nf-core/deepmutscan

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 storage on Cloud infrastructure.

Email address for completion summary.

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

Path to a FASTA file with the wildtype reference sequence of the mutagenised gene (exactly one sequence).

Nucleotide coordinates of the mutagenised open reading frame within the reference FASTA, in the format ‘start-stop’ (1-based, inclusive), e.g. ‘352-1383’.

Codons programmed at each position of the library. When using ‘custom’, also provide ‘–custom_codon_library’.

Path to a .csv file defining a custom codon library. Required when ‘–mutagenesis_type custom’ is set. Provide either one global comma-separated list of codons without header (e.g. ‘AAA,AAC,AAG’), or a position-wise list with a header line containing ‘Position’, followed by one row per codon position with the position and its allowed codons (e.g. ‘1,ACG,AAA,ACA’ and ‘2,AAA,TTT,ACA’ on separate lines).

Minimum base quality (Phred) for a mismatch to be counted as a mutation, and for a base to contribute to sequencing coverage.

Minimum distance (nt) a mutation or covered base must be from a read edge; also excludes those bases from coverage. Set to 0 to disable edge trimming.

Sequencing-error correction of variant counts. ‘false_doubles’ (default) estimates the error rate of every single-nucleotide variant from reads that carry it together with a nearby programmed multi-nucleotide codon variant; ‘wildtype’ subtracts the background measured by additional deep sequencing of the unmutated template (requires samplesheet rows with type ‘wildtype’); ‘none’ disables correction.

Estimator used by the false-doubles correction. ‘mle’ (default) is a per-variant maximum-likelihood error rate; ‘eb’ is an empirical-Bayes estimate that pools across variants and shrinks per substitution class (steadier for sparse variants). Only applies when error_correction = ‘false_doubles’.

Window (in codons, upstream and downstream) within which programmed multi-nucleotide codon variants are used to estimate the error rate of a single-nucleotide variant during false-doubles correction.

Sliding-window size (in codons) used to smooth the positional coverage and count profiles in the library QC plots.

Targeted number of counts per amino acid variant. Used to draw the sequencing coverage that would be required (assuming an even spread) in the positional coverage plots and the run report.

Estimate sequencing-depth saturation of every library by closed-form hypergeometric rarefaction (on by default).

Estimate variant fitness from matched ‘input’ and ‘output’ libraries of each sample, using the default log-ratio estimator.

Minimum number of reads a variant needs in every ‘input’ replicate to receive a fitness estimate. Applied to the default estimator, DiMSum (‘–fitnessMinInputCountAll’) and mutscan. Variant counting, error correction and library QC are not filtered.

Pseudocount for ‘output’ replicates in which a variant observed in the input was not detected (dropouts), so that strongly depleted variants still receive a finite fitness value. Applied to the default estimator and DiMSum (‘–fitnessDropoutPseudocount’). Set to 0 to disable; dropout variants then receive no fitness estimate in that replicate.

Additionally estimate fitness with DiMSum (Faure et al., 2020). Requires ‘–fitness’.

Additionally estimate variant enrichment with mutscan (Soneson et al., 2023), using edgeR and limma. Requires ‘–fitness’.

Optional wildtype 3D structure (PDB). When supplied together with --fitness, an interactive variant effect inspection tool (self-contained HTML) is built that projects fitness, counts and error-correction biases onto the structure.

Custom MultiQC yaml file containing HTML including a methods description.

Display the full detailed help message.

Display hidden parameters in the help message (only works when –help or –help_full are provided).