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
./results
Email 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.
string
Options specific to the SSDS pipeline.
SSDS enrichment can be tested in defined genomic intervals by the pipeline. Intervals are specified in a config file.
string
conf/spot_intervals.conf
Index to the genome in —spot_intervals config file. If not provided, the pipeline will attempt to use the genome (if defined).
string
null
Should not be provided manually; autogenerated from —spot_intervals.
string
SSDS 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).
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to the BWA index folder.
string
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean
Method used to save pipeline results to output directory.
string