Commit b6deadc0 authored by lrodrig1's avatar lrodrig1
Browse files

add list of reference index fasta files in nextflow.config

parent 786fad21
......@@ -10,16 +10,9 @@
params {
//Files
fastq = [ "data/fastq_simple/SRR081254_{1,2}.fastq.gz", "data/fastq_simple/SRR078847_{1,2}.fastq.gz" ]
generate_bwa_indexes = false
reference_amb = "data/hs37d5.fa.amb"
reference_ann = "data/hs37d5.fa.ann"
reference_bwt = "data/hs37d5.fa.bwt"
reference_pac = "data/hs37d5.fa.pac"
reference_sa = "data/hs37d5.fa.sa"
reference_fai = "data/hs37d5.fa.fai"
generate_bwa_indexes = false
reference_fasta = "data/hs37d5.fa"
reference_fasta_indexs = [ "data/hs37d5.fa.{amb,ann,bwt,pac,sa,fai}" ]
samples = "data/samples_test.txt"
bed = "data/gencode.v19.genes.v7_model.patched_contigs.gtf.bed.*"
blacklist = "data/hg19-blacklist.v2.num.bed.gz"
......@@ -37,14 +30,12 @@ params {
merge_all_script = "templates/merge_all.sh"
//params
threads_fastqc = 2
threads_fastp = 12
//threads_fastqc = 2
//threads_fastp = 12
//threads_bwa_mem = 24
threads_bwa_mem = 1
threads_samtools = 8
threads_gridss = 8
//threads_bwa_mem = 1
//threads_samtools = 8
//threads_gridss = 8
cut_right = true
cut_right_window_size = 5
cut_right_mean_quality = 24
......@@ -93,7 +84,7 @@ profiles {
}
manifest {
name = 'StructuralVariants Workflow'
name = 'CNV_pipeline'
author = 'Adrián Muñoz-Civico, Laura Rodríguez-Navas'
homePage = 'https://gitlab.bsc.es/lrodrig1/structuralvariants_poc/-/tree/master/structuralvariants/nextflow'
defaultBranch = 'master'
......
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