Merge branch 'filtlong-in-tests' into json-schema

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 +26,7 @@ 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
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true

conf/test_noprofiling.config

@@ -26,6 +26,7 @@ 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
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true

nextflow.config

@@ -58,18 +58,18 @@ params {
     perform_shortread_qc             = false
     shortread_qc_tool                = 'fastp'
     shortread_qc_skipadaptertrim     = false
-    shortread_qc_mergepairs          = false
+    shortread_qc_mergepairs          = true
     shortread_qc_excludeunmerged     = false
     shortread_qc_adapter1            = null
     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_skipqualityfilter         = 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

@@ -10,11 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
+            "required": ["input", "databases", "outdir"],
-                "input",
-                "databases",
-                "outdir"
-            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -83,10 +79,7 @@
                 "shortread_qc_tool": {
                     "type": "string",
                     "default": "fastp",
-                    "enum": [
+                    "enum": ["fastp", "adapterremoval"],
-                        "fastp",
-                        "adapterremoval"
-                    ],
                     "fa_icon": "fas fa-tools",
                     "description": "Specify which tool to use for read QC"
                 },
@@ -131,11 +124,7 @@
                 "shortread_complexityfilter_tool": {
                     "type": "string",
                     "default": "bbduk",
-                    "enum": [
+                    "enum": ["bbduk", "prinseqplusplus", "fastp"],
-                        "bbduk",
-                        "prinseqplusplus",
-                        "fastp"
-                    ],
                     "fa_icon": "fas fa-hammer",
                     "description": "Specify which tool to use for complexity filtering"
                 },
@@ -165,10 +154,7 @@
                 "shortread_complexityfilter_prinseqplusplus_mode": {
                     "type": "string",
                     "default": "entropy",
-                    "enum": [
+                    "enum": ["entropy", "dust"],
-                        "entropy",
-                        "dust"
-                    ],
                     "fa_icon": "fas fa-check-square",
                     "description": "Specify the complexity filter mode for PRINSEQ++"
                 },
@@ -323,15 +309,7 @@
                 "diamond_output_format": {
                     "type": "string",
                     "default": "tsv",
-                    "enum": [
+                    "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
-                        "blast",
-                        "xml",
-                        "txt",
-                        "daa",
-                        "sam",
-                        "tsv",
-                        "paf"
-                    ],
                     "fa_icon": "fas fa-file",
                     "description": "Specify output format from DIAMOND profiling."
                 },
@@ -348,14 +326,7 @@
                 "kaiju_taxon_rank": {
                     "type": "string",
                     "default": "species",
-                    "enum": [
+                    "enum": ["phylum", "class", "order", "family", "genus", "species"],
-                        "phylum",
-                        "class",
-                        "order",
-                        "family",
-                        "genus",
-                        "species"
-                    ],
                     "fa_icon": "fas fa-tag",
                     "description": "Specify taxonomic rank to be displayed in Kaiju taxon table"
                 },
@@ -540,14 +511,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
                     "hidden": true
                 },
                 "email_on_fail": {

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_skipqualityfilter) {
         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_skipqualityfilter) {
 
         ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())

workflows/taxprofiler.nf

@@ -22,7 +22,6 @@ 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.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'"