nf-core/chipseq

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row. See usage docs.

Read length together with the genome fasta are used to calculate MACS3 genome size using the khmer program as explained here. For all the genomes present in the igenomes.config the genome size has been already precomputed and the read length is then used to retrieve the corresponding value

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

This parameter is mandatory if --genome is not specified. If you don't have the appropriate alignment index available this will be generated for you automatically. Combine with --save_reference to save alignment index for future runs.

Either this parameter or --gff is mandatory if --genome is not specified.

Either this parameter or --gtf is mandatory if --genome is not specified.

Effective genome size parameter required by MACS3. If using an iGenomes reference these have been provided for any of the genomes available in the igenomes.config, and for the following read lengths (50,75,100,150,200) that should be set using the --read_length parameter. For other genomes, if this parameter is not specified it will be inferred using the provided --read_length or otherwise the pipeline execution will stop with an error.

If provided, alignments that overlap with the regions in this file will be filtered out (see ENCODE blacklists). The file should be in BED format. Blacklisted regions for GRCh37, GRCh38, GRCm38, hg19, hg38, mm10 are bundled with the pipeline in the /assets/blacklists directory, and as such will be automatically used if any of those genomes are specified with the --genome parameter.

If the BWA index is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times.

This enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.

Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.

By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.

By default, intermediate BAM files will not be saved. The final BAM files created after the appropriate filtering step are always saved to limit storage usage. Set this parameter to also save other intermediate BAM files.

This may either be in the form of FastQ or BAM files depending on the options available for that particular tool.

MACS3 is run by default with the --broad flag. Specify this flag to call peaks in narrowPeak mode.

If you are confident you have good reproducibility amongst your replicates then you can increase the value of this parameter to create a 'reproducible' set of consensus peaks. For example, a value of 2 will mean peaks that have been called in at least 2 replicates will contribute to the consensus set of peaks, and as such peaks that are unique to a given replicate will be discarded.

See DESeq2 docs.