Revert recent changes made to some of the modules (#1463)

* revert changes to modules

* fix tests

* fix kraken2

* fix untar

* fix cat

* add blank lines

* fix typo

modules/cat/cat/main.nf

@@ -30,7 +30,7 @@ process CAT_CAT {
     // | ungzipped | gzipped    | cat      | pigz     |
 
     // Use input file ending as default
-    prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
+    prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
     out_zip  = prefix.endsWith('.gz')
     in_zip   = file_list[0].endsWith('.gz')
     command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'

modules/deepvariant/main.nf

@@ -46,7 +46,7 @@ process DEEPVARIANT {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vcf.gz
     touch ${prefix}.g.vcf.gz

modules/gatk4/createsequencedictionary/main.nf

@@ -39,9 +39,8 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.dict
+    touch test.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/manta/germline/main.nf

@@ -8,9 +8,10 @@ process MANTA_GERMLINE {
         'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
 
     input:
-    tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
+    tuple val(meta), path(input), path(index)
     path fasta
     path fasta_fai
+    tuple path(target_bed), path(target_bed_tbi)
 
 
     output:

modules/tiddit/cov/main.nf

@@ -40,8 +40,8 @@ process TIDDIT_COV {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch $prefix.wig
+    touch ${prefix}.wig
-    touch $prefix.tab
+    touch ${prefix}.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/tiddit/sv/main.nf

@@ -42,9 +42,9 @@ process TIDDIT_SV {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch $prefix.vcf
+    touch ${prefix}.vcf
-    touch $prefix.ploidy.tab
+    touch ${prefix}.ploidy.tab
-    touch $prefix.signals.tab
+    touch ${prefix}.signals.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/modules/manta/germline/main.nf

@@ -7,28 +7,30 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
 workflow test_manta_germline {
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
-        [],[]
     ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [[],[]]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }
 
 workflow test_manta_germline_target_bed {
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
     ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }
 
 workflow test_manta_germline_target_bed_jointcalling {
@@ -37,12 +39,14 @@ workflow test_manta_germline_target_bed_jointcalling {
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),]
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
     ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }