nf-core/captnseq
CAPTn-seq is an extended Tn-seq pipeline that goes 1) from raw reads to gene essentiality then 2) to gene-gene interaction calls (fron HTTM experiments).
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.
stringOptions specific to the CAPTn-seq trimming/alignment/insertion-site-calling steps.
Path to the reference genome FASTA to align reads against (bwa index is built from this).
stringPath to the gene-feature BED file used by intersect/sites2genes to map insertion sites onto genes.
stringAdapter sequence trimmed by cutadapt from both R1 and R2.
stringACTGTCTCTTATACACATCTMinimum read length kept by cutadapt/fastp trimming.
integer10Mean quality threshold for fastp’s cut_right sliding-window trimming.
integer10Minimum mapping quality kept when filtering aligned reads in samtools view.
integer10Refuse to start if any input FASTQ is smaller than this, in bytes.
integer10000Minimum mapped-read count required per sample after alignment, or the run fails for that sample.
integer1000Selects which tier of the params.resources cpu/memory/time map is applied per process.
stringPer-process cpus/memory/time, keyed by process then by execution_mode tier (‘single’/‘multi’). See conf/modules.config.
objectEmpirical, transposon/library-prep-specific tuning for bin/sam2sites.py.
objectGene-length trim percentages for bin/sites2genes.py.
objectParameters 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.
booleanCustom 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