cores	8
ram	30
scratch	100
partition	user
process_mode	DATASET
samples	S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff
nfcorePipeline	chipseq
pipelineVersion	2.1.0
inputType	samplesheet
samplesheetMapping	"{""sample"":""Name"",""fastq_1"":""Read1 [File]"",""fastq_2"":""Read2 [File]"",""replicate"":""Replicate"",""antibody"":""Antibody"",""control"":""Control""}"
fasta	/srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa
fragment_size	200
seq_center	""
read_length	50
multiqc_title	""
genome	""
gtf	""
gff	""
bwa_index	""
bowtie2_index	""
chromap_index	""
star_index	""
gene_bed	""
macs_gsize	""
blacklist	""
save_reference	false
clip_r1	2
clip_r2	2
three_prime_clip_r1	0
three_prime_clip_r2	0
trim_nextseq	0
skip_trimming	false
save_trimmed	false
aligner	bwa
keep_dups	false
keep_multi_map	false
bwa_min_score	0
save_align_intermeds	false
save_unaligned	false
narrow_peak	false
broad_cutoff	0.1
macs_fdr	""
macs_pvalue	""
min_reps_consensus	1
save_macs_pileup	false
skip_peak_qc	false
skip_peak_annotation	false
skip_consensus_peaks	false
skip_fastqc	false
skip_picard_metrics	false
skip_preseq	false
deseq2_vst	true
skip_plot_profile	false
skip_plot_fingerprint	false
skip_spp	false
skip_deseq2_qc	false
skip_igv	false
skip_multiqc	false
skip_qc	false
sushi_app	NfCoreChipseqApp
refBuild	Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03