config.yaml

# ======================== INPUT DIRECTORIES ==================
fastq_dir: fastq
bams_dir: bams

# ======================== FASTQ READS ========================

# FASTQ file extension: "fastq.gz" or "fastq" or "fq.gz" or "fq", etc.
fastq_ext: "fastq.gz"

# Force single end processing
fastq_single_end_only: False

# ======================== TRIM READS ========================
trim_reads: False

# ======================== Alignment ========================
# UCSC genome: e.g. hg19, hg38, mm9, mm10, ..
genome: hg38

# For ATAC-Seq used: "-X 2000 --dovetail"
bowtie2_params: ""
#bowtie2_params: "-X 2000 --dovetail"

# Compute NRF, PBC for BAM alignment
bams_additional_qc: False

# Option if all will start with bams
start_with_bams: False

# ======================== Visualization ================

bw: False
# Produce normalized coverage ignoring duplicated reads
bamCoverage_params: "--normalizeUsing CPM --ignoreDuplicates"

tagsbw: False
tags2bw_fragment: 150

# ======================== MACS2 ========================
macs2: False
# MACS2 Narrow:
macs2_mode: narrow
macs2_params: "-q 0.05"
macs2_suffix: q0.05 # do not use underscores here otherwise wrong sample wildcards

# MACS2 Broad
#macs2_mode: broad
#macs2_params: "--broad --broad-cutoff 0.1"
#macs2_suffix: broad0.1 # do not use underscores here otherwise wrong sample wildcards

# MACS2 ATAC-seq:
#macs2_mode: narrow
#macs2_params: "-q 0.05 -f BAMPE --nomodel --nolambda -B --call-summits"
#macs2_suffix: q0.05 # do not use underscores here otherwise wrong sample wildcards

# ======================== SICER ========================
sicer: False
sicer_fragment: 150
sicer_window: 200
sicer_gap: 600
sicer_fdr: 0.01
sicer_evalue: 100

# ======================== SPAN ========================
span: False
span_workdir: "span"
span_bin: 100
span_fragment: "auto"
span_fdr: 0.05
span_iterations: 10
span_threshold: 1e-4
span_params: ""
span_threads: 8