nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a samplesheet with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row. See usage docs.
Estimated fragment size used to extend single-end reads.
integer200Sequencing center information to be added to read group of BAM files.
stringRead length used to calculate or retrieve pre-computed MACS2 genome size for peak calling if --macs_gsize isn't provided.
integerRead length together with the genome fasta are used to calculate MACS2 genome size using the khmer program as explained here. For all the genomes present in the igenomes.config the genome size has been already precomputed and the read length is then used to retrieve the corresponding value
Use controls.
booleanUse this to indicate that your samplesheet lists controls.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
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.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have the appropriate alignment index available this will be generated for you automatically. Combine with --save_reference to save alignment index for future runs.
Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$This parameter is mandatory if --genome is not specified.
Path to GFF3 annotation file.
string^\S+\.gff(\.gz)?$This parameter must be specified if --genome or --gtf are not specified.
Path to directory or tar.gz archive for pre-built BWA index.
stringPath to directory or tar.gz archive for pre-built Bowtie2 index.
stringPath to directory or tar.gz archive for pre-built Chromap index.
stringPath to directory or tar.gz archive for pre-built STAR index.
stringPath to BED file containing gene intervals. This will be created from the GTF file if not specified.
string^\S+\.bed(\.gz)?$Path to BED file containing transcription start sites. This will be created from the gene BED file if not specified.
string^\S+\.bed(\.gz)?$Effective genome size parameter required by MACS2.
numberEffective 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 aligner index (e.g. BWA) in the results directory.
booleanIf the index generated by the aligner 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/igenomesDo 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.
Reads mapping to mitochondrial contig are not filtered from alignments.
booleanSets the value of the ataqv --mitochondrial-reference-name argument
stringBy default takes the value of the mito_name parameter, if set. However, some plants and algae have chloroplast genomes in addition to a mitochondrial genome and thus mito_name can have values as multiple names that are separated by a | symbol that will break ataqv, in these cases this parameter can be used to overwrite these values.
Options to adjust adapter trimming criteria.
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.
Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.
integer10000Skip 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.
Options to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are 'bwa', 'bowtie2', 'chromap' and 'star'.
stringDuplicate 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.
Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
booleanThis may either be in the form of FastQ or BAM files depending on the options available for that particular tool.
BAMTools JSON file with custom filters for paired-end data.
string$projectDir/assets/bamtools_filter_pe.jsonBAMTools JSON file with custom filters for single-end data.
string$projectDir/assets/bamtools_filter_se.jsonOptions to adjust peak calling criteria.
Run 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.
booleanOptions to adjust differential analysis criteria.
Skip DESeq2 PCA and heatmap plotting.
booleanOptions to skip various steps within the workflow.
Skip FastQC.
booleanSkip Picard CollectMultipleMetrics.
booleanSkip Preseq.
booleantrueSkip deepTools plotProfile.
booleanSkip deepTools plotFingerprint.
booleanSkip IGV.
booleanSkip MultiQC.
booleanSkip all QC steps except for MultiQC.
booleanSkip Ataqv.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git 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 config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum 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.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use 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.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Number of genomic bins to use when calculating deepTools fingerprint plot.
integer500000Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.