Commit 2a273d29 authored by Xavier Grand's avatar Xavier Grand
Browse files

Output directory name BigWig modification

parent 4e34d7f2
......@@ -23,7 +23,7 @@ chrom_sizes: "/home/adminxavier/CTCF/Ref/genomeindex/sizes.genome"
idx: "/home/adminxavier/CTCF/Ref/genomeindex/"
# output folder under results/ directory
project: "CTCF_peak_calling_input_Genome"
project: "CTCF_peak_calling_input_Genome_part2"
input:
......
# A row defines some features to describe a sample to analyse.
# You can add as many row as you want below each other. Be sure that
# the name of the row is the same as the file name witout extension.
# boolean value to setup sequencing type (paired-end or single-end)
# true or false
paired_end: false
# directory containing fastq files (rawdata)
fastq_folder: "/home/adminxavier/MYCN/SRA293647_MYCN_BE2/fastq/"
# the genome of interest (fasta file)
genome: "/home/adminxavier/CTCF/Ref/genomeindex/genome.fasta"
# corresponding entire genome size
genome_size: 2913022398
# A file containing chromosome sizes (usualy "chrom.sizes" file)
chrom_sizes: "/home/adminxavier/CTCF/Ref/genomeindex/sizes.genome"
# Does the genome is allready indexed with bowtie2 ?
# directory containing indexed genome files or ""
idx: "/home/adminxavier/CTCF/Ref/genomeindex/"
# output folder under results/ directory
project: "SRA293647_MYCN_BE2"
input:
row1:
# sample must be a string. It corresponds to the name of the sample
sample: "SRR2229590_MYCN"
# fastq is the corresponding fastq file, can be compressed as gz file.
fastq: "SRR2229590_MYCN.fastq.gz"
# condition
condition: "SRA293647_MYCN_BE2"
# type is related to ChIP type: Input or IP
type: "IP"
row2:
sample: "SRR2229591_IgG"
fastq: "SRR2229591_IgG.fastq.gz"
condition: "SRA293647_MYCN_BE2"
type: "Input"
# Under construction:
# Organism (hg19, GRCH38, HBV...) default hg19 for FasterDB compatibility
# organism: ""
\ No newline at end of file
......@@ -17,7 +17,7 @@ params.peak_calling_out = "$params.project/Peak_calling/"
params.bam_to_bed_out = "$params.project/Bed/"
params.bed_slop_out = "$params.project/Bed_sloped/"
params.bedGraph_out = "$params.project/BedGraph/"
params.chipseq_bam2BW_out = "$params.project/chipseq_BigGig"
params.chipseq_bam2BW_out = "$params.project/chipseq_BigWig"
/*
****************************************************************
......
Supports Markdown
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