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refactor: change parameter exclude unmerged to include
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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
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@ -28,10 +28,10 @@ jobs:
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- "--perform_longread_qc false"
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- "--perform_longread_qc false"
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- "--perform_shortread_qc false"
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- "--perform_shortread_qc false"
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- "--shortread_qc_tool fastp"
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- "--shortread_qc_tool fastp"
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- "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
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- "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_includeunmerged"
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- "--shortread_qc_tool fastp --shortread_qc_mergepairs"
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- "--shortread_qc_tool fastp --shortread_qc_mergepairs"
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- "--shortread_qc_tool adapterremoval"
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- "--shortread_qc_tool adapterremoval"
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- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
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- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_includeunmerged"
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- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
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- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseqplusplus"
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- "--shortread_complexityfilter_tool prinseqplusplus"
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@ -79,7 +79,7 @@ process {
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withName: FASTP_PAIRED {
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withName: FASTP_PAIRED {
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ext.args = [
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ext.args = [
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// collapsing options - option to retain singletons
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// collapsing options - option to retain singletons
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params.shortread_qc_excludeunmerged ? '' : "--include_unmerged",
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params.shortread_qc_includeunmerged ? '--include_unmerged' : '',
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// trimming options
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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@ -204,7 +204,7 @@ It is highly recommended to run this on raw reads to remove artifacts from seque
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There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
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There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
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For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_qc_adapter1` and `--shortread_qc_adapter2`)
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For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_qc_adapter1` and `--shortread_qc_adapter2`)
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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`).
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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`).
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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`).
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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`).
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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.
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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.
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@ -66,7 +66,7 @@ params {
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shortread_qc_tool = 'fastp'
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shortread_qc_tool = 'fastp'
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shortread_qc_skipadaptertrim = false
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shortread_qc_skipadaptertrim = false
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shortread_qc_mergepairs = true
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shortread_qc_mergepairs = true
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shortread_qc_excludeunmerged = false
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shortread_qc_includeunmerged = false
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shortread_qc_adapter1 = null
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shortread_qc_adapter1 = null
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shortread_qc_adapter2 = null
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shortread_qc_adapter2 = null
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shortread_qc_adapterlist = null
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shortread_qc_adapterlist = null
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@ -125,11 +125,11 @@
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"default": true,
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"default": true,
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"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"
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"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"
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},
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},
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"shortread_qc_excludeunmerged": {
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"shortread_qc_includeunmerged": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "far fa-times-circle",
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"fa_icon": "far fa-times-circle",
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"description": "Discard unmerged reads from paired-end merging",
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"description": "Include unmerged reads from paired-end merging in the downstream processing",
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"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"
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"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"
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},
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},
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"shortread_qc_minlength": {
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"shortread_qc_minlength": {
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"type": "integer",
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"type": "integer",
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@ -30,7 +30,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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* has to be exported in a separate channel and we must manually recombine when necessary.
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* has to be exported in a separate channel and we must manually recombine when necessary.
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*/
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*/
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if ( params.shortread_qc_mergepairs && !params.shortread_qc_excludeunmerged ) {
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if ( params.shortread_qc_mergepairs && params.shortread_qc_includeunmerged ) {
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ch_concat_fastq = Channel.empty()
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ch_concat_fastq = Channel.empty()
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.mix(
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.mix(
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@ -55,7 +55,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else if ( params.shortread_qc_mergepairs && params.shortread_qc_excludeunmerged ) {
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} else if ( params.shortread_qc_mergepairs && !params.shortread_qc_includeunmerged ) {
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ch_concat_fastq = Channel.empty()
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ch_concat_fastq = Channel.empty()
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.mix(
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.mix(
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@ -28,7 +28,7 @@ if ( params.input ) {
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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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."
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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."
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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"
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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"
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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'"
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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'"
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