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Unclear how to submit multiple reads with webin-cli #23

Open peterjc opened 3 years ago

peterjc commented 3 years ago

https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html has an example for submitting a pair of FASTQ files:

STUDY TODO
SAMPLE TODO
NAME TODO
INSTRUMENT Illumina Genome Analyzer II
INSERT_SIZE 200
LIBRARY_SOURCE GENOMIC
LIBRARY_SELECTION RANDOM
LIBRARY_STRATEGY WGS
FASTQ read1.fastq.gz
FASTQ read2.fastq.gz

What is not clear is if and how to submit lots of paired FASTQ files. Must you prepare a separate manifest file for each FASTQ pair, and call webin-cli many times? Or can the manifest file describe multiple samples? If so, can an example be added please?

sholt6 commented 3 years ago

Hi Peter, As you've found, it's not possible to make multiple Webin-CLI submissions at once, each requiring its own manifest file and command. If you'd like to discuss this further, we'd appreciate you making a ticket through our official helpdesk form: https://www.ebi.ac.uk/ena/browser/support

peterjc commented 3 years ago

That's fine - would you like me to make a pull request clarifying that in the documentation?