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.
stringThe default list of fields used by the pipeline can be found at the top of the bin/sra_ids_to_runinfo.py script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. 'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'. Full list of accepted metadata fields can be obtained from the ENA API.
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.
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'.
stringautoThe default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.
Method to download FastQ files. Available options are 'aspera', 'ftp' or 'sratools'. Default is 'ftp'.
stringFTP and Aspera CLI download FastQ files directly from the ENA FTP whereas sratools uses sra-tools to download *.sra files and convert to FastQ.
Only download metadata for public data database ids and don't download the FastQ files.
booleandbGaP repository key.
stringPath to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.
The 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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional 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.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
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.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
List of parameters that have been deprecated.
This parameter has been deprecated. Please use '--download_method sratools' instead.
boolean