Standardise QC parameter system and turn on both porechop/filtlong in tests

conf/modules.config

@@ -136,9 +136,9 @@ process {
 
     withName: FILTLONG {
         ext.args = [
-            "--min_length ${params.longread_qc_minlength}",
+            "--min_length ${params.longread_qc_qualityfilter_minlength}",
-            "--keep_percent ${params.longread_qc_keep_percent}",
+            "--keep_percent ${params.longread_qc_qualityfilter_keeppercent}",
-            "--target_bases ${params.longread_qc_target_bases}"
+            "--target_bases ${params.longread_qc_qualityfilter_targetbases}"
         ]
         .join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }

conf/test.config

@@ -26,6 +26,9 @@ params {
     databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
     perform_shortread_qc                  = true
     perform_longread_qc                   = true
+    shortread_qc_mergepairs               = true
+    longread_qc_skipadaptertrim           = false
+    longread_qc_qualityfilter             = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true

conf/test_noprofiling.config

@@ -26,6 +26,9 @@ params {
     databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
     perform_shortread_qc                  = true
     perform_longread_qc                   = true
+    shortread_qc_mergepairs               = true
+    longread_qc_skipadaptertrim           = false
+    longread_qc_qualityfilter             = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true

nextflow.config

@@ -64,12 +64,12 @@ params {
     shortread_qc_adapter2            = null
     shortread_qc_minlength           = 15
 
-    perform_longread_qc              = false
+    perform_longread_qc                   = false
-    longread_qc_run_clip             = false
+    longread_qc_skipadaptertrim           = false
-    longread_qc_run_filter           = false
+    longread_qc_qualityfilter             = false
-    longread_qc_minlength            = 1000
+    longread_qc_qualityfilter_minlength   = 1000
-    longread_qc_keep_percent        = 90
+    longread_qc_qualityfilter_keeppercent = 90
-    longread_qc_target_bases         = 500000000
+    longread_qc_qualityfilter_targetbases = 500000000
 
     save_preprocessed_reads          = false
 

nextflow_schema.json

@@ -404,21 +404,21 @@
             "type": "integer",
             "default": 30
         },
-        "longread_qc_run_clip": {
+        "longread_qc_skipadaptertrim": {
             "type": "boolean"
         },
-        "longread_qc_run_filter": {
+        "longread_qc_qualityfilter": {
             "type": "boolean"
         },
-        "longread_qc_minlength": {
+        "longread_qc_qualityfilter_minlength": {
             "type": "integer",
             "default": 1000
         },
-        "longread_qc_keep_percent": {
+        "longread_qc_qualityfilter_keeppercent": {
             "type": "integer",
             "default": 90
         },
-        "longread_qc_target_bases": {
+        "longread_qc_qualityfilter_targetbases": {
             "type": "integer",
             "default": 500000000
         },

subworkflows/local/longread_preprocessing.nf

@@ -14,7 +14,7 @@ workflow LONGREAD_PREPROCESSING {
     ch_versions      = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-    if ( params.longread_qc_run_clip && !params.longread_qc_run_filter ) {
+    if ( !params.longread_qc_skipadaptertrim && !params.longread_qc_qualityfilter ) {
         PORECHOP ( reads )
 
         ch_processed_reads = PORECHOP.out.reads
@@ -28,7 +28,7 @@ workflow LONGREAD_PREPROCESSING {
         ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
         ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
 
-    } else if ( !params.longread_qc_run_clip && params.longread_qc_run_filter ) {
+    } else if ( params.longread_qc_skipadaptertrim && params.longread_qc_qualityfilter ) {
 
         ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())

workflows/taxprofiler.nf

@@ -22,7 +22,7 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
 
 if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
 if (params.shortread_qc_excludeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_qc_mergepairs"
-if ( (params.longread_qc_run_clip || params.longread_qc_run_filter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_run_clip or --longread_qc_run_filter requested but quality-control not turned on. Please specify --perform_long_qc"
+if ( (!params.longread_qc_skipadaptertrim || params.longread_qc_qualityfilter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_skipadaptertrim false or --longread_qc_qualityfilter requested but quality-control not turned on. Please specify --perform_long_qc"
 
 if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' ))  exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"