Path to comma-separated file containing information about the samples in the experiment.

required
type: string

Specifies that the input is single-end reads.

type: boolean

Estimated fragment size used to extend single-end reads.

type: integer

Sequencing center information to be added to read group of BAM files.

type: string

Path to the output directory where the results will be saved.

type: string
default: ./results

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Name of iGenomes reference.

type: string

Path to Fasta reference file.

type: string

Path to GTF annotation file.

type: string

Full path to directory containing BWA index including base name. i.e. /path/to/index/genome.fa.

type: string

Path to BED file containing gene intervals. This will be created from the GTF file if not specified.

type: string

Path to BED file containing transcription start sites. This will be created from the gene BED file if not specified.

type: string

Effective genome size parameter required by MACS2.

type: string

Path to blacklist regions in BED format, used for filtering alignments.

type: string

Name of Mitochondrial chomosome in reference assembly e.g. chrM.

type: string

If generated by the pipeline save the BWA index in the results directory.

type: boolean

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Do not load the iGenomes reference config.

hidden
type: boolean

Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).

type: integer

Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.

type: integer

Skip the adapter trimming step.

type: boolean

Save the trimmed FastQ files in the results directory.

type: boolean

Reads mapping to mitochondrial contig are not filtered from alignments.

type: boolean

Duplicate reads are not filtered from alignments.

type: boolean

Reads mapping to multiple locations are not filtered from alignments.

type: boolean

Don’t output BWA MEM alignments with score lower than this parameter.

type: integer

Do not perform alignment merging and downstream analysis by merging replicates i.e. only do this by merging resequenced libraries.

type: boolean

Save the intermediate BAM files from the alignment step.

type: boolean

BAMTools JSON file with custom filters for paired-end data.

hidden
type: string
default: $baseDir/assets/bamtools_filter_pe.json

BAMTools JSON file with custom filters for single-end data.

hidden
type: string
default: $baseDir/assets/bamtools_filter_se.json

Run MACS2 in narrowPeak mode.

type: boolean

Specifies broad cutoff value for MACS2. Only used when —narrow_peak isnt specified.

type: number
default: 0.1

Minimum FDR (q-value) cutoff for peak detection, —macs_fdr and —macs_pvalue are mutually exclusive.

type: 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.

type: number

Number of biological replicates required from a given condition for a peak to contribute to a consensus peak.

type: integer
default: 1

Instruct MACS2 to create bedGraph files normalised to signal per million reads.

type: boolean

Skip MACS2 peak QC plot generation.

type: boolean

Skip annotation of MACS2 and consensus peaks with HOMER.

type: boolean

Skip consensus peak generation, annotation and counting.

type: boolean

Use vst transformation instead of rlog with DESeq2.

type: boolean

Skip differential accessibility analysis.

type: boolean

Skip FastQC.

type: boolean

Skip Picard CollectMultipleMetrics.

type: boolean

Skip Preseq.

type: boolean

Skip deepTools plotProfile.

type: boolean

Skip deepTools plotFingerprint.

type: boolean

Skip Ataqv.

type: boolean

Skip IGV.

type: boolean

Skip MultiQC.

type: boolean

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional configs hostname.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h

Display help text.

hidden
type: boolean

Number of genomic bins to use when calculating deepTools fingerprint plot.

hidden
type: integer
default: 500000

Method used to save pipeline results to output directory.

hidden
type: string

Workflow name.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

Do not use coloured log outputs.

hidden
type: boolean

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Arguments passed to Nextflow clusterOptions.

hidden
type: string