Commit 4e34d7f2 authored by Xavier Grand's avatar Xavier Grand
Browse files

creation du parametre genome_size dans le yaml et dans deeptools/main.nf

parent 0634832a
......@@ -12,6 +12,9 @@ fastq_folder: "/home/adminxavier/CTCF/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"
......@@ -23,21 +26,35 @@ idx: "/home/adminxavier/CTCF/Ref/genomeindex/"
project: "CTCF_peak_calling_input_Genome"
input:
row1:
# sample must be a string. It corresponds to the name of the sample
sample: "5Y_Ctrl_DDX5"
# fastq is the corresponding fastq file, can be compressed as gz file.
fastq: "5Y_Ctrl_DDX5.fastq.gz"
# condition
condition: "Ctrl"
condition: "Ctrl_DDX5"
# type is related to ChIP type: Input or IP
type: "IP"
#row2:
# sample: "5Y_Ctrl_input"
# fastq: "5Y_Ctrl_input.fastq.gz"
# condition: "Ctrl"
# type: "Input"
row2:
sample: "5Y_Ctrl_input"
fastq: "5Y_Ctrl_input.fastq.gz"
condition: "Ctrl_DDX5"
type: "Input"
row3:
sample: "5Y_siDDX_CTCF"
fastq: "5Y_siDDX_CTCF.fastq.gz"
condition: "siDDX_CTCF"
type: "IP"
row4:
sample: "5Y_siDDX_input"
fastq: "5Y_siDDX_input.fastq.gz"
condition: "siDDX_CTCF"
type: "Input"
# Under construction:
# Organism (hg19, GRCH38, HBV...) default hg19 for FasterDB compatibility
# organism: ""
\ No newline at end of file
# 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.
# project name,
# boolean value to setup sequencing type (paired-end or single-end)
paired-end: FALSE
# true or false
paired_end: false
# directory containing fastq files (rawdata)
fastq_folder: ""
samples:
fastq_folder: "/home/adminxavier/CTCF/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: "CTCF_peak_calling_input_Genome"
input:
row1:
# sample must be a string. It corresponds to the name of the sample
sample: "5Y_siDDX_CTCF"
sample: "5Y_Ctrl_CTCF"
# fastq is the corresponding fastq file, can be compressed as gz file.
fastq: "5Y_siDDX_CTCF.fastq.gz"
fastq: "5Y_Ctrl_CTCF.fastq.gz"
# condition
condition: "siDDX"
condition: "Ctrl_CTCF"
# type is related to ChIP type: Input or IP
type: "IP"
row2:
sample: "5Y_siDDX_input"
fastq: "5Y_siDDX_input.fastq.gz"
condition: "siDDX"
sample: "5Y_Ctrl_input"
fastq: "5Y_Ctrl_input.fastq.gz"
condition: "Ctrl_CTCF"
type: "Input"
row3:
sample: "5Y_Ctrl_DDX17.fastq.gz"
fastq: "5Y_Ctrl_DDX17.fastq.gz"
condition: "Ctrl_DDX17"
type: "IP"
row4:
sample: "5Y_Ctrl_input"
fastq: "5Y_Ctrl_input.fastq.gz"
condition: "Ctrl_DDX17"
type: "Input"
# Under construction:
# Organism (hg19, GRCH38, HBV...) default hg19 for FasterDB compatibility
# organism: ""
\ No newline at end of file
# Under construction:
# Organism (hg19, GRCH38, HBV...) default hg19 for FasterDB compatibility
# organism: ""
\ No newline at end of file
......@@ -88,7 +88,6 @@ include { mapping_fastq_chipster } from "./nf_modules/bowtie2/main.nf"
include { filter_bam_quality_chipster } from "./nf_modules/samtools/main.nf"
include { sort_bam_chipster } from "./nf_modules/samtools/main.nf"
include { index_bam_chipster } from "./nf_modules/samtools/main.nf"
include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
include { chipseq_bam2BW_chipster } from "./nf_modules/deeptools/main.nf"
include { peak_calling } from "./nf_modules/macs3/main.nf"
......@@ -121,7 +120,7 @@ workflow {
//############ GENOME INDEXATION AND MAPPING ###################
if (! params.idx) {
if (params.idx == "") {
Channel
.fromPath( params.genome )
.ifEmpty { error "Cannot find any files matching: ${params.genome}" }
......
......@@ -110,7 +110,7 @@ plotProfile -m ${matrix} \
// --effectiveGenomeSize in command line
params.chipseq_bam2BW = ""
params.chipseq_bam2BW_out = ""
params.genome_size = 2913022398
// params.genome_size = 2913022398
process chipseq_bam2BW_chipster {
container = "${container_url}"
label "big_mem_multi_cpus"
......
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