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.
integer
200
Sequencing center information to be added to read group of BAM files.
string
Read length used to calculate or retrieve pre-computed MACS2 genome size for peak calling if --macs_gsize
isn’t provided.
integer
Use controls.
boolean
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path 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.
string
Path to directory or tar.gz archive for pre-built Bowtie2 index.
string
Path to directory or tar.gz archive for pre-built Chromap index.
string
Path to directory or tar.gz archive for pre-built STAR index.
string
Path 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.
number
Path to blacklist regions in BED format, used for filtering alignments.
string
Name of Mitochondrial chomosome in reference assembly e.g. chrM.
string
If generated by the pipeline save the aligner index (e.g. BWA) in the results directory.
boolean
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Reads mapping to mitochondrial contig are not filtered from alignments.
boolean
Sets the value of the ataqv —mitochondrial-reference-name argument
string
Options to adjust adapter trimming criteria.
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integer
Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integer
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integer
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.
integer
10000
Skip the adapter trimming step.
boolean
Save the trimmed FastQ files in the results directory.
boolean
Options to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are ‘bwa’, ‘bowtie2’, ‘chromap’ and ‘star’.
string
Duplicate reads are not filtered from alignments.
boolean
Reads mapping to multiple locations are not filtered from alignments.
boolean
Don’t output BWA MEM alignments with score lower than this parameter.
integer
Do not perform alignment merging and downstream analysis by merging replicates i.e. only do this by merging resequenced libraries.
boolean
Save the intermediate BAM files from the alignment step.
boolean
Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
boolean
BAMTools JSON file with custom filters for paired-end data.
string
$projectDir/assets/bamtools_filter_pe.json
BAMTools JSON file with custom filters for single-end data.
string
$projectDir/assets/bamtools_filter_se.json
Options to adjust peak calling criteria.
Run MACS2 in narrowPeak mode.
boolean
Specifies broad cutoff value for MACS2. Only used when —narrow_peak isnt specified.
number
0.1
Minimum FDR (q-value) cutoff for peak detection, —macs_fdr and —macs_pvalue are mutually exclusive.
number
p-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.
number
Number of biological replicates required from a given condition for a peak to contribute to a consensus peak.
integer
1
Instruct MACS2 to create bedGraph files normalised to signal per million reads.
boolean
Skip MACS2 peak QC plot generation.
boolean
Skip annotation of MACS2 and consensus peaks with HOMER.
boolean
Skip consensus peak generation, annotation and counting.
boolean
Options to adjust differential analysis criteria.
Use vst transformation instead of rlog with DESeq2.
boolean
true
Skip DESeq2 PCA and heatmap plotting.
boolean
Options to skip various steps within the workflow.
Skip FastQC.
boolean
Skip Picard CollectMultipleMetrics.
boolean
Skip Preseq.
boolean
true
Skip deepTools plotProfile.
boolean
Skip deepTools plotFingerprint.
boolean
Skip IGV.
boolean
Skip MultiQC.
boolean
Skip all QC steps except for MultiQC.
boolean
Skip Ataqv.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Number of genomic bins to use when calculating deepTools fingerprint plot.
integer
500000
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean