From e94feb6f082d1352a2f7fca03eac57d1fc6b903e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 29 Apr 2021 09:42:19 +0200
Subject: [PATCH] emaze-zero: integrate alntools into named workflow
---
src/nf_modules/emase-zero/main.nf | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index 594d591a..1b3cf3e1 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -2,19 +2,20 @@ version = "0.3.1"
container_url = "lbmc/emase-zero:${version}"
include { tr2g } from "./../kb/main.nf"
+include { bam2ec } from "./../alntools/main.nf"
params.count = "-m 2"
params.count_out = ""
workflow count {
take:
- bin
- transcript_length
+ bam
gtf
main:
tr2g(gtf, channel.of(["NO T2G", ""]))
- emase(bin, transcript_length, tr2g.out.t2g)
+ bam2ec(bam, gtf)
+ emase(bam2ec.out.bin, bam2ec.out.tsv, tr2g.out.t2g)
emit:
count: emase.count
--
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