Merge crey02/nextflow-add_htseq to close #29

src/.docker_modules/htseq/1.99.2/Dockerfile

+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

src/.docker_modules/htseq/1.99.2/docker_init.sh

+#!/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

src/nf_modules/htseq/main.nf

+
+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
+}