Merge pull request #180 from nf-core/rename-exclude-unmerged

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 analysis",
-                    "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 FASTQ file from merging paired-end sequencing data when using `fastp` and/or `AdapterRemoval`. For `fastp` this means the unmerged read pairs are directly included in the output FASTQ file. For `AdapterRemoval`, additional output files containing unmerged reads are all concatenated into one file by the workflow.\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> Adds `fastp` 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(
@@ -40,9 +40,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                 ADAPTERREMOVAL_PAIRED.out.paired_truncated
             )
             .map { meta, reads ->
-                def meta_new = meta.clone()
+                [meta + [single_end: true], reads]
-                meta_new.single_end = true
-                [meta_new, reads]
             }
             .groupTuple()
             // Paired-end reads cause a nested tuple during grouping.
@@ -55,7 +53,7 @@ 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(
@@ -63,9 +61,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                 ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
             )
             .map { meta, reads ->
-                def meta_new = meta.clone()
+                [meta + [single_end: true], reads]
-                meta_new.single_end = true
-                [meta_new, reads]
             }
             .groupTuple()
             .map { meta, fastq -> [meta, fastq.flatten()] }

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'"