Refactor the single_end meta thing to be pulled from the ENA metadata. #9
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Include the Fetch tool metadata into the multiqc report
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I think taking metadata from ENA is good. But we should probably add an ability to user/prefect to push correct library_strategy or library_layout to pipeline. Waiting for ENA to fix data can take time (and we had cases where they must contact users but users are unknown/do not reply..).
Basically, first iteration of pipeline should be with ENA metadata. If something failed, we checked - we should be able to specify fixed args and push assembly and do not delay it.
In my view, we also need to add library_strategy or library_layout to params
Indeed.. I wil add 2 more parameters for that (same logic, if they are there then it will ignore the metadata) |
- Make MEGAHIT fail if the contigs are empty - MultiQC ENA Metadata report (remove the hardcoded name from the process) - Added some more unit tests - Fix the assembler override ( only use single_end auto selection if the assembler is null )
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Perfect. I have enough 👍 to merge... |
Include the Fetch tool metadata into the multiqc report