From f27bf1489ab141ecff93b2df667a351686c8dbcc Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 28 Apr 2022 15:13:41 +0200
Subject: [PATCH] Merge crey02/nextflow-add_htseq to close #29
---
src/.docker_modules/htseq/1.99.2/Dockerfile | 11 ++++
.../htseq/1.99.2/docker_init.sh | 4 ++
src/nf_modules/htseq/main.nf | 53 +++++++++++++++++++
3 files changed, 68 insertions(+)
create mode 100644 src/.docker_modules/htseq/1.99.2/Dockerfile
create mode 100755 src/.docker_modules/htseq/1.99.2/docker_init.sh
create mode 100644 src/nf_modules/htseq/main.nf
diff --git a/src/.docker_modules/htseq/1.99.2/Dockerfile b/src/.docker_modules/htseq/1.99.2/Dockerfile
new file mode 100644
index 00000000..ba82320c
--- /dev/null
+++ b/src/.docker_modules/htseq/1.99.2/Dockerfile
@@ -0,0 +1,11 @@
+FROM ubuntu:20.04
+LABEL maintainer= Laurent Modolo
+
+RUN apt-get update \
+ && apt-get install -y \
+ procps \
+ build-essential \
+ python3 \
+ python3-pip
+
+RUN pip install HTSeq==1.99.2
\ No newline at end of file
diff --git a/src/.docker_modules/htseq/1.99.2/docker_init.sh b/src/.docker_modules/htseq/1.99.2/docker_init.sh
new file mode 100755
index 00000000..a0aa6479
--- /dev/null
+++ b/src/.docker_modules/htseq/1.99.2/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/htseq:1.99.2
+docker build src/.docker_modules/htseq/1.99.2 -t 'lbmc/htseq:1.99.2'
+docker push lbmc/htseq:1.99.2
diff --git a/src/nf_modules/htseq/main.nf b/src/nf_modules/htseq/main.nf
new file mode 100644
index 00000000..93377467
--- /dev/null
+++ b/src/nf_modules/htseq/main.nf
@@ -0,0 +1,53 @@
+
+version = "1.99.2"
+container_url = "lbmc/htseq:${version}"
+
+params.htseq_out = ""
+
+
+
+process gff3_2_gtf {
+ container = "dceoy/cufflinks"
+ label "small_mem_mono_cpus"
+
+ input:
+ tuple val(genome_id), path(gff3_file)
+ output:
+ path "${genome_id}.gtf", emit: gtf
+ script:
+"""
+gffread ${gff3_file} -T -o ${genome_id}.gtf
+"""
+}
+
+
+process htseq_count {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "file_id: $file_id"
+ if (params.htseq_out != "") {
+ publishDir "results/${params.htseq_out}", mode: 'copy'
+ }
+ input:
+ tuple val(file_id), path(bam), path(bai)
+ path (gtf)
+
+ output:
+ path "${file_id}.tsv", emit: counts
+
+ script:
+"""
+htseq-count -n ${task.cpus} -r pos -a 10 -s yes -t exon -i gene_id $bam $gtf > ${file_id}.tsv
+"""
+}
+
+workflow htseq_count_with_gff {
+ take:
+ bam_tuple
+ gff_file
+ main:
+ gff3_2_gtf(gff_file)
+ htseq_count(bam_tuple,gff3_2_gtf.out.gtf)
+ emit:
+ counts = htseq_count.out.counts
+}
--
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