Nextflow pipeline designed for peak calling using MACS and IDR, coupled with QC generation using deeptools. The saturation option generates peaks by successively considering increasing percentages of the total reads, repeating the operation multiple times within the range of 0.05 to 0.95.

1. Nextflow : for common installation procedures see the IARC-nf repository.

2. MACS2 or MACS3

3. IDR

4. Deeptools

A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")

• Mandatory

• Optional

• Flags

Flags are special parameters without value.

To run the pipeline for ATAC, one can type:

nextflow run iarcbioinfo/bam2peaks-nf -r latest -profile singularity --input_file input.tsv --ref hg38 --output_folder output --ignoreDuplicates

To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

To use the pipeline for Chip-seq, add the --chip flag :

nextflow run iarcbioinfo/bam2peaks-nf -r latest -profile singularity --input_file input.tsv --ref hg38 --output_folder output --chip --broad --extsize 320