nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
1.2.0). The latest
stable release is
2.1.2
.
Path to comma-separated file containing information about the samples in the experiment.
stringYou 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.
Specifies that the input is single-end reads.
booleanBy 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.
Estimated fragment size used to extend single-end reads.
integerSequencing center information to be added to read group of BAM files.
stringPath to the output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed.
Name of iGenomes reference.
stringIf 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.
Path to Fasta reference file.
stringThis 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.
Path to GTF annotation file.
stringThis parameter is mandatory if --genome is not specified.
Full path to directory containing BWA index including base name. i.e. /path/to/index/genome.fa.
stringPath to BED file containing gene intervals. This will be created from the GTF file if not specified.
stringPath to BED file containing transcription start sites. This will be created from the gene BED file if not specified.
stringEffective genome size parameter required by MACS2.
stringEffective 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.
stringIf 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.
Name of Mitochondrial chomosome in reference assembly e.g. chrM.
stringReads aligning to this contig are filtered out if a valid identifier is provided otherwise this step is skipped. Where possible these have been provided in the igenomes.config.
If generated by the pipeline save the BWA index in the results directory.
booleanIf 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.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
integerInstructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
integerInstructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.
integerThis 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.
Skip the adapter trimming step.
booleanUse 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.
Save the trimmed FastQ files in the results directory.
booleanBy 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.
Reads mapping to mitochondrial contig are not filtered from alignments.
booleanDuplicate reads are not filtered from alignments.
booleanReads mapping to multiple locations are not filtered from alignments.
booleanDon’t output BWA MEM alignments with score lower than this parameter.
integerDo not perform alignment merging and downstream analysis by merging replicates i.e. only do this by merging resequenced libraries.
booleanAn 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.
booleanBy 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.
BAMTools JSON file with custom filters for paired-end data.
string$baseDir/assets/bamtools_filter_pe.jsonBAMTools JSON file with custom filters for single-end data.
string$baseDir/assets/bamtools_filter_se.jsonRun MACS2 in narrowPeak mode.
booleanMACS2 is run by default with the --broad flag. Specify this flag to call peaks in narrowPeak mode.
Specifies broad cutoff value for MACS2. Only used when --narrow_peak isnt specified.
number0.1Minimum FDR (q-value) cutoff for peak detection, --macs_fdr and --macs_pvalue are mutually exclusive.
numberp-value cutoff for peak detection, --macs_fdr and --macs_pvalue are mutually exclusive. If --macs_pvalue cutoff is set, q-value will not be calculated and reported as -1 in the final .xls file.
numberNumber of biological replicates required from a given condition for a peak to contribute to a consensus peak.
integer1If 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.
Instruct MACS2 to create bedGraph files normalised to signal per million reads.
booleanSkip MACS2 peak QC plot generation.
booleanSkip annotation of MACS2 and consensus peaks with HOMER.
booleanSkip consensus peak generation, annotation and counting.
booleanSkip differential accessibility analysis.
booleanSkip FastQC.
booleanSkip Picard CollectMultipleMetrics.
booleanSkip Preseq.
booleanSkip deepTools plotProfile.
booleanSkip deepTools plotFingerprint.
booleanSkip Ataqv.
booleanSkip IGV.
booleanSkip MultiQC.
booleanGit commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringMaximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GBUse to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.hUse to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Display help text.
booleanNumber of genomic bins to use when calculating deepTools fingerprint plot.
integer500000Method used to save pipeline results to output directory.
stringThe 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.
Workflow name.
stringA 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.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoArguments passed to Nextflow clusterOptions.
string