Commit c4792fa5 authored by Xavier Grand's avatar Xavier Grand
Browse files

idx genome mod

parent b412a7fa
......@@ -32,7 +32,7 @@ params.genome = "data/tinyTestDataset/*.fasta"
@type: File
*/
params.idxgenome = ""
params.idxgenome = "data/tinyTestDataset/*.fasta.fai*"
/* already indexed reference genome
@Type: String
......@@ -117,13 +117,17 @@ workflow {
fastqc_preprocessed.out.report
).collect()
)
mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
// index reference genome & mapping preprocessed reads
if (!params.idxgenome) {
/*if (!params.idxgenome) {
index_fasta(genome_file)
mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq)
} else {
mapping_fastq(genome_idx.collect(), fastp_default.out.fastq)
}
*/
// filter bam - remove reads with quality <30
filter_bam_quality(mapping_fastq.out.bam)
......
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