From 4eef11221b267bf46b3ac795057743dd29b03633 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 26 May 2021 09:39:07 +0200
Subject: [PATCH] emaze: change imput from gtf to fasta to compute transcript
length
---
src/nf_modules/emase-zero/main.nf | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index 36ff276f..01134781 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -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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