I'm downloading files with fetchngs. in the SRA_FA...
# fetchngs
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I'm downloading files with fetchngs. in the SRA_FASTQ_FTP step it downloads files directly from ftp.sra.ebi.ac.uk using wget. The issue is that no protocol is specified and wget uses http as default. the server rejects the request because it is not ftp and the pipeline fails after many retries. Is there a setting I need to change for this to work or should I submit a pull request appneindg 'ftp://' to the fastq file url? I suspect this is a breaking change from the EMBL side since there is an issue on github with the same problem Thread in Slack conversation
I fixed the issues (container is already fixed in dev) and made a PR as a patch (directly to master). I hope I did everything correctly https://github.com/nf-core/fetchngs/pull/338