nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
1.0
). The latest
stable release is
1.12.0
.
Define where the pipeline should find input data and save output data.
File containing SRA/ENA/GEO identifiers one per line to download their associated metadata and FastQ files.
string
\.txt$
Comma-separated list of ENA metadata fields to fetch before downloading data.
string
Name of supported nf-core pipeline e.g. ‘rnaseq’. A samplesheet for direct use with the pipeline will be created with the appropriate columns.
string
Only download metadata for public data database ids and don’t download the FastQ files.
boolean
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})$
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 configs hostname.
string
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
Method used to save pipeline results to output directory.
string
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
Do not use coloured log outputs.
boolean
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
Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
boolean