From 9c64bd7b2e0b14ba1a9ecfbc1cd97c36979a9418 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 16:35:38 +0100
Subject: [PATCH] g2gtools: add convert process
---
src/nf_modules/g2gtools/main.nf | 57 +++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index 39a1c7e6..8954ceec 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -59,4 +59,61 @@ g2gtools transform \
-c ${vci} \
-o ${file_id}_snp_indel.fasta
"""
+}
+
+process convert_gtf {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(vci)
+ tuple val(annot_id), path(gtf)
+ output:
+ tuple val(file_id), path("${file_id}.gtf"), emit: gtf
+ script:
+"""
+g2gtools convert \
+ -i ${gtf} \
+ -c ${vci} \
+ -o ${file_id}.gtf
+"""
+}
+
+process convert_bed {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(vci)
+ tuple val(annot_id), path(bed)
+ output:
+ tuple val(file_id), path("${file_id}.bed"), emit: bed
+ script:
+"""
+g2gtools convert \
+ -i ${bed} \
+ -c ${vci} \
+ -o ${file_id}.bed
+"""
+}
+
+process convert_bam {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${bam_id} ${file_id}"
+
+ input:
+ tuple val(file_id), path(vci)
+ tuple val(bam_id), path(bam)
+ output:
+ tuple val(file_id), path("${file_id}_${bam_id}.bam"), emit: bam
+ script:
+"""
+g2gtools convert \
+ -i ${bam} \
+ -c ${vci} \
+ -o ${file_id}_${bam_id}.bam
+"""
}
\ No newline at end of file
--
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