nf-core/seqinspector
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
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$Take a subset of reads for analysis.
numberThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringComma-separated string of tools to run
stringSelect some default setup for the tools to be run, tools can still be used to add tools
stringdefaultComma-separated string of tools to skip - overrides any other means of tools selection
stringOptions for validating and screening FASTQ files.
Arguments to pass to FQ lint
stringWhether to continue with the pipeline if linting fails for a single sample.
booleantruePath to custom CheckQC config
stringOptions for Kraken2
Path to Kraken2 database file, either a gzipped file or the path to the uncompressed database.
stringTurn on saving of Kraken2-aligned reads
booleanTurn on saving of Kraken2 per-read taxonomic assignment file
booleanTurn on saving of uncompressed Kraken2 DB
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringDo not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/A .csv of reference genomes to be mapped against by FastQ Screen
string${projectDir}/assets/example_fastq_screen_references.csvPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to bwamem2 indices.
stringSequence dictionary for the reference fasta file provided.
string^\S+.dict$Fasta index for the reference fasta file provided.
string^\S+.fai$Path to target intervals file.
string^\S+.(bed|bed.gz|interval_list)$Path to bait intervals file.
string^\S+.(bed|bed.gz|interval_list)$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.
booleanBase path / URL for data used in the modules
strings3://ngi-igenomes/testdata/nf-core/modules/Custom 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/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when —help or —help_full are provided).
boolean