perf: datavzrd wrapper v3.12.1, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules
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this then uses `datavzrd=2.36.10`
fxwiegand
reviewed
May 27, 2024
based on this very approximate statement, but started with a lower estimate here: pachterlab/sleuth#139 (comment) so we should increase this if we see this failing with out of memory on any real datasets
…out-of-space errors
dlaehnemann
changed the title
v3.10.2 datavzrd.smkv3.11.0, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb
…nakemake-workflows/rna-seq-kallisto-sleuth into perf/update-datavzrd-wrapper-to-3-10-2
…is seems to be handled automatically by the bioconductor recipes nowadays
…ading script via `input:` instead of `params:`
…his branch, will fix on a new branch where we also fix the ensembl cdna reference (see https://www.r-bloggers.com/2020/01/comparing-ensembl-gtf-and-cdna/ for discrepancies between the Ensembl GTF and cDNA FASTA)
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For now, I'll turn off the reactivated testing of isoformSwitchAnalyzer, to get the tests to pass here and merge this PR. And then, I'll fix isoformSwitchAnalyzer on a new branch, where we'll also fix the Ensembl cDNA fasta file, as the current failure is due to the Ensembl GTF and the Ensembl cDNA FASTA file being out of sync, see here: Removing Ensembl cDNA FASTA redundancies (the same HGNC gene symbol appearing with multiple Ensembl |
….org), so switch to 112 to get tests to pass -- sigh
dlaehnemann
changed the title
v3.11.0, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mbv3.11.0, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules
johanneskoester
requested changes
Jun 13, 2024
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It would probably also makes sense to upgrade to 2.36.15 as this will probably save loads of space in the resulting reports 😊 |
…nfig["report"]["offer_excel"]
dlaehnemann
changed the title
v3.11.0, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrulesv3.12.1, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules
Co-authored-by: Johannes Köster <[email protected]>
johanneskoester
approved these changes
Jun 13, 2024
johanneskoester
pushed a commit
that referenced
this pull request
Aug 16, 2024
🤖 I have created a release *beep* *boop* --- ## [2.7.0](v2.6.0...v2.7.0) (2024-08-15) ### Features * Improve datavzrd tables ([#93](#93)) ([93512b8](93512b8)) ### Bug Fixes * Fix missing output in spia.R when no significant genes are found ([#103](#103)) ([bc0d017](bc0d017)) * Handle missing bam columns in units.tsv ([#105](#105)) ([bae88d0](bae88d0)) * Remove non-existent outputs in spia rule ([#102](#102)) ([0fbb930](0fbb930)) * update to latest datavzrd ([417ec3b](417ec3b)) ### Performance Improvements * datavzrd wrapper `v3.12.1`, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules ([#92](#92)) ([70850fb](70850fb)) * Update datavzrd wrapper ([#98](#98)) ([e5eb0e0](e5eb0e0)) * Update samtools fast separate wrapper ([#100](#100)) ([65d8f41](65d8f41)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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this then uses
datavzrd=2.36.10