Fix more version commands (#750)

* Fix outstanding tests

* Fix more version commands

* Fix remaining modules

modules/bismark/summary/main.nf

@@ -35,7 +35,7 @@ process BISMARK_SUMMARY {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/chromap/chromap/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
 params.options = [:]
 options        = initOptions(params.options)
 
-def VERSION = 0.1 // No version information printed
+def VERSION = '0.1' // No version information printed
 
 process CHROMAP_CHROMAP {
     tag "$meta.id"

modules/graphmap2/align/main.nf

@@ -43,7 +43,7 @@ process GRAPHMAP2_ALIGN {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/graphmap2/index/main.nf

@@ -36,7 +36,7 @@ process GRAPHMAP2_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gunzip/main.nf

@@ -29,10 +29,14 @@ process GUNZIP {
     def software = getSoftwareName(task.process)
     gunzip       = archive.toString() - '.gz'
     """
-    gunzip -f $options.args $archive
+    gunzip \\
+        -f \\
+        $options.args \\
+        $archive
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gunzip --version 2>&1 | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/ivar/consensus/main.nf

@@ -44,7 +44,7 @@ process IVAR_CONSENSUS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/ivar/trim/main.nf

@@ -40,7 +40,7 @@ process IVAR_TRIM {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/ivar/variants/main.nf

@@ -47,7 +47,7 @@ process IVAR_VARIANTS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/kraken2/kraken2/main.nf

@@ -50,7 +50,7 @@ process KRAKEN2_KRAKEN2 {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(kraken2 --version 2>&1 | sed 's/^.*Kraken version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/lofreq/call/main.nf

@@ -39,7 +39,7 @@ process LOFREQ_CALL {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
     END_VERSIONS
     """
 }

modules/lofreq/callparallel/main.nf

@@ -41,7 +41,7 @@ process LOFREQ_CALLPARALLEL {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
     END_VERSIONS
     """
 }

modules/lofreq/filter/main.nf

@@ -37,7 +37,7 @@ process LOFREQ_FILTER {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
     END_VERSIONS
     """
 }

modules/lofreq/indelqual/main.nf

@@ -37,7 +37,7 @@ process LOFREQ_INDELQUAL {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^.*lofreq //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
     END_VERSIONS
     """
 }

modules/minia/main.nf

@@ -40,7 +40,7 @@ process MINIA {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(minia --version 2>&1 | sed 's/^.*Minia version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/preseq/lcextrap/main.nf

@@ -42,7 +42,7 @@ process PRESEQ_LCEXTRAP {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(preseq 2>&1 | sed 's/^.*Version: //; s/Usage:.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
     END_VERSIONS
     """
 }

modules/qualimap/bamqc/main.nf

@@ -58,7 +58,7 @@ process QUALIMAP_BAMQC {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(qualimap 2>&1 | sed 's/^.*QualiMap v.//; s/Built.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
     END_VERSIONS
     """
 }

modules/tabix/bgzip/main.nf

@@ -33,7 +33,7 @@ process TABIX_BGZIP {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/tabix/bgziptabix/main.nf

@@ -34,7 +34,7 @@ process TABIX_BGZIPTABIX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/tabix/tabix/main.nf

@@ -32,7 +32,7 @@ process TABIX_TABIX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/ucsc/wigtobigwig/main.nf

@@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
 params.options = [:]
 options        = initOptions(params.options)
 
+def VERSION = '377' // No version information printed
+
 process UCSC_WIGTOBIGWIG {
     tag '$wig'
     label 'process_medium'
@@ -38,7 +40,7 @@ process UCSC_WIGTOBIGWIG {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(wigToBigWig 2>&1 | sed 's/wigToBigWig v //; s/ - Convert.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo "$VERSION")
     END_VERSIONS
     """
 }

modules/untar/main.nf

@@ -22,17 +22,21 @@ process UNTAR {
     path archive
 
     output:
-    path "$untar"       , emit: untar
+    path "$untar"      , emit: untar
-    path "versions.yml" , emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)
     untar        = archive.toString() - '.tar.gz'
     """
-    tar -xzvf $options.args $archive
+    tar \\
+        -xzvf \\
+        $options.args \\
+        $archive
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(tar --version 2>&1 | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
     END_VERSIONS
     """
 }

modules/unzip/main.nf

@@ -40,7 +40,7 @@ process UNZIP {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        7za: \$( 7za --help) grep Version | sed 's/.*p7zip Version//; s/(.*//' )
+        7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
     END_VERSIONS
     """
 }

tests/modules/bwa/sampe/main.nf

@@ -3,18 +3,23 @@
 nextflow.enable.dsl = 2
 
 include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
-include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
+include { BWA_ALN   } from '../../../../modules/bwa/aln/main.nf'   addParams( options: [:] )
 include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
 
 workflow test_bwa_sampe {
 
-    input = [ [ id:'test', single_end:false ], // meta map
+    Channel
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        .fromList(
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            [
+                [ id:'test', single_end:false ],
+                [ [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
             ]
+        ).collect()
+        .set { input }
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWA_INDEX ( fasta )
     BWA_ALN ( input, BWA_INDEX.out.index )
-    BWA_SAMPE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
+    BWA_SAMPE ( input.join(BWA_ALN.out.sai), BWA_INDEX.out.index )
 }

tests/modules/bwa/samse/main.nf

@@ -3,17 +3,20 @@
 nextflow.enable.dsl = 2
 
 include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
-include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
+include { BWA_ALN   } from '../../../../modules/bwa/aln/main.nf'   addParams( options: [:] )
 include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf' addParams( options: [:] )
 
 workflow test_bwa_samse {
 
-    input = [ [ id:'test', single_end:true ], // meta map
+    Channel
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+        .fromList(
-            ]
+            [ [ id:'test', single_end:true ],
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+        ).collect()
+        .set { input }
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWA_INDEX ( fasta )
     BWA_ALN ( input, BWA_INDEX.out.index )
-    BWA_SAMSE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
+    BWA_SAMSE ( input.join(BWA_ALN.out.sai, by:[0]), BWA_INDEX.out.index )
 }

tests/modules/bwameth/align/main.nf

@@ -2,9 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { BWAMETH_INDEX                     } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:]                               )
+include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
-include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
+include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf' addParams( options: [:] )
-include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
 
 //
 // Test with single-end data
@@ -16,7 +15,7 @@ workflow test_bwameth_align_single_end {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWAMETH_INDEX ( fasta )
-    BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index )
+    BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
 }
 
 //
@@ -30,5 +29,5 @@ workflow test_bwameth_align_paired_end {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWAMETH_INDEX ( fasta )
-    BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index )
+    BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
 }

tests/modules/bwameth/align/test.yml

@@ -4,7 +4,7 @@
     - bwameth
     - bwameth/align
   files:
-    - path: output/test_single_end/test.bam
+    - path: output/bwameth/test.bam
 
 - name: bwameth align paired-end test workflow
   command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
@@ -12,5 +12,5 @@
     - bwameth
     - bwameth/align
   files:
-    - path: output/test_paired_end/test.bam
+    - path: output/bwameth/test.bam
 

tests/modules/genmap/index/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [:] )
+include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [publish_dir:'genmap'] )
 
 workflow test_genmap_index {
 

tests/modules/genmap/index/test.yml

@@ -4,45 +4,45 @@
     - genmap
     - genmap/index
   files:
-    - path: output/index/genmap/index.ids.concat
+    - path: output/genmap/genmap/index.ids.concat
       md5sum: da6caa25f62c5407ccdfbcce1fa92408
-    - path: output/index/genmap/index.ids.limits
+    - path: output/genmap/genmap/index.ids.limits
       md5sum: f82636c5da188aec131d3a809473eff1
-    - path: output/index/genmap/index.info.concat
+    - path: output/genmap/genmap/index.info.concat
       md5sum: 8ba5273aa9e58722bf45b9cc39fc6bfe
-    - path: output/index/genmap/index.info.limits
+    - path: output/genmap/genmap/index.info.limits
       md5sum: 3522f2811f4ddf04598809fc84a1459e
-    - path: output/index/genmap/index.lf.drp
+    - path: output/genmap/genmap/index.lf.drp
       md5sum: dd85d6a23af2c7adf2695658e3056c08
-    - path: output/index/genmap/index.lf.drp.sbl
+    - path: output/genmap/genmap/index.lf.drp.sbl
       md5sum: f1d3ff8443297732862df21dc4e57262
-    - path: output/index/genmap/index.lf.drs
+    - path: output/genmap/genmap/index.lf.drs
       md5sum: 93b885adfe0da089cdf634904fd59f71
-    - path: output/index/genmap/index.lf.drv
+    - path: output/genmap/genmap/index.lf.drv
       md5sum: e06b605496bd91b32afa3c4f56d934ac
-    - path: output/index/genmap/index.lf.drv.sbl
+    - path: output/genmap/genmap/index.lf.drv.sbl
       md5sum: 8dd6bb7329a71449b0a1b292b5999164
-    - path: output/index/genmap/index.lf.pst
+    - path: output/genmap/genmap/index.lf.pst
       md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/index/genmap/index.rev.lf.drp
+    - path: output/genmap/genmap/index.rev.lf.drp
       md5sum: 5d9107e3aeec0721553dd661d4365fef
-    - path: output/index/genmap/index.rev.lf.drp.sbl
+    - path: output/genmap/genmap/index.rev.lf.drp.sbl
       md5sum: f1d3ff8443297732862df21dc4e57262
-    - path: output/index/genmap/index.rev.lf.drs
+    - path: output/genmap/genmap/index.rev.lf.drs
       md5sum: 93b885adfe0da089cdf634904fd59f71
-    - path: output/index/genmap/index.rev.lf.drv
+    - path: output/genmap/genmap/index.rev.lf.drv
       md5sum: df7e795edc0a034577a9d2599fe8cfeb
-    - path: output/index/genmap/index.rev.lf.drv.sbl
+    - path: output/genmap/genmap/index.rev.lf.drv.sbl
       md5sum: 8dd6bb7329a71449b0a1b292b5999164
-    - path: output/index/genmap/index.rev.lf.pst
+    - path: output/genmap/genmap/index.rev.lf.pst
       md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/index/genmap/index.sa.ind
+    - path: output/genmap/genmap/index.sa.ind
       md5sum: e21e5c7ce887cc8e3d0fa44ab1019cab
-    - path: output/index/genmap/index.sa.len
+    - path: output/genmap/genmap/index.sa.len
       md5sum: 5dfc20cfe8ed9892451461a8d402f51c
-    - path: output/index/genmap/index.sa.val
+    - path: output/genmap/genmap/index.sa.val
       md5sum: 400ee7f2fe93b2000ae3a5da5e509730
-    - path: output/index/genmap/index.txt.concat
+    - path: output/genmap/genmap/index.txt.concat
       md5sum: b4303962e0c176107945f3405370e6ae
-    - path: output/index/genmap/index.txt.limits
+    - path: output/genmap/genmap/index.txt.limits
       md5sum: 4480a068db603e4c9a27bc4fa9ceaf14

tests/modules/ivar/trim/test.yml

@@ -5,4 +5,4 @@
     - ivar/trim
   files:
     - path: output/ivar/test.bam
-      md5sum: 8705d032b28a1c3dbfe78fa762a2132f
+      md5sum: 12cff17d43b1efdba8120a6bff5311e3

tests/modules/qualimap/bamqc/test.yml

@@ -6,7 +6,7 @@
   files:
     - path: ./output/qualimap/test/qualimapReport.html
     - path: ./output/qualimap/test/genome_results.txt
-      md5sum: 00ad697dbec5141428ac8d850c13e1c5
+      md5sum: 5ec87ea86ad734d512c8c76fe8eb37b1
     - path: ./output/qualimap/test/css/plus.png
       md5sum: 0125e6faa04e2cf0141a2d599d3bb220
     - path: ./output/qualimap/test/css/down-pressed.png

tests/modules/rsem/calculateexpression/main.nf

@@ -2,20 +2,21 @@
 
 nextflow.enable.dsl = 2
 
-include { RSEM_PREPAREREFERENCE }       from '../../../../modules/rsem/preparereference/main.nf'   addParams(options: [args: "--star"])
+include { RSEM_PREPAREREFERENCE    } from '../../../../modules/rsem/preparereference/main.nf'    addParams(options: [args: "--star"])
-include { RSEM_CALCULATEEXPRESSION }    from '../../../../modules/rsem/calculateexpression/main.nf'   addParams(options: [args: "--star --star-gzipped-read-file"])
+include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
 
 workflow test_rsem_calculateexpression {
 
+    input = [
+        [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
-    input = [ [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
-                [file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)]
-            ]
-
     RSEM_PREPAREREFERENCE ( fasta, gtf )
-
     RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
 }

tests/modules/rsem/preparereference/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { RSEM_PREPAREREFERENCE }   from '../../../../modules/rsem/preparereference/main.nf'   addParams(options: [:])
+include { RSEM_PREPAREREFERENCE }   from '../../../../modules/rsem/preparereference/main.nf'   addParams(options: [publish_dir:'rsem'])
 
 workflow test_rsem_preparereference {
 

tests/modules/rsem/preparereference/test.yml

@@ -4,19 +4,19 @@
     - rsem
     - rsem/preparereference
   files:
-    - path: output/index/rsem/genome.chrlist
+    - path: output/rsem/rsem/genome.chrlist
       md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/index/rsem/genome.fasta
+    - path: output/rsem/rsem/genome.fasta
       md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/index/rsem/genome.grp
+    - path: output/rsem/rsem/genome.grp
       md5sum: c2848a8b6d495956c11ec53efc1de67e
-    - path: output/index/rsem/genome.idx.fa
+    - path: output/rsem/rsem/genome.idx.fa
       md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/index/rsem/genome.n2g.idx.fa
+    - path: output/rsem/rsem/genome.n2g.idx.fa
       md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/index/rsem/genome.seq
+    - path: output/rsem/rsem/genome.seq
       md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
-    - path: output/index/rsem/genome.ti
+    - path: output/rsem/rsem/genome.ti
       md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
-    - path: output/index/rsem/genome.transcripts.fa
+    - path: output/rsem/rsem/genome.transcripts.fa
       md5sum: 050c521a2719c2ae48267c1e65218f29

tests/modules/star/genomegenerate/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [:] )
+include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [publish_dir:'star'] )
 
 workflow test_star_genomegenerate {
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/star/genomegenerate/test.yml

@@ -4,34 +4,34 @@
     - star/genomegenerate
     - star
   files:
-    - path: output/index/star/Genome
+    - path: output/star/star/Genome
       md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/index/star/Log.out
+    - path: output/star/star/Log.out
-    - path: output/index/star/SA
+    - path: output/star/star/SA
       md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/index/star/SAindex
+    - path: output/star/star/SAindex
       md5sum: d0fbf2789ee1e9f60c352ba3655d9de4
-    - path: output/index/star/chrLength.txt
+    - path: output/star/star/chrLength.txt
       md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/index/star/chrName.txt
+    - path: output/star/star/chrName.txt
       md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/index/star/chrNameLength.txt
+    - path: output/star/star/chrNameLength.txt
       md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/index/star/chrStart.txt
+    - path: output/star/star/chrStart.txt
       md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/index/star/exonGeTrInfo.tab
+    - path: output/star/star/exonGeTrInfo.tab
       md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/index/star/exonInfo.tab
+    - path: output/star/star/exonInfo.tab
       md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/index/star/geneInfo.tab
+    - path: output/star/star/geneInfo.tab
       md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/index/star/genomeParameters.txt
+    - path: output/star/star/genomeParameters.txt
       md5sum: 5a1ec027e575c3d7c1851e6b80fb8c5d
-    - path: output/index/star/sjdbInfo.txt
+    - path: output/star/star/sjdbInfo.txt
       md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/index/star/sjdbList.fromGTF.out.tab
+    - path: output/star/star/sjdbList.fromGTF.out.tab
       md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/index/star/sjdbList.out.tab
+    - path: output/star/star/sjdbList.out.tab
       md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/index/star/transcriptInfo.tab
+    - path: output/star/star/transcriptInfo.tab
       md5sum: 0c3a5adb49d15e5feff81db8e29f2e36

tests/modules/stringtie/merge/main.nf

@@ -2,37 +2,45 @@
 
 nextflow.enable.dsl = 2
 
-include { STRINGTIE as STRINGTIE_FORWARD            } from '../../../../modules/stringtie/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_forward' ] )
+include { STRINGTIE       } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
-include { STRINGTIE as STRINGTIE_REVERSE            } from '../../../../modules/stringtie/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
+include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'     addParams( options: [:] )
-include { STRINGTIE_MERGE as STRINGTIE_FORWARD_MERGE} from '../../../../modules/stringtie/merge/main.nf'      addParams( options: [ publish_dir:'test_stringtie_forward_merge'] )
+
-include { STRINGTIE_MERGE as STRINGTIE_REVERSE_MERGE} from '../../../../modules/stringtie/merge/main.nf'      addParams( options: [ publish_dir:'test_stringtie_reverse_merge'] )
 /*
  * Test with forward strandedness
  */
 workflow test_stringtie_forward_merge {
-    input = [ [ id:'test', strandedness:'forward' ], // meta map
+    input = [
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
+        [ id:'test', strandedness:'forward' ], // meta map
-    annotation_gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    
+    ]
-    STRINGTIE_FORWARD ( input, annotation_gtf )
+    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    STRINGTIE_FORWARD.out.transcript_gtf
+
-       .map { it -> it[1] }
+    STRINGTIE ( input, annotation_gtf )
-       .set { stringtie_gtf }
+    STRINGTIE
-    STRINGTIE_FORWARD_MERGE ( stringtie_gtf, annotation_gtf )
+        .out
+        .transcript_gtf
+        .map { it -> it[1] }
+        .set { stringtie_gtf }
+
+    STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
 }
 
 /*
  * Test with reverse strandedness
  */
 workflow test_stringtie_reverse_merge {
-    input = [ [ id:'test', strandedness:'reverse' ], // meta map
+    input = [
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
+        [ id:'test', strandedness:'reverse' ], // meta map
-            ]
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    annotation_gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    ]
-    
+    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    STRINGTIE_REVERSE ( input, annotation_gtf )
+
-    STRINGTIE_REVERSE.out.transcript_gtf
+    STRINGTIE ( input, annotation_gtf )
-       .map { it -> it[1] }
+    STRINGTIE
-       .set { stringtie_gtf }
+        .out
-    STRINGTIE_REVERSE_MERGE ( stringtie_gtf, annotation_gtf )
+        .transcript_gtf
+        .map { it -> it[1] }
+        .set { stringtie_gtf }
+
+    STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
 }

tests/modules/stringtie/merge/test.yml

@@ -1,22 +1,22 @@
-- name: stringtie forward-strand merge
+- name: stringtie merge forward-strand
   command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_forward_merge -c tests/config/nextflow.config
   tags:
     - stringtie
     - stringtie/merge
   files:
-    - path: ./output/test_stringtie_forward_merge/stringtie.merged.gtf
+    - path: ./output/stringtie/stringtie.merged.gtf
       contains:
       - 'stringtie'
       - 'merge'
       - 'chr22'
 
-- name: stringtie reverse-strand merge
+- name: stringtie merge reverse-strand
   command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
   tags:
     - stringtie
     - stringtie/merge
   files:
-    - path: ./output/test_stringtie_reverse_merge/stringtie.merged.gtf
+    - path: ./output/stringtie/stringtie.merged.gtf
       contains:
       - 'stringtie'
       - 'merge'

tests/modules/stringtie/stringtie/main.nf

@@ -2,27 +2,29 @@
 
 nextflow.enable.dsl = 2
 
-include { STRINGTIE as STRINGTIE_FORWARD            } from '../../../../modules/stringtie/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_forward' ] )
+include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
-include { STRINGTIE as STRINGTIE_REVERSE            } from '../../../../modules/stringtie/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
-
 //
 // Test with forward strandedness
 //
 workflow test_stringtie_forward {
-    input = [ [ id:'test', strandedness:'forward' ], // meta map
+    input = [
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
+        [ id:'test', strandedness:'forward' ], // meta map
-    annotation_gtf   = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE_FORWARD ( input, annotation_gtf )
+    STRINGTIE ( input, annotation_gtf )
 }
 
 //
 // Test with reverse strandedness
 //
 workflow test_stringtie_reverse {
-    input = [ [ id:'test', strandedness:'reverse' ], // meta map
+    input = [
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
+        [ id:'test', strandedness:'reverse' ], // meta map
-    annotation_gtf   = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE_REVERSE ( input, annotation_gtf )
+    STRINGTIE ( input, annotation_gtf )
 }

tests/modules/stringtie/stringtie/test.yml

@@ -1,43 +1,43 @@
-- name: test_stringtie_forward
+- name: stringtie stringtie forward
   command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
   tags:
     - stringtie
     - stringtie/stringtie
   files:
-    - path: ./output/test_stringtie_forward/test.transcripts.gtf
+    - path: ./output/stringtie/test.transcripts.gtf
-    - path: ./output/test_stringtie_forward/test.gene.abundance.txt
+    - path: ./output/stringtie/test.gene.abundance.txt
       md5sum: 7d8bce7f2a922e367cedccae7267c22e
-    - path: ./output/test_stringtie_forward/test.coverage.gtf
+    - path: ./output/stringtie/test.coverage.gtf
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: ./output/test_stringtie_forward/test.ballgown/e_data.ctab
+    - path: ./output/stringtie/test.ballgown/e_data.ctab
       md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
-    - path: ./output/test_stringtie_forward/test.ballgown/i_data.ctab
+    - path: ./output/stringtie/test.ballgown/i_data.ctab
       md5sum: be3abe09740603213f83d50dcf81427f
-    - path: ./output/test_stringtie_forward/test.ballgown/t_data.ctab
+    - path: ./output/stringtie/test.ballgown/t_data.ctab
       md5sum: 3b66c065da73ae0dd41cc332eff6a818
-    - path: ./output/test_stringtie_forward/test.ballgown/i2t.ctab
+    - path: ./output/stringtie/test.ballgown/i2t.ctab
       md5sum: 8a117c8aa4334b4c2d4711932b006fb4
-    - path: ./output/test_stringtie_forward/test.ballgown/e2t.ctab
+    - path: ./output/stringtie/test.ballgown/e2t.ctab
       md5sum: e981c0038295ae54b63cedb1083f1540
 
-- name: test_stringtie_reverse
+- name: stringtie stringtie reverse
   command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
   tags:
     - stringtie
     - stringtie/stringtie
   files:
-    - path: ./output/test_stringtie_reverse/test.transcripts.gtf
+    - path: ./output/stringtie/test.transcripts.gtf
-    - path: ./output/test_stringtie_reverse/test.gene.abundance.txt
+    - path: ./output/stringtie/test.gene.abundance.txt
       md5sum: 7385b870b955dae2c2ab78a70cf05cce
-    - path: ./output/test_stringtie_reverse/test.coverage.gtf
+    - path: ./output/stringtie/test.coverage.gtf
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: ./output/test_stringtie_reverse/test.ballgown/e_data.ctab
+    - path: ./output/stringtie/test.ballgown/e_data.ctab
       md5sum: 879b6696029d19c4737b562e9d149218
-    - path: ./output/test_stringtie_reverse/test.ballgown/i_data.ctab
+    - path: ./output/stringtie/test.ballgown/i_data.ctab
       md5sum: be3abe09740603213f83d50dcf81427f
-    - path: ./output/test_stringtie_reverse/test.ballgown/t_data.ctab
+    - path: ./output/stringtie/test.ballgown/t_data.ctab
       md5sum: 3b66c065da73ae0dd41cc332eff6a818
-    - path: ./output/test_stringtie_reverse/test.ballgown/i2t.ctab
+    - path: ./output/stringtie/test.ballgown/i2t.ctab
       md5sum: 8a117c8aa4334b4c2d4711932b006fb4
-    - path: ./output/test_stringtie_reverse/test.ballgown/e2t.ctab
+    - path: ./output/stringtie/test.ballgown/e2t.ctab
       md5sum: e981c0038295ae54b63cedb1083f1540