mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-14 07:13:09 +00:00
425 lines
16 KiB
Text
425 lines
16 KiB
Text
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
Config file for defining DSL2 per module options and publishing paths
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
Available keys to override module options:
|
|
ext.args = Additional arguments appended to command in module.
|
|
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
|
|
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
|
|
ext.prefix = File name prefix for output files.
|
|
----------------------------------------------------------------------------------------
|
|
*/
|
|
|
|
process {
|
|
|
|
withName: SAMPLESHEET_CHECK {
|
|
publishDir = [
|
|
path: { "${params.outdir}/pipeline_info" },
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
|
|
]
|
|
}
|
|
|
|
withName: DATABASE_CHECK {
|
|
publishDir = [
|
|
path: { "${params.outdir}/pipeline_info" },
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
|
|
]
|
|
}
|
|
|
|
withName: FASTQC {
|
|
ext.args = '--quiet'
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/fastqc/raw" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.html'
|
|
]
|
|
}
|
|
|
|
withName: FASTQC_PROCESSED {
|
|
ext.args = '--quiet'
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/fastqc/processed" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.html'
|
|
]
|
|
}
|
|
|
|
withName: FASTP_SINGLE {
|
|
ext.args = [
|
|
// trimming options
|
|
params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
|
|
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
|
|
// filtering options
|
|
"--length_required ${params.shortread_qc_minlength}",
|
|
(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
|
|
].join(' ').trim()
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/fastp" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.fastq.gz',
|
|
enabled: params.save_preprocessed_reads
|
|
]
|
|
}
|
|
|
|
withName: FASTP_PAIRED {
|
|
ext.args = [
|
|
// collapsing options - option to retain singletons
|
|
params.shortread_qc_excludeunmerged ? '' : "--include_unmerged",
|
|
// trimming options
|
|
params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
|
|
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
|
|
params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
|
|
// filtering options
|
|
"--length_required ${params.shortread_qc_minlength}",
|
|
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
|
|
].join(' ').trim()
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/fastp" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.fastq.gz',
|
|
enabled: params.save_preprocessed_reads
|
|
]
|
|
}
|
|
|
|
withName: ADAPTERREMOVAL_SINGLE {
|
|
ext.args = [
|
|
// trimming options
|
|
params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
|
|
params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
|
|
// filtering options
|
|
"--minlength ${params.shortread_qc_minlength}"
|
|
].join(' ').trim()
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/adapterremoval" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.fastq.gz',
|
|
enabled: params.save_preprocessed_reads
|
|
]
|
|
}
|
|
|
|
withName: ADAPTERREMOVAL_PAIRED {
|
|
ext.args = [
|
|
// collapsing options
|
|
params.shortread_qc_mergepairs ? "--collapse" : "",
|
|
// trimming options
|
|
params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
|
|
params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
|
|
params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
|
|
// filtering options
|
|
"--minlength ${params.shortread_qc_minlength}"
|
|
].join(' ').trim()
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/adapterremoval" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.fastq.gz',
|
|
enabled: params.save_preprocessed_reads
|
|
]
|
|
}
|
|
|
|
withName: PORECHOP {
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/porechop" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.fastq.gz',
|
|
enabled: params.save_preprocessed_reads
|
|
]
|
|
}
|
|
|
|
withName: FILTLONG {
|
|
ext.args = [
|
|
"--min_length ${params.longread_qc_qualityfilter_minlength}",
|
|
"--keep_percent ${params.longread_qc_qualityfilter_keeppercent}",
|
|
"--target_bases ${params.longread_qc_qualityfilter_targetbases}"
|
|
]
|
|
.join(' ').trim()
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/filtlong" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{fastq.gz,log}',
|
|
enabled: params.save_preprocessed_reads
|
|
]
|
|
}
|
|
|
|
withName: BOWTIE2_BUILD {
|
|
publishDir = [
|
|
path: { "${params.outdir}/bowtie2/build" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_index,
|
|
pattern: 'bowtie2'
|
|
]
|
|
}
|
|
|
|
withName: BOWTIE2_ALIGN {
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
[
|
|
path: { "${params.outdir}/bowtie2/align" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.log'
|
|
],
|
|
[
|
|
path: { "${params.outdir}/bowtie2/align" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_mapped,
|
|
pattern: '*.bam'
|
|
],
|
|
[
|
|
path: { "${params.outdir}/bowtie2/align" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_unmapped,
|
|
pattern: '*.fastq.gz'
|
|
]
|
|
]
|
|
}
|
|
|
|
withName: MINIMAP2_INDEX {
|
|
ext.args = '-x map-ont'
|
|
publishDir = [
|
|
path: { "${params.outdir}/minimap2/index" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_index,
|
|
pattern: 'minimap2'
|
|
]
|
|
}
|
|
|
|
withName: MINIMAP2_ALIGN {
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/minimap2/align" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_mapped,
|
|
pattern: '*.bam'
|
|
]
|
|
}
|
|
|
|
withName: SAMTOOLS_VIEW {
|
|
ext.args = '-f 4'
|
|
ext.prefix = { "${meta.id}.mapped.sorted" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/samtools/view" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_unmapped,
|
|
pattern: '*.bam'
|
|
]
|
|
}
|
|
|
|
withName: SAMTOOLS_BAM2FQ {
|
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/samtools/bam2fq" },
|
|
mode: params.publish_dir_mode,
|
|
enabled: params.save_hostremoval_unmapped,
|
|
pattern: '*.fq.gz'
|
|
]
|
|
}
|
|
|
|
withName: BBMAP_BBDUK {
|
|
ext.args = [
|
|
"entropy=${params.shortread_complexityfilter_entropy}",
|
|
"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
|
|
params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
|
|
].join(' ').trim()
|
|
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/bbduk/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{fastq.gz,log}',
|
|
enabled: params.save_complexityfiltered_reads
|
|
]
|
|
}
|
|
|
|
withName: PRINSEQPLUSPLUS {
|
|
ext.args = [
|
|
params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
|
|
"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
|
|
"-VERBOSE 2"
|
|
].join(' ').trim()
|
|
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/prinseqplusplus/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
|
|
enabled: params.save_complexityfiltered_reads
|
|
]
|
|
}
|
|
|
|
withName: CAT_FASTQ {
|
|
ext.prefix = { "${meta.id}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/run_merging/" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.fastq.gz',
|
|
enabled: params.save_runmerged_reads
|
|
]
|
|
}
|
|
|
|
withName: MALT_RUN {
|
|
ext.args = { "${meta.db_params}" }
|
|
// one run with multiple samples, so fix ID to just db name to ensure clean log name
|
|
ext.prefix = { "${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/malt/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{rma6,log,sam}'
|
|
]
|
|
}
|
|
|
|
withName: 'NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO' {
|
|
ext.args = "-c2c Taxonomy"
|
|
ext.prefix = { "${meta.id}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/malt/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt.gz,megan}'
|
|
]
|
|
}
|
|
|
|
withName: KRAKEN2_KRAKEN2 {
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/kraken2/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt,report,fastq.gz}'
|
|
]
|
|
}
|
|
|
|
withName: KRONA_CLEANUP {
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/krona" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{html}'
|
|
]
|
|
}
|
|
|
|
withName: KRONA_KTIMPORTTEXT {
|
|
ext.prefix = { "${meta.tool}-${meta.id}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/krona" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{html}'
|
|
]
|
|
}
|
|
|
|
withName: 'NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO' {
|
|
ext.args = { "--read2class Taxonomy" }
|
|
ext.prefix = { "${meta.id}-${meta.db_name}" }
|
|
}
|
|
|
|
withName: KRONA_KTIMPORTTAXONOMY {
|
|
ext.args = "-i"
|
|
ext.prefix = { "${meta.tool}-${meta.id}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/krona" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{html}'
|
|
]
|
|
}
|
|
|
|
withName: METAPHLAN3 {
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{biom,txt}'
|
|
]
|
|
}
|
|
|
|
withName: CENTRIFUGE_CENTRIFUGE {
|
|
publishDir = [
|
|
path: { "${params.outdir}/centrifuge/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt,sam,gz}'
|
|
]
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
|
|
}
|
|
|
|
withName: CENTRIFUGE_KREPORT {
|
|
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/centrifuge/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt}'
|
|
]
|
|
}
|
|
|
|
withName: KAIJU_KAIJU {
|
|
publishDir = [
|
|
path: { "${params.outdir}/kaiju/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.tsv'
|
|
]
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
}
|
|
|
|
withName: KAIJU_KAIJU2TABLE {
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/kaiju/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{txt}'
|
|
]
|
|
}
|
|
|
|
withName: KAIJU_KAIJU2KRONA {
|
|
ext.args = '-v -u'
|
|
}
|
|
|
|
withName: DIAMOND_BLASTX {
|
|
ext.args = { "${meta.db_params}" }
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/diamond/${meta.db_name}" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
|
|
]
|
|
}
|
|
|
|
withName: MOTUS_PROFILE {
|
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
|
publishDir = [
|
|
path: { "${params.outdir}/motus/${meta.db_name}" },
|
|
mode: params.publish_dir_mode
|
|
]
|
|
}
|
|
|
|
withName: MOTUS_MERGE {
|
|
publishDir = [
|
|
path: { "${params.outdir}/motus/" },
|
|
mode: params.publish_dir_mode
|
|
]
|
|
}
|
|
|
|
withName: CUSTOM_DUMPSOFTWAREVERSIONS {
|
|
publishDir = [
|
|
path: { "${params.outdir}/pipeline_info" },
|
|
mode: params.publish_dir_mode,
|
|
pattern: '*_versions.yml'
|
|
]
|
|
}
|
|
|
|
withName: MULTIQC {
|
|
publishDir = [
|
|
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
|
|
]
|
|
}
|
|
}
|