nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
1.2.1
). The latest
stable release is
2.1.2
.
Path to comma-separated file containing information about the samples in the experiment.
string
Specifies that the input is single-end reads.
boolean
Estimated fragment size used to extend single-end reads.
integer
Sequencing center information to be added to read group of BAM files.
string
Path to the output directory where the results will be saved.
string
./results
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Name of iGenomes reference.
string
Path to Fasta reference file.
string
Path to GTF annotation file.
string
Full path to directory containing BWA index including base name. i.e. /path/to/index/genome.fa
.
string
Path to BED file containing gene intervals. This will be created from the GTF file if not specified.
string
Path to BED file containing transcription start sites. This will be created from the gene BED file if not specified.
string
Effective genome size parameter required by MACS2.
string
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 BWA index in the results directory.
boolean
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
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
Skip the adapter trimming step.
boolean
Save the trimmed FastQ files in the results directory.
boolean
Reads mapping to mitochondrial contig are not filtered from alignments.
boolean
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
BAMTools JSON file with custom filters for paired-end data.
string
$baseDir/assets/bamtools_filter_pe.json
BAMTools JSON file with custom filters for single-end data.
string
$baseDir/assets/bamtools_filter_se.json
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
Use vst transformation instead of rlog with DESeq2.
boolean
Skip differential accessibility analysis.
boolean
Skip FastQC.
boolean
Skip Picard CollectMultipleMetrics.
boolean
Skip Preseq.
boolean
Skip deepTools plotProfile.
boolean
Skip deepTools plotFingerprint.
boolean
Skip Ataqv.
boolean
Skip IGV.
boolean
Skip MultiQC.
boolean
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional configs hostname.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
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
Maximum amount of time that can be requested for any single job.
string
240.h
Display help text.
boolean
Number of genomic bins to use when calculating deepTools fingerprint plot.
integer
500000
Method used to save pipeline results to output directory.
string
Workflow name.
string
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
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Arguments passed to Nextflow clusterOptions.
string