nf-core/dartseq
Pipeline for m6A detection in RNAseq data
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.
stringReference 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/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.
stringRead trimming tool to use.
stringRead aligner to use.
stringSkip alignment stage (useful for smoke tests).
booleanRun Bullseye downstream stage on aligned BAM files.
booleanRun Bullseye in mock mode without invoking Perl scripts.
booleanPath to Bullseye Code directory containing parseBAM.pl, Find_edit_site.pl, summarize_sites.pl and quant/quantify_sites.pl.
stringOptional container image URI or local SIF for Bullseye local modules.
stringAnnotation file for Find_edit_site.pl (refFlat or compatible).
stringSample group label to use as control when pairing matrices for Bullseye.
stringcontrolMinimum coverage passed to parseBAM.pl.
integer10Conversion type for Find_edit_site.pl (for example C2U).
stringC2UMinimum edit percentage for Find_edit_site.pl.
number10Maximum edit percentage for Find_edit_site.pl.
number80Minimum edit fold threshold over control for Find_edit_site.pl.
number1.5Minimum number of edits to report a site.
integer2Minimum edited matrix coverage for Find_edit_site.pl.
integer10Minimum control matrix coverage for Find_edit_site.pl.
integer10Minimum replicate count used by summarize_sites.pl.
integer1Coverage threshold for quantify_sites.pl.
integer10Run RAC motif filtering on Bullseye quantified BED files.
booleanIf true, remove RAC sequence column from RAC-filtered output BED.
booleantrueAggregate Bullseye site-level outputs across samples using gather_sites.pl.
booleanRequest score matrix output from gather_sites.pl.
booleantrueRequest coverage matrix output from gather_sites.pl.
booleantrueRequest mutation-count matrix output from gather_sites.pl.
booleantrueRun Bullseye R GLM helper on gathered coverage and mutation tables.
booleanRun Bullseye GLM module in mock mode.
booleanOptional container image URI for Bullseye R GLM module.
stringPath to functions.R used by the Bullseye GLM helper.
string/opt/bullseye/example_data/markdown/functions.RPath to a tab-delimited sample metadata file containing at least a ‘sample’ column.
stringR formula string used as design in Bullseye GLM helper.
string~groupLink/model option passed to Bullseye helper function.
stringMinimum coverage threshold passed to Bullseye GLM helper.
integer10Run RustQC on aligned BAM files.
booleanCommand template used to run RustQC. Supports placeholders {bam} and {prefix}; if omitted, the module appends ’
stringContainer image URI or local SIF path used for the RUSTQC process.
stringEmit mock RustQC outputs instead of executing RustQC (for testing).
booleanPath to STAR index directory.
stringWhen using pre-built STAR index, do not pass the GTF file at the mapping step.
booleanPath to annotation GTF file.
stringPath to HISAT2 index directory.
stringPath to HISAT2 splice sites file.
stringMinimum memory threshold for HISAT2 index build to include splice-site/exon hints.
string8.GBDisplay 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).
booleanRoot directory for test data and caches. Defaults to DARTSEQ_TEST_ROOT environment variable.
string