nf-core/deepmutscan
nf-core/deepmutscan is a reproducible, scalable, and community-curated pipeline for analyzing deep mutational scanning (DMS) data using shotgun DNA sequencing.
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.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringStart and stop codon positions in the format ‘start-stop’, e.g., ‘352-1383’.
string^\d+-\d+$Minimum number of variant observations required.
integer3Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using ‘custom’, also provide the parameter ‘custom_codon_library’
stringnnkPath to a comma-separated .txt file listing custom codons (e.g., ‘AAA,AAC,AAG,…’). Required when mutagenesis_type is ‘custom’.
stringEnable DiMSum execution.
booleanEnable basic fitness calculation and preceded data preparation (group and merge counts per sample into counts_merged.tsv, create a specific experimental design file and find a high-count 2nt synonymous mutation). All data prepared serves also as input for the dimsum fitness calculator.
booleanWhether to run the SeqDepth simulation module. This is computationally intensive and optional.
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string