style: Remove newline at end of files

.editorconfig

@@ -3,10 +3,10 @@ root = true
 [*]
 charset = utf-8
 end_of_line = lf
-insert_final_newline = true
+insert_final_newline = false
 trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
 [*.{yml,yaml}]
-indent_size = 2
+indent_size = 2

.gitattributes

@@ -1 +1 @@
-*.config linguist-language=nextflow
+*.config linguist-language=nextflow

.gitignore

@@ -4,4 +4,4 @@ results/
 test_output/
 output/
 .DS_Store
-*.code-workspace
+*.code-workspace

.markdownlint.yml

@@ -8,4 +8,4 @@ header-increment: false
 no-duplicate-header:
     siblings_only: true
 ul-indent:
-  indent: 4
+  indent: 4

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

README.md

@@ -40,11 +40,11 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
     ```console
     $ nf-core modules list
 
-                                              ,--./,-.
+                                            ,--./,-.
-              ___     __   __   __   ___     /,-._.--~\
+            ___     __   __   __   ___     /,-._.--~\
         |\ | |__  __ /  ` /  \ |__) |__         }  {
         | \| |       \__, \__/ |  \ |___     \`-._,-`-,
-                                              `._,._,'
+                                            `._,._,'
 
         nf-core/tools version 1.10.2
 
@@ -67,11 +67,11 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
     ```console
     $ nf-core modules install . fastqc
 
-                                              ,--./,-.
+                                            ,--./,-.
-              ___     __   __   __   ___     /,-._.--~\
+            ___     __   __   __   ___     /,-._.--~\
         |\ | |__  __ /  ` /  \ |__) |__         }  {
         | \| |       \__, \__/ |  \ |___     \`-._,-`-,
-                                              `._,._,'
+                                            `._,._,'
 
         nf-core/tools version 1.10.2
 
@@ -99,11 +99,11 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
     ...truncated...
 
     Commands:
-      list     List available software modules.
+    list     List available software modules.
-      install  Add a DSL2 software wrapper module to a pipeline.
+    install  Add a DSL2 software wrapper module to a pipeline.
-      update   Update one or all software wrapper modules.             (NOT YET IMPLEMENTED)
+    update   Update one or all software wrapper modules.             (NOT YET IMPLEMENTED)
-      remove   Remove a software wrapper from a pipeline.              (NOT YET IMPLEMENTED)
+    remove   Remove a software wrapper from a pipeline.              (NOT YET IMPLEMENTED)
-      check    Check that imported module code has not been modified.  (NOT YET IMPLEMENTED)
+    check    Check that imported module code has not been modified.  (NOT YET IMPLEMENTED)
     ```
 
 ## Adding a new module file
@@ -305,4 +305,4 @@ nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
 > Note that the nf-core/tools helper package has a `download` command to download all required pipeline
 > files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
 
--->
+-->

software/SOFTWARE/TOOL/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/SOFTWARE/TOOL/main.nf

@@ -86,4 +86,4 @@ process SOFTWARE_TOOL {
 
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
     """
-}
+}

software/SOFTWARE/TOOL/meta.yml

@@ -75,4 +75,4 @@ output:
         pattern: "*.{version.txt}"
 ## TODO nf-core: Add your GitHub username below
 authors:
-    - "@your_github_username"
+    - "@your_github_username"

software/bowtie/align/functions.nf

@@ -57,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bowtie/align/main.nf

@@ -56,4 +56,4 @@ process BOWTIE_ALIGN {
 
     echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
-}
+}

software/bowtie/align/meta.yml

@@ -66,4 +66,4 @@ output:
           description: Unaligned FastQ files
           pattern: "*.fastq.gz"
 authors:
-    - "@kevinmenden"
+    - "@kevinmenden"

software/bowtie/build/functions.nf

@@ -57,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bowtie/build/main.nf

@@ -32,4 +32,4 @@ process BOWTIE_BUILD {
     bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
     echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
-}
+}

software/bowtie/build/meta.yml

@@ -49,4 +49,4 @@ output:
           pattern: "*.{version.txt}"
 authors:
     - "@kevinmenden"
-    - "@drpatelh"
+    - "@drpatelh"

software/bowtie2/align/functions.nf

@@ -57,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bowtie2/align/main.nf

@@ -69,4 +69,4 @@ process BOWTIE2_ALIGN {
         echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
         """
     }
-}
+}

software/bowtie2/align/meta.yml

@@ -71,4 +71,4 @@ output:
         pattern: "*.log"
 authors:
     - "@joseespinosa"
-    - "@drpatelh"
+    - "@drpatelh"

software/bowtie2/build/functions.nf

@@ -57,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bowtie2/build/main.nf

@@ -32,4 +32,4 @@ process BOWTIE2_BUILD {
     bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
     echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
-}
+}

software/bowtie2/build/meta.yml

@@ -50,4 +50,4 @@ output:
           pattern: "*.{version.txt}"
 authors:
     - "@joseespinosa"
-    - "@drpatelh"
+    - "@drpatelh"

software/bwa/index/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bwa/index/main.nf

@@ -31,4 +31,4 @@ process BWA_INDEX {
     bwa index $options.args $fasta
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """
-}
+}

software/bwa/index/meta.yml

@@ -49,4 +49,4 @@ output:
         pattern: "*.{version.txt}"
 authors:
     - "@drpatelh"
-    - "@maxulysse"
+    - "@maxulysse"

software/bwa/mem/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bwa/mem/main.nf

@@ -42,4 +42,4 @@ process BWA_MEM {
 
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """
-}
+}

software/bwa/mem/meta.yml

@@ -66,4 +66,4 @@ output:
         pattern: "*.{version.txt}"
 authors:
     - "@drpatelh"
-    - "@jeremy1805"
+    - "@jeremy1805"

software/cutadapt/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/cutadapt/main.nf

@@ -39,4 +39,4 @@ process CUTADAPT {
         > ${prefix}.cutadapt.log
     echo \$(cutadapt --version) > ${software}.version.txt
     """
-}
+}

software/cutadapt/meta.yml

@@ -63,4 +63,4 @@ output:
       pattern: "*.{version.txt}"
 authors:
   - "@drpatelh"
-  - "@kevinmenden"
+  - "@kevinmenden"

software/deeptools/computematrix/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/deeptools/computematrix/main.nf

@@ -41,4 +41,4 @@ process DEEPTOOLS_COMPUTEMATRIX {
 
     computeMatrix --version | sed -e "s/computeMatrix //g" > ${software}.version.txt
     """
-}
+}

software/deeptools/plotfingerprint/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/deeptools/plotfingerprint/main.nf

@@ -43,4 +43,4 @@ process DEEPTOOLS_PLOTFINGERPRINT {
 
     plotFingerprint --version | sed -e "s/plotFingerprint //g" > ${software}.version.txt
     """
-}
+}

software/deeptools/plotheatmap/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/deeptools/plotheatmap/main.nf

@@ -38,4 +38,4 @@ process DEEPTOOLS_PLOTHEATMAP {
 
     plotHeatmap --version | sed -e "s/plotHeatmap //g" > ${software}.version.txt
     """
-}
+}

software/deeptools/plotprofile/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/deeptools/plotprofile/main.nf

@@ -38,4 +38,4 @@ process DEEPTOOLS_PLOTPROFILE {
 
     plotProfile --version | sed -e "s/plotProfile //g" > ${software}.version.txt
     """
-}
+}

software/dsh/filterbed/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/dsh/filterbed/main.nf

@@ -36,4 +36,4 @@ process DSH_FILTERBED {
 
     echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt
     """
-}
+}

software/dsh/filterbed/meta.yml

@@ -56,4 +56,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@heuermh"
+    - "@heuermh"

software/dsh/splitbed/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/dsh/splitbed/main.nf

@@ -37,4 +37,4 @@ process DSH_SPLITBED {
 
     echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt
     """
-}
+}

software/dsh/splitbed/meta.yml

@@ -56,4 +56,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@heuermh"
+    - "@heuermh"

software/fastp/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/fastp/main.nf

@@ -69,4 +69,4 @@ process FASTP {
         echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
         """
     }
-}
+}

software/fastp/meta.yml

@@ -76,4 +76,4 @@ output:
       pattern: "*fail.fastq.gz"
 authors:
   - "@drpatelh"
-  - "@kevinmenden"
+  - "@kevinmenden"

software/fastqc/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/fastqc/main.nf

@@ -44,4 +44,4 @@ process FASTQC {
         fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
         """
     }
-}
+}

software/fastqc/meta.yml

@@ -69,4 +69,4 @@ authors:
     - "@drpatelh"
     - "@grst"
     - "@ewels"
-    - "@FelixKrueger"
+    - "@FelixKrueger"

software/gffread/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/gffread/main.nf

@@ -30,4 +30,4 @@ process GFFREAD {
     gffread $gff $options.args -o ${gff.baseName}.gtf
     echo \$(gffread --version 2>&1) > ${software}.version.txt
     """
-}
+}

software/hisat2/align/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/hisat2/align/main.nf

@@ -90,4 +90,4 @@ process HISAT2_ALIGN {
         echo $VERSION > ${software}.version.txt
         """
     }
-}
+}

software/hisat2/build/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/hisat2/build/main.nf

@@ -64,4 +64,4 @@ process HISAT2_BUILD {
 
     echo $VERSION > ${software}.version.txt
     """
-}
+}

software/hisat2/extractsplicesites/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/hisat2/extractsplicesites/main.nf

@@ -31,4 +31,4 @@ process HISAT2_EXTRACTSPLICESITES {
     hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
     echo $VERSION > ${software}.version.txt
     """
-}
+}

software/homer/annotatepeaks/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/homer/annotatepeaks/main.nf

@@ -43,4 +43,4 @@ process HOMER_ANNOTATEPEAKS {
 
     echo $VERSION > ${software}.version.txt
     """
-}
+}

software/lib/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/macs2/callpeak/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/macs2/callpeak/main.nf

@@ -48,4 +48,4 @@ process MACS2_CALLPEAK {
 
     macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
     """
-}
+}

software/multiqc/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/multiqc/main.nf

@@ -32,4 +32,4 @@ process MULTIQC {
     multiqc -f $options.args .
     multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
     """
-}
+}

software/multiqc/meta.yml

@@ -57,4 +57,4 @@ output:
 authors:
     - "@abhi18av"
     - "@bunop"
-    - "@drpatelh"
+    - "@drpatelh"

software/pangolin/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/pangolin/main.nf

@@ -36,4 +36,4 @@ process PANGOLIN {
 
     pangolin --version | sed "s/pangolin //g" > ${software}.version.txt
     """
-}
+}

software/pangolin/meta.yml

@@ -54,4 +54,4 @@ output:
       pattern: "*.{version.txt}"
 
 authors:
-  - "@kevinmenden"
+  - "@kevinmenden"

software/phantompeakqualtools/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/phantompeakqualtools/main.nf

@@ -37,4 +37,4 @@ process PHANTOMPEAKQUALTOOLS {
     Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
     echo $VERSION > ${software}.version.txt
     """
-}
+}

software/picard/collectmultiplemetrics/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/picard/collectmultiplemetrics/main.nf

@@ -47,4 +47,4 @@ process PICARD_COLLECTMULTIPLEMETRICS {
 
     echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt
     """
-}
+}

software/picard/collectmultiplemetrics/meta.yml

@@ -67,4 +67,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@drpatelh"
+    - "@drpatelh"

software/picard/markduplicates/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/picard/markduplicates/main.nf

@@ -46,4 +46,4 @@ process PICARD_MARKDUPLICATES {
 
     echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
     """
-}
+}

software/picard/markduplicates/meta.yml

@@ -64,4 +64,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@drpatelh"
+    - "@drpatelh"

software/picard/mergesamfiles/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/picard/mergesamfiles/main.nf

@@ -51,4 +51,4 @@ process PICARD_MERGESAMFILES {
         echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
         """
     }
-}
+}

software/picard/mergesamfiles/meta.yml

@@ -58,4 +58,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@drpatelh"
+    - "@drpatelh"

software/preseq/lcextrap/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/preseq/lcextrap/main.nf

@@ -42,4 +42,4 @@ process PRESEQ_LCEXTRAP {
 
     echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt
     """
-}
+}

software/qualimap/rnaseq/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/qualimap/rnaseq/main.nf

@@ -54,4 +54,4 @@ process QUALIMAP_RNASEQ {
 
     echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt
     """
-}
+}

software/quast/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/quast/main.nf

@@ -45,4 +45,4 @@ process QUAST {
     ln -s ${prefix}/report.tsv
     echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
     """
-}
+}

software/quast/meta.yml

@@ -65,4 +65,4 @@ output:
 
 authors:
   - "@drpatelh"
-  - "@kevinmenden"
+  - "@kevinmenden"

software/rsem/calculateexpression/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/rsem/calculateexpression/main.nf

@@ -58,4 +58,4 @@ process RSEM_CALCULATEEXPRESSION {
 
     rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
     """
-}
+}

software/rsem/preparereference/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/rsem/preparereference/main.nf

@@ -65,4 +65,4 @@ process RSEM_PREPAREREFERENCE {
         rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
         """
     }
-}
+}

software/rseqc/bamstat/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/rseqc/bamstat/main.nf

@@ -36,4 +36,4 @@ process RSEQC_BAMSTAT {
 
     bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt
     """
-}
+}

software/rseqc/inferexperiment/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/rseqc/inferexperiment/main.nf

@@ -38,4 +38,4 @@ process RSEQC_INFEREXPERIMENT {
 
     infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt
     """
-}
+}

software/rseqc/innerdistance/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/rseqc/innerdistance/main.nf

@@ -50,4 +50,4 @@ process RSEQC_INNERDISTANCE {
         inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
         """
     }
-}
+}

software/rseqc/junctionannotation/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/rseqc/junctionannotation/main.nf

@@ -45,4 +45,4 @@ process RSEQC_JUNCTIONANNOTATION {
 
     junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt
     """
-}
+}

software/rseqc/junctionsaturation/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}