nextclade 2.0 updates #430
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kevinlibuit
reviewed
Jun 29, 2022
kevinlibuit
reviewed
Jun 29, 2022
| ~{"--input-gene-map " + gene_annotations_json} \ | ||
| ~{"--input-pcr-primers " + pcr_primers_csv} \ | ||
| ~{"--input-virus-properties " + virus_properties} \ | ||
| --output-basename "~{basename}" \ |
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This was also throwing things off for me. Seemed as if it was looking for intermediate files that weren't tagged appropriately. Removing this and explicitly naming the output files below seemed to suffice.
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Which was throwing things off, --output-basename? I think in combination with --output-all it works.
I managed to get the nextclade_one_sample passing in Github Actions, and I tested the nextclade_many_samples task on some recent production data just fine
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Update nextclade docker from 1.11.0 to 2.0.0.
nextclade --helpPlease adjust your scripts and workflows accordingly to avoid sudden breakage.