publishdir is now a map; forgot nums

README.md

@@ -187,6 +187,7 @@ dependencies:
   - r-base
   - r-ggplot2
   - r-dplyr
+  - nodejs
 ```
 
 Perl packages needed for original workflow
@@ -243,7 +244,24 @@ snakemake --profile sm_profile/ -F
 
 #### Linter
 
-TODO
+For this pipeline, we use [npm-groovy-lint](https://www.npmjs.com/package/npm-groovy-lint) as the linter for the nextflow pipeline. Also, check out its [ruleset](https://codenarc.org/)
+
+##### Install
+
+```
+conda activate backmap-development
+npm install -g npm-groovy-lint
+```
+
+##### Run
+
+```
+npm-groovy-lint --output "txt" --no-insight --verbose -p nextflow/
+```
+
+##### Notes
+
+Consider changing the file `.groovylintrc.json`, if the linter shows unexpected behavior.
 
 ----------------------------------------
 

nextflow/backmap.nf

@@ -2,7 +2,6 @@
 
 final String VERSION = 'v0.4'
 final String NO_FILE = 'NO_FILE'
-final Map<String, String> COPYMODE = ['mode': 'copy']
 final int PROCESSMAXTHREADS = 8
 final String HELP = """
 
@@ -116,9 +115,6 @@ fileSeparator  = params['file-separator']
 
 output         = params['output']
 
-//specific subfolders
-final String BWAINDEX = "${output} /bwa_index"
-
 prefix         = params['prefix']
 threads        = params['threads']
 
@@ -205,6 +201,10 @@ if (printVersion) {
     exit 1
 }
 
+final Map<String, String> COPYMODE = [path: output, mode: 'copy']
+final Map<String, String> COPYMODETMP = [path: output, mode: 'copy', enabled: keepTemporaryFiles]
+final Map<String, String> BWAINDEX = [path: "$output/bwa_index", mode: 'copy', pattern: '*{amb,ann,bwt,pac,sa}']
+final Map<String, String> LOGFILES = [path: output, mode: 'copy', pattern: '*.{log,err}']
 /*
 * Process declarations
 */
@@ -231,8 +231,8 @@ if (bamAvailable) {
 
     // Create index files for bwa mapping
     process bwaIndexing {
-        publishDir BWAINDEX, COPYMODE, pattern: '*{amb,ann,bwt,pac,sa}'
-        publishDir output,   COPYMODE, pattern: '*.{log,err}'
+        publishDir BWAINDEX
+        publishDir LOGFILES
         cpus 1
         input:
             file genome from chBwaIndexGenome
@@ -248,9 +248,7 @@ if (bamAvailable) {
     // BWA Mapping with Illuminma unpaired reads
     process unpairedMapping {
         cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
-        if (keepTemporaryFiles) {
-            publishDir output, COPYMODE
-        }
+        publishDir COPYMODETMP
         input:
             file u from chUnpairedReadMapping
             file index_name from chBwaIndexFilesUnpaired.collect()
@@ -267,9 +265,7 @@ if (bamAvailable) {
     // BWA Mapping with Illumina paired reads
     process pairedMapping {
         cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
-        if (keepTemporaryFiles) {
-            publishDir output, COPYMODE
-        }
+        publishDir COPYMODETMP
         input:
             file p from chPairedReadMapping
             file index_name from chBwaIndexFilesPaired.collect()
@@ -286,9 +282,7 @@ if (bamAvailable) {
 
     // Minimap2 mapping with PacBio reads
     process pacbioMapping {
-        if (keepTemporaryFiles) {
-            publishDir output, COPYMODE
-        }
+        publishDir COPYMODETMP
         cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
         input:
             file pb from chPacbioReadMapping
@@ -305,9 +299,7 @@ if (bamAvailable) {
 
     // Minimap2 mapping with Nanopore reads
     process nanoporeMapping {
-        if (keepTemporaryFiles) {
-            publishDir output, COPYMODE
-        }
+        publishDir COPYMODETMP
         cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
         input:
             file ont from chNanoporeReadMapping
@@ -329,9 +321,7 @@ if (bamAvailable) {
 
 // Merging of Illumina mapped reads
 process mergeIlluminaBamFiles {
-    if (keepTemporaryFiles) {
-        publishDir output, COPYMODE
-    }
+    publishDir COPYMODETMP
     cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
     input:
         path(bams) from chIlluminaBamMerge.collect()
@@ -345,9 +335,7 @@ process mergeIlluminaBamFiles {
 
 // Merging of PacBio mapped reads
 process mergePacbioBamFiles {
-    if (keepTemporaryFiles) {
-        publishDir output, COPYMODE
-    }
+    publishDir COPYMODETMP
     cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
     input:
         file pbs from chPacbioBamMerge.collect()
@@ -361,9 +349,7 @@ process mergePacbioBamFiles {
 
 // Merging of Nanopore mapped reads
 process mergeNanoporeBamFiles {
-    if (keepTemporaryFiles) {
-        publishDir output, COPYMODE
-    }
+    publishDir COPYMODETMP
     cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
     input:
         file onts from chNanoporeBamMerge.collect()
@@ -377,7 +363,7 @@ process mergeNanoporeBamFiles {
 
 // Sorting all Bam files
 process sortAllBamFiles {
-    publishDir output, COPYMODE
+    publishDir COPYMODE
     cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
     input:
         tuple val(tech), file(bam) from chSortIlluminaBamFile.mix(chSortPacbioBamFile).mix(chSortNanoporeBamFile)
@@ -395,7 +381,7 @@ process sortAllBamFiles {
 // Qualimap QC of sorted BAM files
 if (qualityControl) {
     process qualimap {
-        publishDir output, COPYMODE
+        publishDir COPYMODE
         cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
         input:
             tuple val(tech), file(bam) from chQualimapSortedBams
@@ -411,7 +397,7 @@ if (qualityControl) {
 
     // Multiqc QC with qualimap results
     process multiqc {
-        publishDir output, COPYMODE
+        publishDir COPYMODE
         cpus 1
         input:
             file qualis from chMultiqcQualimapResults.collect()
@@ -428,7 +414,7 @@ if (qualityControl) {
 if (coverageHistogram) {
     process bedtoolsGenomecov {
         cpus { 3 > threads ? threads : 3 }
-        publishDir output, COPYMODE
+        publishDir COPYMODE
         input:
             tuple val(tech), file(bam) from chComputeCoverageSortedBams
         output:
@@ -444,7 +430,7 @@ if (coverageHistogram) {
 
     // R script for single coverage
     process RcoveragePlotSingle {
-        publishDir output, COPYMODE
+        publishDir COPYMODE
         cpus 1
         input:
             tuple val(tech), file(cov) from chRCoverageSinglePlot
@@ -487,7 +473,7 @@ if (coverageHistogram) {
 
     // Coverage comparison R script for coverage
     process RMultiCoveragePlot {
-        publishDir output, COPYMODE
+        publishDir COPYMODE
         cpus 1
         input:
             val(techCov) from chRCoverageMultiPlot.collect()
@@ -495,7 +481,7 @@ if (coverageHistogram) {
             file '*.pdf' into globAll
     //  only when more than one technology
         when:
-            techoCov.size() / 2 > 1
+            techCov.size() / 2 > 1
         script:
             """
             #!/usr/bin/env Rscript
@@ -543,7 +529,7 @@ if (coverageHistogram) {
     if (genomeSizeEstimation) {
         //calculate samtools stats
         process samtoolsStats {
-            publishDir output, COPYMODE
+            publishDir COPYMODE
             cpus 1
             input:
                 tuple val(tech), file(bam) from chSamtoolsStatsSortedBams
@@ -603,8 +589,8 @@ if (coverageHistogram) {
         /*
         * Print results
         */
-        chPeakAsInteger = chPeak.map { [num[0], Integer.parseInt(num[1])] }
-        chTotalNucleotidesAsInteger = chTotalNucleotidesResults.map { [num[0], Integer.parseInt(num[1])] }
+        chPeakAsInteger = chPeak.map { num -> [num[0], Integer.parseInt(num[1])] }
+        chTotalNucleotidesAsInteger = chTotalNucleotidesResults.map { num -> [num[0], Integer.parseInt(num[1])] }
         chGenomeSizeEstimationResults = chTotalNucleotidesAsInteger
             .join(chPeakAsInteger)
             .join(chGenomeEstimationSortedBams)