refactor: change parameter exclude unmerged to include

.github/workflows/ci.yml

@@ -28,10 +28,10 @@ jobs:
           - "--perform_longread_qc false"
           - "--perform_shortread_qc false"
           - "--shortread_qc_tool fastp"
-          - "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
+          - "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_includeunmerged"
           - "--shortread_qc_tool fastp --shortread_qc_mergepairs"
           - "--shortread_qc_tool adapterremoval"
-          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
+          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_includeunmerged"
           - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
           - "--shortread_complexityfilter_tool bbduk"
           - "--shortread_complexityfilter_tool prinseqplusplus"

conf/modules.config

@@ -79,7 +79,7 @@ process {
     withName: FASTP_PAIRED {
         ext.args   = [
             // collapsing options - option to retain singletons
-            params.shortread_qc_excludeunmerged ? '' : "--include_unmerged",
+            params.shortread_qc_includeunmerged ? '--include_unmerged' : '',
             // trimming options
             params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
             params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",

docs/usage.md

@@ -204,7 +204,7 @@ It is highly recommended to run this on raw reads to remove artifacts from seque
 There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
 
 For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_qc_adapter1` and `--shortread_qc_adapter2`)
-By default, paired-end merging is not activated and paired-end profiling is performed where supported otherwise pairs will be independently profiled. If paired-end merging is activated you can also specify whether to exclude unmerged reads in the reads sent for profiling (`--shortread_qc_mergepairs` and `--shortread_qc_excludeunmerged`).
+By default, paired-end merging is not activated and paired-end profiling is performed where supported otherwise pairs will be independently profiled. If paired-end merging is activated you can also specify whether to include unmerged reads in the reads sent for profiling (`--shortread_qc_mergepairs` and `--shortread_qc_includeunmerged`).
 You can also turn off clipping and only perform paired-end merging, if requested. This can be useful when processing data downloaded from the ENA, SRA, or DDBJ (`--shortread_qc_skipadaptertrim`).
 Both tools support length filtering of reads and can be tuned with `--shortread_qc_minlength`. Performing length filtering can be useful to remove short (often low sequencing complexity) sequences that result in unspecific classification and therefore slow down runtime during profiling, with minimal gain.
 

nextflow.config

@@ -66,7 +66,7 @@ params {
     shortread_qc_tool                = 'fastp'
     shortread_qc_skipadaptertrim     = false
     shortread_qc_mergepairs          = true
-    shortread_qc_excludeunmerged     = false
+    shortread_qc_includeunmerged     = false
     shortread_qc_adapter1            = null
     shortread_qc_adapter2            = null
     shortread_qc_adapterlist         = null

nextflow_schema.json

@@ -125,11 +125,11 @@
                     "default": true,
                     "help_text": "Turn on the merging of read-pairs of paired-end short read sequencing data for AdapterRemoval (this is performed automatically with fastp).\n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--collapse`\n"
                 },
-                "shortread_qc_excludeunmerged": {
+                "shortread_qc_includeunmerged": {
                     "type": "boolean",
                     "fa_icon": "far fa-times-circle",
-                    "description": "Discard unmerged reads from paired-end merging",
+                    "description": "Include unmerged reads from paired-end merging in the downstream processing",
-                    "help_text": "Turns off the inclusion of unmerged reads in resulting processing FASTQ file of paired-end sequencing data when using `fastp`.\n\nThis can be useful in cases where you prefer to have very short reads (e.g. aDNA), thus excluding longer-reads or possibly faulty reads where one of the pair was discarded.\n\n> Modifies tool parameter(s):\n> - removed from reads `--include_unmerged`\n"
+                    "help_text": "Turns on the inclusion of unmerged reads in resulting processing FASTQ file of paired-end sequencing data when using `fastp`.\n\nExcluding unmerged reads can be useful in cases where you prefer to have very short reads (e.g. aDNA), thus excluding longer-reads or possibly faulty reads where one of the pair was discarded.\n\n> Modifies tool parameter(s):\n> - adds option `--include_unmerged`\n"
                 },
                 "shortread_qc_minlength": {
                     "type": "integer",

subworkflows/local/shortread_adapterremoval.nf

@@ -30,7 +30,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
      * has to be exported in a separate channel and we must manually recombine when necessary.
      */
 
-    if ( params.shortread_qc_mergepairs && !params.shortread_qc_excludeunmerged ) {
+    if ( params.shortread_qc_mergepairs && params.shortread_qc_includeunmerged ) {
 
         ch_concat_fastq = Channel.empty()
             .mix(
@@ -55,7 +55,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
         ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
             .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
-    } else if ( params.shortread_qc_mergepairs && params.shortread_qc_excludeunmerged ) {
+    } else if ( params.shortread_qc_mergepairs && !params.shortread_qc_includeunmerged ) {
 
         ch_concat_fastq = Channel.empty()
             .mix(

workflows/taxprofiler.nf

@@ -28,7 +28,7 @@ if ( params.input ) {
 if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
 
 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.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
 
 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'"