adding kalisto

src/RNASeq.nf

@@ -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)
 }