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)$Comma-separated list of ENA metadata fields to fetch before downloading data.
stringComma-separated list of ENA metadata fields used to create a separate ‘id_mappings.csv’ and ‘multiqc_config.yml’ with selected fields that can be used to rename samples in general and in MultiQC.
stringexperiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_descriptionName of supported nf-core pipeline e.g. ‘rnaseq’. A samplesheet for direct use with the pipeline will be created with the appropriate columns.
stringValue for ‘strandedness’ entry added to samplesheet created when using ‘—nf_core_pipeline rnaseq’.
stringautoMethod to download FastQ files. Available options are ‘aspera’, ‘ftp’ or ‘sratools’. Default is ‘ftp’.
stringOnly download metadata for public data database ids and don’t download the FastQ files.
booleandbGaP repository key.
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
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.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail 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.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of modules test dataset files
strings3://ngi-igenomes/testdata/nf-core/modules/Base URL or local path to location of pipeline test dataset files
strings3://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.
booleanSuffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string