v1.13

• WRAPPER_SLURM detects Snakemake version and uses appropriate env var (LCDBWF_SNAKEMAKE_PROFILE or LCDBWF_SNAKEMAKE_PROFILE_V8). This means you can keep your existing env var for backwards compatibility in older projects using snakemake <8.
• deploy.py accepts an --additional-main argument, which defaults to the value of LCDBWF_ADDITIONAL_MAIN env var. This lets you configure additional package[s] to install in a cluster-specific manner.
• Updated env yaml files
• Updated docs
• Updated dmel references config since existing URLs appear to be broken
• Default to using conda instead of mamba as conda front-end (since libmamba has been incorporated into conda itself for a while now)

v1.12

• Fixed render_r1_r2 function(s) in Snakefiles (#413) which cleans up some Snakefile functions

• add Plodia interpunctella reference config (#417) which adds some postprocessing functionality for dealing with references in zip files, and adds references for Plodia interpunctella

• Make strand_arg a param (#415) which moves strandedness arguments to params: directive, letting jobs re-run if strandedness changed in config. Previously, rules needed to be manually re-run after changing strandedness in config.

• Update plotting.R (#423) to fix a typo in the (infrequently-used) lcdbwf::vargenes_heatmap() function

• Change SRA fastq directory (#418) which improves how SRA-configured runs are handled, addressing #408

• Use tempdir, if configured, for STAR (#425) which allows STAR to use a temp dir if configured

v1.11

• Add samtools stats and samtools flagstat for additional QC options (#397)
• Overhauls the way output Rds objects are made from RNA-seq downstream RMarkdown files (#399, thanks @mitraak)
  • This prepares for integration with Carnation, an interactive web interface currently still in development but being used internally
  • Rds files are dramatically smaller after stripping out superfluous data
  • Better support for running rnaseq.Rmd followed by functional-enrichment.Rmd, and/or gene-patterns.Rmd without overwriting existing Rds files.
• Support universe of expressed genes by default when running functional enrichment, while also supporting customization if needed (#401, thanks @Mira0507 )
• Support LRT in the lcdb::make_results machinery (#396, thanks @menoldmt)

v1.10.2

Merge pull request #376 from lcdb/v1.10.2rc

V1.10.2rc

v1.10.1

updt changelog

v1.10

v1.10

v1.7

See https://lcdb.github.io/lcdb-wf/changelog.html for changelog.

v1.5.3

See https://lcdb.github.io/lcdb-wf/changelog.html for changelog.