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taxprofiler/subworkflows/local/shortread_hostremoval.nf

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//
// Remove host reads via alignment and export off-target reads
//
include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
workflow SHORTREAD_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.shortread_hostremoval_index ) {
ch_bowtie2_index = BOWTIE2_BUILD ( [ [], reference ] ).index
ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
} else {
ch_bowtie2_index = index.first()
}
// Map, generate BAM with all reads and unmapped reads in FASTQ for downstream
BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true, true)
ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
// Indexing whole BAM for host removal statistics
SAMTOOLS_INDEX ( BOWTIE2_ALIGN.out.bam )
ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
bam_bai = BOWTIE2_ALIGN.out.bam
.join(SAMTOOLS_INDEX.out.bai, remainder: true)
SAMTOOLS_STATS ( bam_bai, reference )
ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
emit:
stats = SAMTOOLS_STATS.out.stats
reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}