Fix some module tests after switching to config data (#386)

* Adding tar.gz kraken2 db to test data

* Update test path files for untar module

* Update test path files for kraken2/run module

* Update test path files for cat/fastq module

tests/config/test_data.config

@@ -21,6 +21,7 @@ params {
                 baits_bed                                 = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
 
                 kraken2                                   = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
+                kraken2_tar_gz                            = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
             }
             'illumina' {
                 test_single_end_bam                       = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"

tests/software/cat/fastq/main.nf

@@ -6,8 +6,8 @@ include { CAT_FASTQ } from '../../../../software/cat/fastq/main.nf' addParams( o
 
 workflow test_cat_fastq_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
             ]
 
     CAT_FASTQ ( input )
@@ -15,10 +15,10 @@ workflow test_cat_fastq_single_end {
 
 workflow test_cat_fastq_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("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_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),
+                file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
             ]
 
     CAT_FASTQ ( input )

tests/software/kraken2/run/main.nf

@@ -6,19 +6,19 @@ include { KRAKEN2_RUN } from '../../../../software/kraken2/run/main.nf' addParam
 
 workflow test_kraken2_run_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    db    = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/db/kraken2", checkIfExists: true) ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
 
     KRAKEN2_RUN ( input, db )
 }
 
 workflow test_kraken2_run_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) ]
             ]
-    db    = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/db/kraken2", checkIfExists: true) ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
 
     KRAKEN2_RUN ( input, db )
 }

tests/software/kraken2/run/test.yml

@@ -28,4 +28,4 @@
     - path: output/kraken2/test.unclassified_2.fastq.gz
       should_exist: true
     - path: output/kraken2/test.kraken2.report.txt
-      md5sum: 5fb165fd0bdf920ff6cf6f734371a4cf
+      md5sum: 4227755fe40478b8d7dc8634b489761e

tests/software/untar/main.nf

@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { UNTAR } from '../../../software/untar/main.nf' addParams( options: [:] )
 
 workflow test_untar {
-    input = file("${launchDir}/tests/data/generic/test.txt.tar.gz", checkIfExists: true)
+    input = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
 
     UNTAR ( input )
 }

tests/software/untar/test.yml

@@ -3,5 +3,9 @@
   tags:
     - untar
   files:
-    - path: output/untar/test.txt
-      md5sum: 7171d4ec2ad0882fab4b0142536d93a1
+    - path: output/untar/kraken2/hash.k2d
+      md5sum: 8b8598468f54a7087c203ad0190555d9
+    - path: output/untar/kraken2/opts.k2d
+      md5sum: a033d00cf6759407010b21700938f543
+    - path: output/untar/kraken2/taxo.k2d
+      md5sum: 094d5891cdccf2f1468088855c214b2c