nf-core/tbanalyzer
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
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.
stringSelect which part of the MTBseq workflow to run.
Which bundled MTBC analysis pipeline to run.
stringRun read QC only and stop before the MTBseq analysis.
booleanRun the per-sample MTBseq steps as separate parallel processes instead of the single TBfull step.
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.
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).
booleanMTBseq variant-calling and reference settings. These are exposed as parameters so they can be swept via a -params-file for parameter optimization.
Name/path of the MTBseq executable inside the container. Rarely needs changing.
stringMTBseqOptional cohort TSV (sample/library per line) for the joint analysis. Derived from the samplesheet when not provided.
stringAdd an additional filter that excludes all variants except SNPs.
booleanCall low-frequency / subpopulation variants distinct from wild type. Output from this detection mode must not be used for phylogenetic analysis.
booleanMinimum base quality used for the mpileup creation.
integer13Minimum forward read coverage threshold. Alleles with lower forward coverage are not considered.
integer4Project/analysis name used by MTBseq to label output files.
stringmtbseqnfMinimum number of reads indicating an allele with a phred score of at least 20.
integer4Minimum allele frequency (percentage) for an allele to be called.
integer75Minimum percentage of samples with unambiguous information for a position.
integer95Window size in which multiple variants within the same sample cause the positions to be excluded.
integer12SNP distance used to classify samples into groups via agglomerative clustering.
integer12Minimum reverse read coverage threshold. Alleles with lower reverse coverage are not considered.
integer4stringrootDirectory holding the reference genome and its BWA indexes.
stringdata/mtbseq-references/ref/List of known resistance-associated variant positions for resistance prediction.
stringdata/mtbseq-references/res/MTB_Resistance_Mediating.txtList of interesting regions used for annotation of detected variants.
stringdata/mtbseq-references/res/MTB_Extended_Resistance_Mediating.txtGene categories file annotating essential/non-essential genes and repetitive regions (excluded from phylogeny).
stringdata/mtbseq-references/cat/MTB_Gene_Categories.txtVCF of known SNPs used for base quality recalibration.
stringdata/mtbseq-references/res/MTB_Base_Calibration_List.vcf