nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
1.8
). The latest
stable release is
1.12.0
.
Define where the pipeline should find input data and save output data.
File containing SRA/ENA/DDBJ identifiers one per line to download their associated metadata and FastQ files.
string
^\S+\.(csv|tsv|txt)$
Specifies the type of identifier provided via --input
- available options are ‘sra’ and ‘synapse’.
string
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,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
Force download FASTQ files via sra-tools instead of via the ENA FTP.
boolean
Only download metadata for public data database ids and don’t download the FastQ files.
boolean
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})$
Path to Synapse configuration file
string
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
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
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