nf-core/cutandrun

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

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

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Save genome reference data to the output directory

Save any technical replicate FASTQ files that were merged to the output directory

Save trimmed FASTQ files to the output directory

Save BAM files aligned to the spike-in genome to the output directory

Save unaligned sequences to the output directory

Save alignment intermediates to the output directory (WARNING: can be very large)

Email address for completion summary.

Name of iGenomes reference.

Path to bowtie2 index

Path to GTF annotation file

Path to gene BED file

Path to genome blacklist

Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6

Path to spike-in bowtie2 index

Path to spike-in fasta

Path to FASTA genome file.

Run pipeline up to input checking

Run pipeline up to reference preparation

Run pipeline up to pre-alignment

Run pipeline up to alignment

Run pipeline up to q-filtering

Run pipeline up to peak calling

Skips fastqc reporting

Skips trimming

Skips de-duplication

Skips reporting

Skips preseq reporting

Skips igv session generation

Skips deeptools QC repoting

Skips deeptools heatmap generation

Skips peak QC reporting

Skips multiqc

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

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

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

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

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

Filter reads below a q-score threshold

Filter mitochondrial reads

Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome.

De-duplicate target reads AND control reads (default is control only)

De-duplicate reads based on read 1 5’ start position. Relevant for assays using linear amplification with tagmentation (default is false).

Use —end-to-end mode of Bowtie2 during alignment

Sets the target read normalisation mode. Options are: [“Spikein”, “RPKM”, “CPM”, “BPM”, “None” ]

If normsalisation option is one of “RPKM”, “CPM”, “BPM” - then the binsize that the reads count is calculated on is used.

Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary peak callers will be run and outputed to the results folder.

Specifies whether to use a control to normalise peak calls against (e.g. IgG)

Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks

Specifies whether the background control is scaled prior to being used to normalise peaks.

SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if --use_control is false

SEACR normalization.

SEACR stringency.

Q-value threshold for MACS2 peak caller.

P-value threshold for macs2 peak caller. If set it will overide the qvalue.

parameter required by MACS2. If using an iGenomes reference these have been provided when --genome is set as GRCh37, GRCh38, GRCm38, WBcel235, BDGP6, R64-1-1, EF2, hg38, hg19 and mm10. Otherwise the gsize will default to GRCh38.

Determines whether MACS2 broad or narrow peak mode is used for the peak caller

MACS2 broad cutoff parameter

Specifies what samples to group together for consensus peaks. Options are [group, all]

Minimum number of overlapping replicates needed for a consensus peak

Show gene names instead of symbols in IGV browser sessions

Deeptools multiBamSummary bam bin size

Deeptools Correlation Plot statistical calculation method

Deeptools heatmap gene plot before length (bases)

Deeptools heatmap gene plot body length (bases)

Deeptools heatmap gene plot after length (bases)

Deeptools heatmap peak plot before length (bases)

Deeptools heatmap peak plot after length (bases)

Flag for whether to generate a heatmap for all samples together

Minimum fragment overlap for FriP score

Minimum peak overlap for peak reproducibility plot

Pull Docker container.

Custom MultiQC yaml file containing HTML including a methods description.