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Add ability to download more than 2 FastQ files via FTP and Aspera

Open drpatelh opened this issue 6 months ago • 3 comments

Description of feature

As raised in https://github.com/nf-core/fetchngs/pull/259#discussion_r1470946683 and https://github.com/nf-core/fetchngs/pull/259#discussion_r1470960788 we need to revisit why we restricted downloading a max of 2 FastQ files via FTP and Aspera.

I vaguely remember this was added because they may have been discrepancies in some files have 3 FastQ files but only 2 md5sum files which broke the pipeline. We need to find some examples of database ids that have 3 FastQ files and take a proper look to see if we can accommodate them in the pipeline.

If you do have more than 2 FastQ files e.g. single-cell data like in this issue https://github.com/nf-core/fetchngs/issues/144 then you should be able to retrieve these by using the --force_sratools_download parameter.

drpatelh avatar Jan 30 '24 11:01 drpatelh