Commit 351bda15 authored by Xavier Grand's avatar Xavier Grand
Browse files

RNAseq_XGR test with Tiny dataset

parent 8285f90f
......@@ -26,7 +26,7 @@ def helpMessage() {
nextflow ./src/RNAseq_XGR.nf -c ./src/nextflow.config -profile singularity
Mandatory arguments:
--project [path] Path to the project folder. Results are saved in this folder.
--project [path] Path to the fastq folder.
-profile [str] Configuration profile to use.
Available: docker, singularity, podman, psmn, ccin2p3
......@@ -59,16 +59,15 @@ if (params.help || params.h) {
*/
/* Arguments */
project = params.project
params.fastq = "${project}/fastq/*_{1,2}.fastq"
params.fastq = "$params.project/*.fastq*"
params.gtf = ""
params.fasta = ""
params.idx = ""
params.filter_bam_mapped = "-F 268 -f 1 -q 10"
params.fastp_out = "$params.project/fastp/"
params.star_mapping_fastq_out = "$params.project/STAR/"
params.star_index_out = "$params.project/STARindex/"
params.fastp_out = "fastp/"
params.star_mapping_fastq_out = "STAR/"
params.star_index_out = "STARindex/"
/*
****************************************************************
......
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