Path to comma-separated file containing information about the samples in the experiment.
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 4 columns, and a header row. See usage docs.
By default, the pipeline expects paired-end data. If you have single-end data, specify this parameter on the command line when you launch the pipeline. It is not possible to run a mixture of single-end and paired-end files in one 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.
This parameter is *mandatory* if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Effective genome size parameter required by MACS2.
Effective genome size parameter required by MACS2. If using an iGenomes reference these have been provided when --genome is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. For other genomes, if this parameter is not specified then the MACS2 peak-calling and differential analysis will be skipped.
Path to blacklist regions in BED format, used for filtering alignments.
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 blacklists directory, and as such will be automatically used if any of those genomes are specified with the --genome parameter.
Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.
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.
Do not perform alignment merging and downstream analysis by merging replicates i.e. only do this by merging resequenced libraries.
An additional series of steps are performed by the pipeline for merging the replicates from the same experimental group. This is primarily to increase the sequencing depth in order to perform downstream analyses such as footprinting. Specifying this parameter means that these steps will not be performed.
Save the intermediate BAM files from the alignment step.
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.
Number of biological replicates required from a given condition for a peak to contribute to a consensus peak.
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.
If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Method used to save pipeline results to output directory.
The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
A custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.