nf-core/ssds
Single-stranded DNA Sequencing (SSDS) nf-core pipeline
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$Path to the output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions specific to the SSDS pipeline.
SSDS enrichment can be tested in defined genomic intervals by the pipeline. Intervals are specified in a config file.
stringconf/spot_intervals.confIndex to the genome in —spot_intervals config file. If not provided, the pipeline will attempt to use the genome (if defined).
stringnullShould not be provided manually; autogenerated from —spot_intervals.
stringSSDS identifies ssDNA using the micro-homology structure at the 5’ end of reads. When set to true, the SSDS pipeline also infers three additional, but low confidence fragment types; importantly, reads of these thress types are a best guess, but could be incorrect (i.e. fragments classified as dsDNA may instead come from ssDNA in a sufficiently enriched library).
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)?$Path to the BWA index folder.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanMethod used to save pipeline results to output directory.
string