HTSeq: add nf and tests files

src/nf_modules/HTSeq/htseq.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $counting {
+        container = "htseq:0.8.0"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load HTSeq/0.8.0"
+      }
+    }
+  }
+}

src/nf_modules/HTSeq/htseq.nf

+/*
+* htseq :
+* Imputs : sorted bams files
+* Imputs : gtf
+* Output : counts files
+*/
+/*                      quality trimming                                     */
+
+params.bam = "$baseDir/data/bam/*.bam"
+params.gtf = "$baseDir/data/annotation/*.gtf"
+
+log.info "bam files : ${params.bam}"
+log.info "gtf files : ${params.gtf}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+  .set { bam_files }
+Channel
+  .fromPath( params.gtf )
+  .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
+  .set { gtf_file }
+
+process counting {
+  tag "$bam.baseName"
+  publishDir "results/quantification/", mode: 'copy'
+
+  input:
+  file bam from bam_files
+  file gtf from gtf_file
+
+  output:
+  file "*.count" into count_files
+
+  script:
+"""
+htseq-count -r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
+--format=bam ${bam} ${gtf} > ${bam.baseName}.count
+"""
+}

src/nf_modules/HTSeq/tests/counting.nf

+params.bam = "$baseDir/data/bam/*.bam"
+params.gtf = "$baseDir/data/annotation/*.gtf"
+
+log.info "bam files : ${params.bam}"
+log.info "gtf files : ${params.gtf}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+  .set { bam_files }
+Channel
+  .fromPath( params.gtf )
+  .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
+  .set { gtf_file }
+
+process counting {
+  tag "$bam.baseName"
+  publishDir "results/quantification/", mode: 'copy'
+
+  input:
+  file bam from bam_files
+  file gtf from gtf_file
+
+  output:
+  file "*.count" into count_files
+
+  script:
+"""
+htseq-count -r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
+--format=bam ${bam} ${gtf} > ${bam.baseName}.count
+"""
+}
+

src/nf_modules/HTSeq/tests/tests.sh

+nextflow src/nf_modules/HTSeq/tests/counting.nf \
+  -c src/nf_modules/HTSeq/htseq.config \
+  -profile docker \
+  --gtf "data/tiny_dataset/annot/tiny.gff" \
+  --bam "data/tiny_dataset/map/tiny_v2.bam"
+