Verified Commit 4eef1122 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

emaze: change imput from gtf to fasta to compute transcript length

parent 6231fc3f
......@@ -3,6 +3,7 @@ container_url = "lbmc/emase-zero:${version}"
include { tr2g } from "./../kb/main.nf"
include { bam2ec } from "./../alntools/main.nf"
include { fasta_to_transcripts_lengths } from "./../bioawk/main.nf"
params.count = "-m 2"
......@@ -10,7 +11,7 @@ params.count_out = ""
workflow count {
take:
bam_idx
gtf
fasta
transcript_to_gene
main:
......@@ -18,7 +19,8 @@ workflow count {
.ifEmpty(["NO T2G", ""])
.set{ transcript_to_gene_optional }
tr2g(gtf, transcript_to_gene_optional)
bam2ec(bam_idx, gtf)
fasta_to_transcripts_lengths(fasta)
bam2ec(bam_idx, fasta_to_transcripts_lengths.out.tsv.collect())
emase(bam2ec.out.bin, bam2ec.out.tsv, tr2g.out.t2g)
emit:
......
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