Commit 5a252dbe authored by nlecouvr's avatar nlecouvr
Browse files

adding kalisto

parent ec7128a5
......@@ -3,6 +3,7 @@ nextflow.enable.dsl=2
include { fastp } from "./nf_modules/fastp/main.nf"
include { fasta_from_bed } from "./nf_modules/bedtools/main.nf"
include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main.nf'
params.fastq = "data/fastq/*_{1,2}.fastq"
......@@ -29,4 +30,6 @@ channel
workflow {
fastp(fastq_files)
fasta_from_bed(fasta_files, bed_files)
index_fasta(fasta_from_bed.out.fasta)
mapping_fastq(index_fasta.out.index.collect(), fastp.out.fastq)
}
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