mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 05:53:09 +00:00
refactor: change parameter exclude unmerged to include
This commit is contained in:
parent
7992edd181
commit
4529e7e545
7 changed files with 11 additions and 11 deletions
4
.github/workflows/ci.yml
vendored
4
.github/workflows/ci.yml
vendored
|
@ -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"
|
||||
|
|
|
@ -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}" : "",
|
||||
|
|
|
@ -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.
|
||||
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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",
|
||||
"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"
|
||||
"description": "Include unmerged reads from paired-end merging in the downstream processing",
|
||||
"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",
|
||||
|
|
|
@ -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(
|
||||
|
|
|
@ -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'"
|
||||
|
||||
|
|
Loading…
Reference in a new issue