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Implement hostremoval

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This commit is contained in:
ljmesi 2022-05-03 09:34:27 +02:00
parent a821f748ee
commit 5e6be52fab
3 changed files with 72 additions and 10 deletions
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18
nextflow.config
View file

@ -81,12 +81,18 @@ params {
save_runmerged_reads = false
// Host Removal
perform_shortread_hostremoval = false
shortread_hostremoval_reference = null
shortread_hostremoval_index = null
save_hostremoval_index = false
save_hostremoval_mapped = false
save_hostremoval_unmapped = false
perform_shortread_hostremoval = false
shortread_hostremoval_reference = null
shortread_hostremoval_index = null
longread_hostremoval_index = null
save_hostremoval_index = false
save_hostremoval_mapped = false
save_hostremoval_unmapped = false
save_minimap2_hostremoval_index = false
save_minimap2_hostremoval_mapped = false
save_minimap2_hostremoval_unmapped = false
save_samtools_unmapped_bam = false
save_minimap2_unmapped_fq = false
// MALT
run_malt = false

47
subworkflows/local/longread_hostremoval.nf Normal file
View file

@ -0,0 +1,47 @@
//
// Remove host reads via alignment and export off-target reads
//
include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main'
include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main'
include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main'
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main'
workflow LONGREAD_HOSTREMOVAL {
take:
reads // [ [ meta ], [ reads ] ]
reference // /path/to/fasta
index // /path/to/index
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( !params.longread_hostremoval_index ) {
ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
ch_versions = ch_versions.mix( MINIMAP2_INDEX.out.versions )
} else {
ch_minimap2_index = index
}
MINIMAP2_ALIGN ( reads, ch_minimap2_index, true, false, false )
ch_versions = ch_versions.mix( MINIMAP2_ALIGN.out.versions.first() )
ch_minimap2_mapped = MINIMAP2_ALIGN.out.bam
.map {
meta, reads ->
[ meta, reads, [] ]
}
SAMTOOLS_VIEW ( ch_minimap2_mapped , [] )
ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
emit:
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
}

17
workflows/taxprofiler.nf
View file

@ -26,7 +26,8 @@ if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_refere
if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -52,6 +53,7 @@ include { DB_CHECK } from '../subworkflows/local/db_check'
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
include { PROFILING } from '../subworkflows/local/profiling'
@ -141,16 +143,23 @@ workflow TAXPROFILER {
*/
if ( params.perform_shortread_hostremoval ) {
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_shortread_reference_index ).reads
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
} else {
ch_shortreads_hostremoved = ch_shortreads_filtered
}
if ( params.perform_longread_hostremoval ) {
ch_longreads_hostremoved = LONGREAD_HOSTREMOVAL ( ch_longreads_preprocessed, ch_reference, ch_longread_reference_index ).reads
ch_versions = ch_versions.mix(LONGREAD_HOSTREMOVAL.out.versions)
} else {
ch_longreads_hostremoved = ch_longreads_preprocessed
}
if ( params.perform_runmerging ) {
ch_reads_for_cat_branch = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed )
.mix( ch_longreads_hostremoved )
.map {
meta, reads ->
def meta_new = meta.clone()
@ -182,7 +191,7 @@ workflow TAXPROFILER {
} else {
ch_reads_runmerged = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
.mix( ch_longreads_hostremoved, INPUT_CHECK.out.fasta )
}
/*