nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
1.10.0). 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/DDBJ identifiers one per line to download their associated metadata and FastQ files.
string^\S+\.(csv|tsv|txt)$Specifies the type of identifier provided via --input - available options are ‘sra’ and ‘synapse’.
stringComma-separated list of ENA metadata fields to fetch before downloading data.
stringComma-separated list of ENA metadata fields used to create a separate ‘id_mappings.csv’ and ‘multiqc_config.yml’ with selected fields that can be used to rename samples in general and in MultiQC.
stringexperiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_descriptionName of supported nf-core pipeline e.g. ‘rnaseq’. A samplesheet for direct use with the pipeline will be created with the appropriate columns.
stringValue for ‘strandedness’ entry added to samplesheet created when using ‘—nf_core_pipeline rnaseq’.
stringautoForce download FASTQ files via sra-tools instead of via the ENA FTP.
booleanOnly download metadata for public data database ids and don’t download the FastQ files.
booleanstringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Path to Synapse configuration file
stringParameters 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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay 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})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
boolean