mv test.sh file from docker_modules to nf_modules

src/nf_modules/BEDtools/bedtools.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fasta_from_bed {
+        container = "bedtools:2.25.0"
+      }
+    }
+  }
+  sge {
+    process{
+      $fasta_from_bed {
+        beforeScript = "module purge; module load BEDtools/2.25.0"
+      }
+    }
+  }
+}

src/nf_modules/BEDtools/bedtools.nf

+/*
+* bedtools :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/*                      fasta extraction                                     */
+
+params.fastq = "$baseDir/data/fasta/*.fasta"
+params.bed = "$baseDir/data/annot/*.bed"
+
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .set { fasta_files }
+Channel
+  .fromPath( params.bed )
+  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+  .set { bed_files }
+
+process fasta_from_bed {
+  tag "$pair_id"
+  cpus 4
+  publishDir "results/fasta/", mode: 'copy'
+
+  input:
+  file fasta from fasta_files
+  file bed from bed_files
+
+  output:
+  file "*_extracted.fasta" into fasta_files_extracted
+
+  script:
+"""
+bedtools getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${fasta.baseName}_extracted.fasta
+"""
+}