Rename subworkflow parameters for consistency

.github/workflows/ci.yml

@@ -29,8 +29,8 @@ jobs:
           - NXF_VER: ""
             NXF_EDGE: "1"
         parameters:
-          - "--longread_clip false"
+          - "--perform_longread_clip false"
-          - "--shortread_clip false"
+          - "--perform_shortread_clipmerge false"
           - "--shortread_clipmerge_tool fastp"
           - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
           - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
@@ -39,8 +39,8 @@ jobs:
           - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
           - "--shortread_complexityfilter_tool bbduk"
           - "--shortread_complexityfilter_tool prinseq"
-          - "--run_merging"
+          - "--perform_runmerging"
-          - "--run_merging --shortread_clipmerge_mergepairs"
+          - "--perform_runmerging --shortread_clipmerge_mergepairs"
 
     steps:
       - name: Check out pipeline code

conf/modules.config

@@ -173,7 +173,7 @@ process {
 
     withName: MALT_RUN {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/malt/${meta.db_name}" },
             mode: params.publish_dir_mode,
@@ -183,7 +183,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
             mode: params.publish_dir_mode,
@@ -193,7 +193,7 @@ process {
 
     withName: METAPHLAN3 {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.run_merging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
             mode: params.publish_dir_mode,

conf/test.config

@@ -28,7 +28,7 @@ params {
     run_malt                      = true
     run_metaphlan3                = true
     run_centrifuge                = true
-    shortread_clipmerge           = true
+    perform_shortread_clipmerge           = true
-    longread_clip                 = false
+    perform_longread_clip                 = false
-    shortread_complexityfilter    = true
+    perform_shortread_complexityfilter    = true
 }

nextflow.config

@@ -55,7 +55,7 @@ params {
     databases = null
 
     // FASTQ preprocessing
-    shortread_clipmerge                     = false
+    perform_shortread_clipmerge             = false
     shortread_clipmerge_tool                = 'fastp'
     shortread_clipmerge_skipadaptertrim     = false
     shortread_clipmerge_mergepairs          = false
@@ -63,11 +63,11 @@ params {
     shortread_clipmerge_adapter1            = null
     shortread_clipmerge_adapter2            = null
     shortread_clipmerge_minlength           = 15
-    longread_clip                           = false
+    perform_longread_clip                   = false
     save_preprocessed_reads                 = false
 
     // Complexity filtering
-    shortread_complexityfilter                           = false
+    perform_shortread_complexityfilter                   = false
     shortread_complexityfilter_tool                      = 'bbduk'
     shortread_complexityfilter_entropy                   = 0.3
     shortread_complexityfilter_bbduk_windowsize          = 50
@@ -77,8 +77,8 @@ params {
     save_complexityfiltered_reads                        = false
 
     // run merging
-    run_merging                = false
+    perform_runmerging          = false
-    save_runmerged_reads       = false
+    save_runmerged_reads        = false
 
     // MALT
     run_malt                   = false
@@ -92,6 +92,7 @@ params {
     centrifuge_save_unaligned  = false
     centrifuge_save_aligned    = false
     centrifuge_sam_format      = false
+
     // metaphlan3
     run_metaphlan3             = false
 }

nextflow_schema.json

@@ -262,15 +262,9 @@
             "type": "string",
             "default": "None"
         },
-        "shortread_clipmerge": {
-            "type": "boolean"
-        },
         "shortread_clipmerge_excludeunmerged": {
             "type": "boolean"
         },
-        "longread_clip": {
-            "type": "boolean"
-        },
         "run_malt": {
             "type": "boolean"
         },
@@ -334,9 +328,6 @@
         "shortread_complexityfilter_bbduk_mask": {
             "type": "boolean"
         },
-        "shortread_complexityfilter": {
-            "type": "boolean"
-        },
         "shortread_complexityfilter_entropy": {
             "type": "number",
             "default": 0.3
@@ -353,10 +344,19 @@
         "save_complexityfiltered_reads": {
             "type": "boolean"
         },
-        "run_merging": {
+        "save_runmerged_reads": {
             "type": "boolean"
         },
-        "save_runmerged_reads": {
+        "perform_shortread_clipmerge": {
+            "type": "boolean"
+        },
+        "perform_longread_clip": {
+            "type": "boolean"
+        },
+        "perform_shortread_complexityfilter": {
+            "type": "boolean"
+        },
+        "perform_runmerging": {
             "type": "boolean"
         }
     }

workflows/taxprofiler.nf

@@ -101,14 +101,14 @@ workflow TAXPROFILER {
     /*
         SUBWORKFLOW: PERFORM PREPROCESSING
     */
-    if ( params.shortread_clipmerge ) {
+    if ( params.perform_shortread_clipmerge ) {
 
         ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
     } else {
         ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
     }
 
-    if ( params.longread_clip ) {
+    if ( params.perform_longread_clip ) {
         ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
                                         .map { it -> [ it[0], [it[1]] ] }
     } else {
@@ -119,7 +119,7 @@ workflow TAXPROFILER {
         SUBWORKFLOW: COMPLEXITY FILTERING
     */
 
-    if ( params.shortread_complexityfilter ) {
+    if ( params.perform_shortread_complexityfilter ) {
         ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
     } else {
         ch_shortreads_filtered = ch_shortreads_preprocessed
@@ -129,7 +129,7 @@ workflow TAXPROFILER {
         STEP: Run merging
     */
 
-    if ( params.run_merging ) {
+    if ( params.perform_runmerging ) {
 
         ch_reads_for_cat_branch = ch_shortreads_filtered
             .mix( ch_longreads_preprocessed )
@@ -190,22 +190,22 @@ workflow TAXPROFILER {
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
 
-    if (params.shortread_clipmerge) {
+    if (params.perform_shortread_clipmerge) {
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
         ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
     }
 
-    if (params.longread_clip) {
+    if (params.perform_longread_clip) {
         ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
         ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
     }
 
-    if (params.shortread_complexityfilter){
+    if (params.perform_shortread_complexityfilter){
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
         ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
     }
 
-    if (params.run_merging){
+    if (params.perform_runmerging){
         ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
     }