From 7ccc789daf47f505bcb3ca9357ea4cf83aa14ac5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 5 May 2021 08:43:45 +0200
Subject: [PATCH] emase-zero: change gtf to bam cardinality to 1 to 1
---
src/nf_modules/emase-zero/main.nf | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index a542da5e..c0191e82 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -11,11 +11,15 @@ workflow count {
take:
bam
gtf
+ transcript_to_gene
main:
- tr2g(gtf, channel.of(["NO T2G", ""]))
- bam2ec(bam, gtf.collect())
- emase(bam2ec.out.bin, bam2ec.out.tsv.collect(), tr2g.out.t2g.collect())
+ transcript_to_gene
+ .ifEmpty(["NO T2G", ""])
+ .set{ transcript_to_gene_optional }
+ tr2g(gtf, transcript_to_gene_optional)
+ bam2ec(bam, gtf)
+ emase(bam2ec.out.bin, bam2ec.out.tsv, tr2g.out.t2g)
emit:
count = emase.out.count
--
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