diff --git a/src/nf_modules/Hisat2/test/index.nf b/src/nf_modules/Hisat2/test/index.nf new file mode 100644 index 0000000000000000000000000000000000000000..7b30f7dbee82e1a94f532e76189dbbebc03f9d72 --- /dev/null +++ b/src/nf_modules/Hisat2/test/index.nf @@ -0,0 +1,32 @@ +/* +* Hisat2 : +* Imputs : fastq files +* Imputs : fasta files +* Output : bam files +*/ + +/* fasta indexing */ +params.fasta = "$baseDir/data/bam/*.fasta" + +log.info "fasta files : ${params.fasta}" + +Channel + .fromPath( params.fasta ) + .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" } + .set { fasta_file } + +process index_fasta { + tag "$fasta.baseName" + publishDir "results/mapping/index/", mode: 'copy' + + input: + file fasta from fasta_file + + output: + file "*.index*" into index_files + + script: +""" +hisat2-build ${fasta} ${fasta.baseName}.index +""" +}