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Fixes a few issues in the ML/issue55 branch #64

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MarieLataretu merged 1 commit into MarieLataretu/issue55 from fix/issue55

Nov 8, 2023

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matthuska commented Nov 6, 2023

Resolves a couple little issues I ran into using the branch that includes work on the --keep functionality (see issue #55 ). What was fixed:

process output file names don't always match the expected file name (mostly typo-type or missing suffix fixes)
some conda envs are broken because of deprecations and removed code. Set maximum version numbers for a few packages to work around this.
filter_fastq_by_name needs the pigz tool, but that was not available. For now I substituted the minimap2 container which happens to have pigz installed.


          Fix some incorrect output names, conda envs, container for pigz

b3df249

matthuska requested a review from MarieLataretu

November 6, 2023 12:48

MarieLataretu approved these changes

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MarieLataretu merged commit f5aeab7 into MarieLataretu/issue55

matthuska deleted the fix/issue55 branch

November 10, 2023 09:25

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