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.

required
type: string
pattern: ^\S+\.csv$

Estimated fragment size used to extend single-end reads.

type: integer
default: 200

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

type: string

Read length used to calculate or retrieve pre-computed MACS2 genome size for peak calling if --macs_gsize isn’t provided.

type: integer

Use controls.

type: boolean

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([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.

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

required
type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Path to GTF annotation file.

type: string
pattern: ^\S+\.gtf(\.gz)?$

Path to GFF3 annotation file.

type: string
pattern: ^\S+\.gff(\.gz)?$

Path to directory or tar.gz archive for pre-built BWA index.

type: string

Path to directory or tar.gz archive for pre-built Bowtie2 index.

type: string

Path to directory or tar.gz archive for pre-built Chromap index.

type: string

Path to directory or tar.gz archive for pre-built STAR index.

type: string

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

type: string
pattern: ^\S+\.bed(\.gz)?$

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

type: string
pattern: ^\S+\.bed(\.gz)?$

Effective genome size parameter required by MACS2.

type: number

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 aligner index (e.g. BWA) 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

Reads mapping to mitochondrial contig are not filtered from alignments.

type: boolean

Sets the value of the ataqv —mitochondrial-reference-name argument

type: string

Options to adjust adapter trimming criteria.

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

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.

type: integer
default: 10000

Skip the adapter trimming step.

type: boolean

Save the trimmed FastQ files in the results directory.

type: 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’.

type: string

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

Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.

type: boolean

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

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

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

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

Options to adjust peak calling criteria.

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

Options to adjust differential analysis criteria.

Use vst transformation instead of rlog with DESeq2.

type: boolean
default: true

Skip DESeq2 PCA and heatmap plotting.

type: boolean

Options to skip various steps within the workflow.

Skip FastQC.

type: boolean

Skip Picard CollectMultipleMetrics.

type: boolean

Skip Preseq.

type: boolean
default: true

Skip deepTools plotProfile.

type: boolean

Skip deepTools plotFingerprint.

type: boolean

Skip IGV.

type: boolean

Skip MultiQC.

type: boolean

Skip all QC steps except for MultiQC.

type: boolean

Skip Ataqv.

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

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 config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

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
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

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

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

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

hidden
type: integer
default: 500000

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
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean