From 950ec4b3756118ae48c33c7671fa2b4526de3c58 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 19 Aug 2021 10:05:24 +0200
Subject: [PATCH] emase-zero: use g2tr instean of tr2g
---
src/nf_modules/emase-zero/main.nf | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index 1df64020..5e342341 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -1,7 +1,7 @@
version = "0.3.1"
container_url = "lbmc/emase-zero:${version}"
-include { tr2g } from "./../kb/main.nf"
+include { g2tr } from "./../kb/main.nf"
include { bam2ec } from "./../alntools/main.nf"
include { fasta_to_transcripts_lengths } from "./../bioawk/main.nf"
@@ -15,10 +15,10 @@ workflow count {
gtf
main:
- tr2g(gtf)
+ g2tr(gtf)
fasta_to_transcripts_lengths(fasta)
bam2ec(bam_idx, fasta_to_transcripts_lengths.out.tsv)
- emase(bam2ec.out.bin, bam2ec.out.tsv, tr2g.out.t2g)
+ emase(bam2ec.out.bin, bam2ec.out.tsv, tr2g.out.g2t)
emit:
count = emase.out.count
@@ -35,7 +35,7 @@ process emase {
input:
tuple val(file_id), path(bin)
tuple val(transcript_length_id), path(transcript_length)
- tuple val(transcript_to_gene_id), path(transcript_to_gene)
+ tuple val(gene_to_transcript_id), path(gene_to_transcript)
output:
tuple val(file_id), path("${bin.simpleName}.quantified"), emit: count
@@ -45,7 +45,7 @@ process emase {
emase-zero ${params.count} \
-o ${bin.simpleName}.quantified \
-l ${transcript_length} \
- -g ${transcript_to_gene} \
+ -g ${gene_to_transcript} \
${bin}
"""
}
\ No newline at end of file
--
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