Fix version commands (#749)

* Fix version commands

* Fix version commands: again

modules/abacas/main.nf

@@ -42,7 +42,7 @@ process ABACAS {
     mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(abacas.pl -v 2>&1 | sed 's/^.*ABACAS.//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/agrvate/main.nf

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

modules/bandage/image/main.nf

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

modules/bismark/align/main.nf

@@ -41,7 +41,7 @@ process BISMARK_ALIGN {
 
     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/bismark/deduplicate/main.nf

@@ -38,7 +38,7 @@ process BISMARK_DEDUPLICATE {
 
     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/bismark/genomepreparation/main.nf

@@ -34,7 +34,7 @@ process BISMARK_GENOMEPREPARATION {
 
     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/bismark/methylationextractor/main.nf

@@ -45,7 +45,7 @@ process BISMARK_METHYLATIONEXTRACTOR {
 
     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/bismark/report/main.nf

@@ -32,7 +32,7 @@ process BISMARK_REPORT {
 
     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/bowtie/align/main.nf

@@ -57,7 +57,7 @@ process BOWTIE_ALIGN {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bowtie --version 2>&1 | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bowtie/build/main.nf

@@ -32,7 +32,7 @@ process BOWTIE_BUILD {
     bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bowtie --version 2>&1 | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bowtie2/align/main.nf

@@ -39,7 +39,7 @@ process BOWTIE2_ALIGN {
         bowtie2 \\
             -x \$INDEX \\
             -U $reads \\
-            --threads ${split_cpus} \\
+            --threads $split_cpus \\
             $unaligned \\
             $options.args \\
             2> ${prefix}.bowtie2.log \\
@@ -47,7 +47,7 @@ process BOWTIE2_ALIGN {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
         END_VERSIONS
         """
     } else {
@@ -58,7 +58,7 @@ process BOWTIE2_ALIGN {
             -x \$INDEX \\
             -1 ${reads[0]} \\
             -2 ${reads[1]} \\
-            --threads ${split_cpus} \\
+            --threads $split_cpus \\
             $unaligned \\
             $options.args \\
             2> ${prefix}.bowtie2.log \\
@@ -72,7 +72,7 @@ process BOWTIE2_ALIGN {
         fi
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
         END_VERSIONS
         """
     }

modules/bowtie2/build/main.nf

@@ -32,7 +32,7 @@ process BOWTIE2_BUILD {
     bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/bwa/aln/main.nf

@@ -24,7 +24,7 @@ process BWA_ALN {
 
     output:
     tuple val(meta), path("*.sai"), emit: sai
-    path "versions.yml"                        , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -43,7 +43,7 @@ process BWA_ALN {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
         END_VERSIONS
         """
     } else {
@@ -66,7 +66,7 @@ process BWA_ALN {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
         END_VERSIONS
         """
     }

modules/bwa/index/main.nf

@@ -22,17 +22,22 @@ process BWA_INDEX {
     path fasta
 
     output:
-    path "bwa"          , emit: index
+    path "bwa"         , emit: index
-    path "versions.yml" , emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
     mkdir bwa
-    bwa index $options.args $fasta -p bwa/${fasta.baseName}
+    bwa \\
+        index \\
+        $options.args \\
+        $fasta \\
+        -p bwa/${fasta.baseName}
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
     END_VERSIONS
     """
 }

modules/bwa/mem/main.nf

@@ -37,14 +37,14 @@ process BWA_MEM {
     bwa mem \\
         $options.args \\
         $read_group \\
-        -t ${split_cpus} \\
+        -t $split_cpus \\
         \$INDEX \\
         $reads \\
         | samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
     END_VERSIONS
     """
 }

modules/bwa/sampe/main.nf

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

modules/bwa/samse/main.nf

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

modules/bwamem2/index/main.nf

@@ -29,10 +29,14 @@ process BWAMEM2_INDEX {
     def software = getSoftwareName(task.process)
     """
     mkdir bwamem2
-    bwa-mem2 index $options.args $fasta -p bwamem2/${fasta}
+    bwa-mem2 \\
+        index \\
+        $options.args \\
+        $fasta -p bwamem2/${fasta}
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bwa-mem2 version 2>&1)
+        ${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
     END_VERSIONS
     """
 }

modules/bwamem2/mem/main.nf

@@ -34,17 +34,18 @@ process BWAMEM2_MEM {
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
 
-    bwa-mem2 mem \\
+    bwa-mem2 \\
+        mem \\
         $options.args \\
         $read_group \\
-        -t ${split_cpus} \\
+        -t $split_cpus \\
         \$INDEX \\
         $reads \\
         | samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bwa-mem2 version 2>&1)
+        ${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
     END_VERSIONS
     """
 }

modules/bwameth/align/main.nf

@@ -44,7 +44,7 @@ process BWAMETH_ALIGN {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bwameth.py --version 2>&1 | cut -f2 -d" ")
+        ${getSoftwareName(task.process)}: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
     END_VERSIONS
     """
 }

modules/bwameth/index/main.nf

@@ -32,7 +32,7 @@ process BWAMETH_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bwameth.py --version 2>&1 | cut -f2 -d" ")
+        ${getSoftwareName(task.process)}: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
     END_VERSIONS
     """
 }

modules/chromap/chromap/main.nf

@@ -75,11 +75,13 @@ process CHROMAP_CHROMAP {
             -1 ${reads.join(',')} \\
             -o ${prefix}.${file_extension}
 
+        $compression_cmds
+
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(echo "$VERSION")
         END_VERSIONS
-        """ + compression_cmds
+        """
     } else {
         """
         chromap ${args.join(' ')} \\
@@ -90,10 +92,12 @@ process CHROMAP_CHROMAP {
             -2 ${reads[1]} \\
             -o ${prefix}.${file_extension}
 
+        $compression_cmds
+
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(echo "$VERSION")
         END_VERSIONS
-        """ + compression_cmds
+        """
     }
 }

modules/chromap/index/main.nf

@@ -35,6 +35,7 @@ process CHROMAP_INDEX {
         -t $task.cpus \\
         -r $fasta \\
         -o ${prefix}.index
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo "$VERSION")

modules/gatk4/applybqsr/main.nf

@@ -44,7 +44,7 @@ process GATK4_APPLYBQSR {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/baserecalibrator/main.nf

@@ -47,7 +47,7 @@ process GATK4_BASERECALIBRATOR {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/bedtointervallist/main.nf

@@ -38,7 +38,7 @@ process GATK4_BEDTOINTERVALLIST {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/createsequencedictionary/main.nf

@@ -42,7 +42,7 @@ process GATK4_CREATESEQUENCEDICTIONARY {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/fastqtosam/main.nf

@@ -38,7 +38,7 @@ process GATK4_FASTQTOSAM {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/getpileupsummaries/main.nf

@@ -45,7 +45,7 @@ process GATK4_GETPILEUPSUMMARIES {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/haplotypecaller/main.nf

@@ -49,7 +49,7 @@ process GATK4_HAPLOTYPECALLER {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/intervallisttools/main.nf

@@ -50,7 +50,7 @@ process GATK4_INTERVALLISTTOOLS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/markduplicates/main.nf

@@ -41,7 +41,7 @@ process GATK4_MARKDUPLICATES {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/mergebamalignment/main.nf

@@ -41,7 +41,7 @@ process GATK4_MERGEBAMALIGNMENT {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/mergevcfs/main.nf

@@ -46,7 +46,7 @@ process GATK4_MERGEVCFS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/mutect2/main.nf

@@ -74,7 +74,7 @@ process GATK4_MUTECT2 {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/revertsam/main.nf

@@ -36,7 +36,7 @@ process GATK4_REVERTSAM {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/samtofastq/main.nf

@@ -37,7 +37,7 @@ process GATK4_SAMTOFASTQ {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/splitncigarreads/main.nf

@@ -38,7 +38,7 @@ process GATK4_SPLITNCIGARREADS {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/gatk4/variantfiltration/main.nf

@@ -41,7 +41,7 @@ process GATK4_VARIANTFILTRATION {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/salmon/index/main.nf

@@ -48,7 +48,7 @@ process SALMON_INDEX {
         -i salmon
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g")
+        ${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
     END_VERSIONS
     """
 }

modules/salmon/quant/main.nf

@@ -74,7 +74,7 @@ process SALMON_QUANT {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g")
+        ${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
     END_VERSIONS
     """
 }

modules/samtools/ampliconclip/main.nf

@@ -48,7 +48,7 @@ process SAMTOOLS_AMPLICONCLIP {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/faidx/main.nf

@@ -31,7 +31,7 @@ process SAMTOOLS_FAIDX {
     samtools faidx $fasta
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/fastq/main.nf

@@ -38,7 +38,7 @@ process SAMTOOLS_FASTQ {
         $bam
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/flagstat/main.nf

@@ -31,7 +31,7 @@ process SAMTOOLS_FLAGSTAT {
     samtools flagstat $bam > ${bam}.flagstat
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/idxstats/main.nf

@@ -31,7 +31,7 @@ process SAMTOOLS_IDXSTATS {
     samtools idxstats $bam > ${bam}.idxstats
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/index/main.nf

@@ -32,7 +32,7 @@ process SAMTOOLS_INDEX {
     samtools index $options.args $bam
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/merge/main.nf

@@ -32,7 +32,7 @@ process SAMTOOLS_MERGE {
     samtools merge ${prefix}.bam $bams
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/mpileup/main.nf

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

modules/samtools/sort/main.nf

@@ -32,7 +32,7 @@ process SAMTOOLS_SORT {
     samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/stats/main.nf

@@ -31,7 +31,7 @@ process SAMTOOLS_STATS {
     samtools stats $bam > ${bam}.stats
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/samtools/view/main.nf

@@ -32,7 +32,7 @@ process SAMTOOLS_VIEW {
     samtools view $options.args $bam > ${prefix}.bam
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/trimgalore/main.nf

@@ -62,7 +62,8 @@ process TRIMGALORE {
             ${prefix}.fastq.gz
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(trim_galore --version 2>&1 | sed 's/^.*version //; s/Last.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
+            cutadapt: \$(cutadapt --version)
         END_VERSIONS
         """
     } else {
@@ -82,7 +83,8 @@ process TRIMGALORE {
             ${prefix}_2.fastq.gz
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(trim_galore --version 2>&1 | sed 's/^.*version //; s/Last.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
+            cutadapt: \$(cutadapt --version)
         END_VERSIONS
         """
     }

tests/modules/bandage/image/main.nf

@@ -5,10 +5,10 @@ nextflow.enable.dsl = 2
 include { BANDAGE_IMAGE } from '../../../../modules/bandage/image/main.nf' addParams( options: [:] )
 
 workflow test_bandage_image {
-    input = [ [ id:'B-3106' ], // meta map
+    input = [
-              [ file("${launchDir}/tests/data/generic/gfa/B-3106.gfa", checkIfExists: true) ]
+        [ id:'B-3106' ], // meta map
-              //[ file("${launchDir}/tests/data/genomics/sarscov2/genome/gfa/test.gfa", checkIfExists: true) ]
+        file( params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)
-            ]
+    ]
 
     BANDAGE_IMAGE ( input )
 }

tests/modules/bbmap/align/main.nf

@@ -7,11 +7,11 @@ include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf' addParams
 include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf' addParams( options: [args: "unpigz=t" ] )
 
 workflow test_bbmap_align_paired_end_fasta_ref {
-    
+
     input = [ [ id:'test', single_end:false ], // meta map
                 [
                     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']['test_2_fastq_gz'], checkIfExists: true)
                 ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@@ -20,11 +20,11 @@ workflow test_bbmap_align_paired_end_fasta_ref {
 }
 
 workflow test_bbmap_align_paired_end_index_ref {
-    
+
     input = [ [ id:'test', single_end:false ], // meta map
                 [
                     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']['test_2_fastq_gz'], checkIfExists: true)
                 ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@@ -34,7 +34,7 @@ workflow test_bbmap_align_paired_end_index_ref {
 }
 
 workflow test_bbmap_align_single_end_index_ref {
-    
+
     input = [ [ id:'test', single_end:true ], // meta map
                 file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
             ]
@@ -45,11 +45,11 @@ workflow test_bbmap_align_single_end_index_ref {
 }
 
 workflow test_bbmap_align_paired_end_index_ref_pigz {
-    
+
     input = [ [ id:'test', single_end:false ], // meta map
                 [
                     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']['test_2_fastq_gz'], checkIfExists: true)
                 ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/bismark/align/test.yml

@@ -1,4 +1,4 @@
-- name: Run bismark align single-end test workflow
+- name: bismark align single-end test workflow
   command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
   tags:
     - bismark
@@ -8,7 +8,7 @@
       md5sum: dca4ba9ff705b70446f812e59bdb1a32
     - path: output/test_single_end/test.methylated_1_bismark_bt2_SE_report.txt
 
-- name: Run bismark align paired-end test workflow
+- name: bismark align paired-end test workflow
   command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
   tags:
     - bismark

tests/modules/bismark/deduplicate/test.yml

@@ -1,4 +1,4 @@
-- name: Run bismark deduplicate test workflow
+- name: bismark deduplicate test workflow
   command: nextflow run ./tests/modules/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
   tags:
     - bismark

tests/modules/bismark/genomepreparation/test.yml

@@ -1,4 +1,4 @@
-- name: Run bismark_genomepreparation test workflow
+- name: bismark genomepreparation test workflow
   command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
   tags:
     - bismark

tests/modules/bismark/methylationextractor/test.yml

@@ -1,4 +1,4 @@
-- name: Run bismark methylation extractor test workflow
+- name: bismark methylation extractor test workflow
   command: nextflow run ./tests/modules/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
   tags:
     - bismark

tests/modules/bismark/report/test.yml

@@ -1,4 +1,4 @@
-- name: Run bismark report test workflow
+- name: bismark report test workflow
   command: nextflow run ./tests/modules/bismark/report -entry test_bismark_report -c tests/config/nextflow.config
   tags:
     - bismark

tests/modules/bismark/summary/test.yml

@@ -1,4 +1,4 @@
-- name: Run bismark summary test workflow
+- name: bismark summary test workflow
   command: nextflow run ./tests/modules/bismark/summary -entry test_bismark_summary -c tests/config/nextflow.config
   tags:
     - bismark

tests/modules/bowtie/build_test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' addParams( options: [:] )
+include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' addParams( options: [publish_dir:'bowtie'] )
 
 workflow test_bowtie_build {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/bowtie/build_test/test.yml

@@ -4,15 +4,15 @@
     - bowtie
     - bowtie/build
   files:
-    - path: ./output/index/bowtie/genome.3.ebwt
+    - path: ./output/bowtie/bowtie/genome.3.ebwt
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/index/bowtie/genome.2.ebwt
+    - path: ./output/bowtie/bowtie/genome.2.ebwt
       md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/index/bowtie/genome.rev.2.ebwt
+    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
       md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/index/bowtie/genome.4.ebwt
+    - path: ./output/bowtie/bowtie/genome.4.ebwt
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/index/bowtie/genome.rev.1.ebwt
+    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
       md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/index/bowtie/genome.1.ebwt
+    - path: ./output/bowtie/bowtie/genome.1.ebwt
       md5sum: d9b76ecf9fd0413240173273b38d8199

tests/modules/bowtie2/build_test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [:] )
+include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [publish_dir:'bowtie2'] )
 
 workflow test_bowtie2_build {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/bowtie2/build_test/test.yml

@@ -4,15 +4,15 @@
     - bowtie2
     - bowtie2/build
   files:
-    - path: ./output/index/bowtie2/genome.3.bt2
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/index/bowtie2/genome.2.bt2
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2
       md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/index/bowtie2/genome.1.bt2
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2
       md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/index/bowtie2/genome.4.bt2
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/index/bowtie2/genome.rev.1.bt2
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
       md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/index/bowtie2/genome.rev.2.bt2
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
       md5sum: e3b4ef343dea4dd571642010a7d09597

tests/modules/bwa/index/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [publish_dir:'bwa'] )
 
 workflow test_bwa_index {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/bwa/index/test.yml

@@ -4,13 +4,13 @@
     - bwa
     - bwa/index
   files:
-    - path: ./output/index/bwa/genome.bwt
+    - path: ./output/bwa/bwa/genome.bwt
       md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/index/bwa/genome.amb
+    - path: ./output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/index/bwa/genome.sa
+    - path: ./output/bwa/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: ./output/index/bwa/genome.pac
+    - path: ./output/bwa/bwa/genome.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/index/bwa/genome.ann
+    - path: ./output/bwa/bwa/genome.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567

tests/modules/bwamem2/index/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [:] )
+include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [publish_dir:'bwamem2'] )
 
 workflow test_bwamem2_index {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/bwamem2/index/test.yml

@@ -4,13 +4,13 @@
     - bwamem2
     - bwamem2/index
   files:
-    - path: ./output/index/bwamem2/genome.fasta.amb
+    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/index/bwamem2/genome.fasta.pac
+    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/index/bwamem2/genome.fasta.0123
+    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
       md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
+    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
       md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/index/bwamem2/genome.fasta.ann
+    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567

tests/modules/bwameth/align/test.yml

@@ -1,4 +1,4 @@
-- name: Run bwameth single-end test workflow
+- name: bwameth align single-end test workflow
   command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_single_end -c tests/config/nextflow.config
   tags:
     - bwameth
@@ -6,7 +6,7 @@
   files:
     - path: output/test_single_end/test.bam
 
-- name: Run bwameth paired-end test workflow
+- 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
   tags:
     - bwameth

tests/modules/bwameth/index/main.nf

@@ -2,7 +2,7 @@
 
 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: [publish_dir:'bwameth'] )
 
 workflow test_bwameth_index {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/bwameth/index/test.yml

@@ -1,18 +1,18 @@
-- name: Run bwameth index test workflow
+- name: bwameth index test workflow
   command: nextflow run ./tests/modules/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
   tags:
     - bwameth
     - bwameth/index
   files:
-    - path: ./output/index/bwameth/genome.fasta.bwameth.c2t
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t
       md5sum: 98039984526a41d04d6bd92fcc040c62
-    - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.pac
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.pac
       md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
-    - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.amb
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.amb
       md5sum: 249a4195069071ce47cd0bae68abe376
-    - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.ann
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.ann
       md5sum: 46524d4359dcdfb203a235ab3b930dbb
-    - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.bwt
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.bwt
       md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
-    - path: ./output/index/bwameth/genome.fasta.bwameth.c2t.sa
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.sa
       md5sum: d25f6486f5134f57ed5b258f6fbb8673

tests/modules/methyldackel/extract/test.yml

@@ -1,4 +1,4 @@
-- name: Run methyldackel extract test workflow
+- name: methyldackel extract
   command: nextflow run ./tests/modules/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
   tags:
     - methyldackel

tests/modules/methyldackel/mbias/test.yml

@@ -1,4 +1,4 @@
-- name: Run methyldackel mbias test workflow
+- name: methyldackel mbias
   command: nextflow run ./tests/modules/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
   tags:
     - methyldackel

tests/modules/minia/test.yml

@@ -1,4 +1,4 @@
-- name: Run tests for minia - test_minia
+- name: minia
   command: nextflow run tests/modules/minia -entry test_minia -c tests/config/nextflow.config
   tags:
     - minia

tests/modules/qualimap/bamqc/test.yml

@@ -1,4 +1,4 @@
-- name: Run qualimap bamqc test workflow
+- name: qualimap bamqc test workflow
   command: nextflow run ./tests/modules/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
   tags:
     - qualimap

tests/modules/salmon/index/main.nf

@@ -2,11 +2,11 @@
 
 nextflow.enable.dsl = 2
 
-include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' addParams( options: [:] )
+include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' addParams( options: [publish_dir:'salmon'] )
 
 workflow test_salmon_index {
     genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    
+
     SALMON_INDEX ( genome_fasta, transcript_fasta )
 }

tests/modules/salmon/index/test.yml

@@ -4,28 +4,28 @@
     - salmon
     - salmon/index
   files:
-    - path: ./output/index/salmon/ref_indexing.log
+    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/index/salmon/refseq.bin
+    - path: ./output/salmon/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/index/salmon/versionInfo.json
+    - path: ./output/salmon/salmon/versionInfo.json
       md5sum: 6c764bd219b7bc17168a99d232c0fe09
-    - path: ./output/index/salmon/complete_ref_lens.bin
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/index/salmon/mphf.bin
+    - path: ./output/salmon/salmon/mphf.bin
       md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/index/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/index/salmon/ctable.bin
+    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/index/salmon/duplicate_clusters.tsv
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
       md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/index/salmon/reflengths.bin
+    - path: ./output/salmon/salmon/reflengths.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/index/salmon/info.json
+    - path: ./output/salmon/salmon/info.json
       md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/index/salmon/refAccumLengths.bin
+    - path: ./output/salmon/salmon/refAccumLengths.bin
       md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/index/salmon/ctg_offsets.bin
+    - path: ./output/salmon/salmon/ctg_offsets.bin
       md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/index/salmon/rank.bin
+    - path: ./output/salmon/salmon/rank.bin
       md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/index/salmon/pos.bin
+    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/index/salmon/seq.bin
+    - path: ./output/salmon/salmon/seq.bin

tests/modules/samtools/faidx/test.yml

@@ -1,4 +1,4 @@
-- name: Run samtools faidx test workflow
+- name: samtools faidx test workflow
   command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
   tags:
     - samtools