e72036eb

tests/software/methyldackel/extract/main.nf

@@ -6,8 +6,8 @@ include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract
 
 workflow test_methyldackel_extract {
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 

tests/software/methyldackel/extract/test.yml

@@ -4,5 +4,5 @@
     - methyldackel
     - methyldackel/extract
   files:
-    - path: output/methyldackel/test_methylated_paired_end.sorted_CpG.bedGraph
-      md5sum: d7c637e2ef20de401fc610206f6bf6b7
+    - path: output/methyldackel/test.paired_end.methylated.sorted_CpG.bedGraph
+      md5sum: abcc9d1db6e48d5aced567c337b563d4

tests/software/methyldackel/mbias/main.nf

@@ -6,8 +6,8 @@ include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/mai
 
 workflow test_methyldackel_mbias {
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 

tests/software/msisensor/msi/main.nf

@@ -20,8 +20,8 @@ workflow test_msisensor_msi {
     def input      = []
 
     input = Channel.from([ [ id:'test', single_end:false ], // meta map
-               file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'],     checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam_bai'], checkIfExists: true),
+               file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'],     checkIfExists: true),
+               file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_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) ])
     //scan.txt.view()