nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
Define where the pipeline should find input data and save output data.
File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files.
string
^\S+\.(csv|tsv|txt)$
Comma-separated list of ENA metadata fields to fetch before downloading data.
string
Comma-separated list of ENA metadata fields used to create a separate ‘id_mappings.csv’ and ‘multiqc_config.yml’ with selected fields that can be used to rename samples in general and in MultiQC.
string
experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description
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
Value for ‘strandedness’ entry added to samplesheet created when using ‘—nf_core_pipeline rnaseq’.
string
auto
Method to download FastQ files. Available options are ‘aspera’, ‘ftp’ or ‘sratools’. Default is ‘ftp’.
string
Only download metadata for public data database ids and don’t download the FastQ files.
boolean
dbGaP repository key.
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
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 config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
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
Incoming hook URL for messaging service
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of modules test dataset files
string
s3://ngi-igenomes/testdata/nf-core/modules/
Base URL or local path to location of pipeline test dataset files
string
s3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/
List of parameters that have been deprecated.
This parameter has been deprecated. Please use ‘—download_method sratools’ instead.
boolean
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string