nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
2.1.1). The latest
stable release is
2.1.2
.
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$Estimated fragment size used to extend single-end reads.
integer200Sequencing center information to be added to read group of BAM files.
stringRead length used to calculate or retrieve pre-computed MACS2 genome size for peak calling if --macs_gsize isn’t provided.
integerUse controls.
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$Path to GFF3 annotation file.
string^\S+\.gff(\.gz)?$Path to directory or tar.gz archive for pre-built BWA index.
stringPath to directory or tar.gz archive for pre-built Bowtie2 index.
stringPath to directory or tar.gz archive for pre-built Chromap index.
stringPath to directory or tar.gz archive for pre-built STAR index.
stringPath to BED file containing gene intervals. This will be created from the GTF file if not specified.
string^\S+\.bed(\.gz)?$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.
numberPath to blacklist regions in BED format, used for filtering alignments.
stringName of Mitochondrial chomosome in reference assembly e.g. chrM.
stringIf generated by the pipeline save the aligner index (e.g. BWA) in the results directory.
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanReads mapping to mitochondrial contig are not filtered from alignments.
booleanSets the value of the ataqv —mitochondrial-reference-name argument
stringOptions 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.
integerMinimum 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.
booleanSave the trimmed FastQ files in the results directory.
booleanOptions 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.
booleanSave the intermediate BAM files from the alignment step.
booleanWhere possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
booleanBAMTools 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.
booleanSpecifies 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.
integer1Instruct 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.
Use vst transformation instead of rlog with DESeq2.
booleantrueSkip 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/masterInstitutional 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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringNumber of genomic bins to use when calculating deepTools fingerprint plot.
integer500000Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
stringCustom 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
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
boolean