BEDtools: update nf structure

src/nf_modules/BEDtools/tests/tests.sh → src/nf_modules/BEDtools/tests.sh

-nextflow src/nf_modules/BEDtools/tests/fasta_from_bed.nf \
-  -c src/nf_modules/BEDtools/bedtools.config \
+nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
+  -c src/nf_modules/BEDtools/fasta_from_bed.config \
   -profile docker \
   --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
   --bed "data/tiny_dataset/annot/tiny.bed" \

src/nf_modules/BEDtools/tests/fasta_from_bed.nf

-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: ${params.bed}" }
-  .set { bed_files }
-
-process fasta_from_bed {
-  tag "${bed.baseName}"
-  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 ${bed.baseName}_extracted.fasta
-"""
-}