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PICRUSt2 v2.2.0-b
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@gavinmdouglas gavinmdouglas released this 29 Jul 14:57
· 125 commits to master since this release
v2.2.0-b
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Learn about vigilant mode.

Major:

  • Long-format ("contributional") stratified output is now the default output stratified table, which greatly reduces memory usage. The wide-format table can still be output when the "--wide_table" option is set.

  • Added option to skip copy number normalization to metagenome_pipeline.py and picrust2_pipeline.py along with new unittests.

  • Fixed bug that caused error when running --per_seq_contrib with picrust2_pipeline.py.

  • Bumped r-castor to 1.3.6 -> 1.4.1 and gappa from 0.2.0 -> 0.4.0

  • Convert ASV ids to be strings to avoid cases where they are treated as floats.

  • Changed output format of "metagenome contributions" filetype. Now both relative and raw ASV abundances are output and column names are simplified.

Minor:

  • Removed exact pinning for most conda dependencies to fit with bioconda distribution best-practices.

  • Added pre-print citation in setup.py

  • Added garbage collector (i.e. gc()) calls to castor R script to help reduce memory usage.

  • Now output an additional unstrat pathway abundance table based on regrouping per-seq-contrib stratified output when --per_sequence_contrib used.

  • Added ability for convert_table.py to convert to legacy contributional format.

  • Made option usage for add_descriptions.py clearer.

  • Moved all MetaCyc pathway descriptions to single file.

  • Gzipped all testfiles.

  • Added test for --per-seq-contrib when running full pipeline.

  • Fixed bug where samples with no ASVs / predictions were blank in the weighted NSTI output (now output as 0).

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