Hello everyone, I have the following table with histone mark groups, each with 2 replicates and their corresponding inputs. I ran the nf-core/chip-seq pipeline, and when checking the results, I noticed that I didn't get the merged replicates in BAM files, and bigwig fikes as I did in other ATAC-Seq or CUT&RUN pipelines. Did I make a mistake in my design or code, or is this a feature that the pipeline doesn't handle? Below, I attach part of my table and the code I used. sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate H3K27ac_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998094_SRR3997337.fastq.gz,,1,H3K27ac,input_mb231,1 H3K27ac_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998095_SRR3997338.fastq.gz,,2,H3K27ac,input_mb231,2 H3K27me3_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998096_SRR3997339.fastq.gz,,1,H3K27me3,input_mb231,1 H3K27me3_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998097_SRR3997340.fastq.gz,,2,H3K27me3,input_mb231,2 H3K9me3_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998108_SRR3997351.fastq.gz,,1,H3K9me3,input_mb231,1 H3K9me3_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998109_SRR3997352.fastq.gz,,2,H3K9me3,input_mb231,2 input_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998110_SRR3997353.fastq.gz,,1,,, input_mb231,/media/epigen/94A006E9A006D222/projects/IRD/chip_histone_marks/GSE85158/fq/nf-core_fetchngs/fastq/SRX1998111_SRR3997354.fastq.gz,,2,,,

nextflow run nf-core/chipseq \

-profile docker \

--input '../extra/nf-chipseq_input.csv' \

--outdir '../results/nf-chipseq_results_hg38_broadPeak' \

-work-dir '../results/nf-chipseq_results_hg38_broadPeak/workdir' \

--multiqc_title 'nfcore-chipseq_hg38_broadPeak' \

--genome 'GRCh38' \

--macs_gsize 2749859687 \

--aligner 'bowtie2' \

--save_reference \

--save_trimmed \

--max_cpus 16 \

--max_memory 32.GB \

-resume

Hi, your table is OK, #CFP55NZ5G pipeline does not merge replicates as you noticed

thanks!