From 3dd05762d8cdf8875b80f2a09853dfc9960c3c22 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 20 May 2021 17:27:46 +0200
Subject: [PATCH] gffread: add main.nf
---
src/nf_modules/gffread/main.nf | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 src/nf_modules/gffread/main.nf
diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
new file mode 100644
index 00000000..2414cbd7
--- /dev/null
+++ b/src/nf_modules/gffread/main.nf
@@ -0,0 +1,30 @@
+version = "0.12.2"
+container_url = "lbmc/gffread:${version}"
+
+params.gffread = ""
+params.gffread_out = ""
+process gffread {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_prefix"
+ if (params.gffread_out != "") {
+ publishDir "results/${params.gffread_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(gtf)
+ tuple val(fasta_id), path(fasta)
+
+ output:
+ tuple val(fasta_id), path("${file_prefix}.fasta"), emit: fasta
+
+ script:
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ } else {
+ file_prefix = file_id
+ }
+ """
+ gffread ${gtf} -g ${fasta} -o ${file_prefix}.fasta
+ """
+}
\ No newline at end of file
--
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