Changed 'manifest' format and merged into 'input' parameter#143
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skrakau merged 5 commits intonf-core:devfrom Dec 15, 2020
Merged
Changed 'manifest' format and merged into 'input' parameter#143skrakau merged 5 commits intonf-core:devfrom
skrakau merged 5 commits intonf-core:devfrom
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d4straub
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Dec 15, 2020
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Looks good, two change requests:
- removing
--manifestso sudden is probably not so good, could you instead (1) raise a warning when--manifestis specified saying that it is deprecated (2) forward--manifestinto--input - add to the main.nf help & docu explicitely that the "tsv" extension is required for the mnaifest file.
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Decided to return an error message when deprecated |
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Changed manifest input format:
sampleId, lr, sr1, sr2->sampleId, groupId, sr1, sr2 [, lr]Needs to be TSV format now and has to be handed over also via
--inputparameter now.I made a PR for the testate s well nf-core/test-datasets#208. The current CI tests will fail.
If you agree to this, the
S3manifest file needs to be updated as well.PR checklist
CHANGELOG.mdis updateddocsis updated