Explicitly declare plugins in nextflow.config #315
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nebfield
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https://pgsc-calc.readthedocs.io/en/latest/how-to/offline.html needs to have information about the plugins and pointers to nextflow documentation: https://www.nextflow.io/docs/latest/plugins.html#offline-usage |
smlmbrt
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Jun 17, 2024
nebfield
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Jun 19, 2024
* use dev version of pygscatalog use dev version of pgscatalog-utils * fix versions * update images * Add match error explanation to docs (#311) * add match explanation * Update match.rst Some edits --------- Co-authored-by: Sam Lambert <sam.a.lambert@gmail.com> * Explicitly declare plugins in nextflow.config (#315) * declare plugins explicitly * add provenance to pipeline_info output * update citation string * remove deprecated parameter * nf-schema migration updates * fix validation parameter case * update help message to use nf-schema * update offline instructions with plugin information * fix typo * bump fraposa_pgsc version * disable nf-schema validateparameters() for now * update conda environments * update pyyaml environment * bump pgscatalog-utils to v1.1.1 * bump version to beta * drop defaults channel from conda environment * bump pgscatalog-utils version * trigger action --------- Co-authored-by: Sam Lambert <sam.a.lambert@gmail.com>
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This should make problems when pulling nf-schema (previously: nf-validation) and nf-prov more immediately obvious
Also, adding nf-prov output to pipeline_info is straightforward