diff --git a/subworkflows/local/shortread_preprocessing.nf b/subworkflows/local/shortread_preprocessing.nf index f961584b..9b7314ff 100644 --- a/subworkflows/local/shortread_preprocessing.nf +++ b/subworkflows/local/shortread_preprocessing.nf @@ -2,18 +2,18 @@ * SHORTREAD_PREPROCESSING: Preprocessing and QC for short reads */ -include { FASTQC as FASTQC_RAW } from '../../modules/nf-core/fastqc/main' -include { FASTQC as FASTQC_TRIMMED } from '../../modules/nf-core/fastqc/main' -include { FASTP } from '../../modules/nf-core/fastp/main' -include { ADAPTERREMOVAL as ADAPTERREMOVAL_PE } from '../../modules/nf-core/adapterremoval/main' -include { ADAPTERREMOVAL as ADAPTERREMOVAL_SE } from '../../modules/nf-core/adapterremoval/main' -include { BOWTIE2_REMOVAL_BUILD as BOWTIE2_HOST_REMOVAL_BUILD } from '../../modules/local/bowtie2_removal_build' -include { BOWTIE2_REMOVAL_ALIGN as BOWTIE2_HOST_REMOVAL_ALIGN } from '../../modules/local/bowtie2_removal_align' -include { BOWTIE2_REMOVAL_BUILD as BOWTIE2_PHIX_REMOVAL_BUILD } from '../../modules/local/bowtie2_removal_build' -include { BOWTIE2_REMOVAL_ALIGN as BOWTIE2_PHIX_REMOVAL_ALIGN } from '../../modules/local/bowtie2_removal_align' -include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' -include { SEQTK_MERGEPE } from '../../modules/nf-core/seqtk/mergepe/main' -include { BBMAP_BBNORM } from '../..//modules/nf-core/bbmap/bbnorm/main' +include { FASTQC as FASTQC_RAW } from '../../modules/nf-core/fastqc/main' +include { FASTQC as FASTQC_TRIMMED } from '../../modules/nf-core/fastqc/main' +include { FASTP } from '../../modules/nf-core/fastp/main' +include { ADAPTERREMOVAL as ADAPTERREMOVAL_PE } from '../../modules/nf-core/adapterremoval/main' +include { ADAPTERREMOVAL as ADAPTERREMOVAL_SE } from '../../modules/nf-core/adapterremoval/main' +include { BOWTIE2_REMOVAL_BUILD as BOWTIE2_HOST_REMOVAL_BUILD } from '../../modules/local/bowtie2_removal_build' +include { BOWTIE2_REMOVAL_ALIGN as BOWTIE2_HOST_REMOVAL_ALIGN } from '../../modules/local/bowtie2_removal_align' +include { BOWTIE2_REMOVAL_BUILD as BOWTIE2_PHIX_REMOVAL_BUILD } from '../../modules/local/bowtie2_removal_build' +include { BOWTIE2_REMOVAL_ALIGN as BOWTIE2_PHIX_REMOVAL_ALIGN } from '../../modules/local/bowtie2_removal_align' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' +include { SEQTK_MERGEPE } from '../../modules/nf-core/seqtk/mergepe/main' +include { BBMAP_BBNORM } from '../../modules/nf-core/bbmap/bbnorm/main' workflow SHORTREAD_PREPROCESSING { take: