Commit bfa008bc authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

updating tags

parent 1f8a21d9
#!/usr/bin/env nextflow
// Default parameter values to run tests
params.pairs="pe"
params.genome="/project/apps_database/hisat2_index/hg38/"
params.gtf="/project/apps_database/iGenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf"
params.design="$baseDir/../test_data/design.txt"
params.fastqs="$baseDir/../test_data/*.fastq.gz"
fastqs=params.fastqs
design_file = file(params.design)
gtf_file = file(params.gtf)
// params genome is the directory
......@@ -100,7 +98,7 @@ process trimpe {
output:
set pair_id, file("${read1.baseName.split("\\.", 2)[0]}_val_1.fq.gz"), file("${read2.baseName.split("\\.", 2)[0]}_val_2.fq.gz") into trimpe
when:
param.pairs == 'pe'
params.pairs == 'pe'
script:
"""
module load trimgalore/0.4.1 cutadapt/1.9.1
......@@ -113,7 +111,7 @@ process trimse {
output:
set pair_id, file("${read1.baseName.split("\\.", 2)[0]}_trimmed.fq.gz") into trimse
when:
param.pairs == 'se'
params.pairs == 'se'
script:
"""
module load trimgalore/0.4.1 cutadapt/1.9.1
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment