Added new version and hitory

biobakery · Nov 16, 2024 · 4809439 · 4809439
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diff --git a/biobakery_workflows/biobakery_workflows.py b/biobakery_workflows/biobakery_workflows.py
@@ -35,7 +35,7 @@
 import os
 import subprocess
 
-VERSION = "3.1"
+VERSION = "4.0.0a1"
 
 WORKFLOW_FOLDER="workflows"
 WORKFLOW_EXTENSION=".py"

diff --git a/history.md b/history.md
@@ -1,6 +1,46 @@
 
 # bioBakery workflows History #
 
+##4.0.0a1 (11-15-2024)
+* Update shotgun workflow to give the merge_pairs function more memory for larger files
+* Add extended IUPAC to reverse complement
+* Chunk taxonomy table for species assignment
+* Add strainphlan_markers_wildcard to allow for new extension with strainphlan task
+* Add bam utility script
+* Allow for strainphlan v4p1 format for marker files
+* Update join for metaphlan outputs with new flag
+* Update regroup table for humann v4
+* Add taxonomic profiling options to wmgx_wmtx workflow
+* Change runtimes and add metaphlan option as default for HUMAnN v4
+* Add utility script to downsample fastq
+* Flip new ratios for DADA2 read counts
+* Remove initial filtered reads file from DADA2 outputs
+* Add more ratios and remove table column from DADA2 qc read count output
+* Add reverse complement to primer removal for DADA2 non-ITs
+* Add reverse complement function to utilities
+* Reduce the min size for a large file in kneaddata time/mem equations
+* Add figaro option for DADA2 workflow
+* Update DADA2 silva database versions
+* Update 16s workflow to track cutadapt tasks
+* For tracking cutadapt tasks to dada2 use workflow tasks instead of files
+* Update primer task to individual task from group to support new target
+* Add tracked directory for remove primers for single end for dada2 so it can be used downstream
+* Make paired function more flexible for checking on matches
+* Allow for dada2 remove primers with single end
+* Init add of two options, min_len and pooling, to allow for long reads with DADA2
+* In 16s workflow, add remove primer option
+* In 16s workflow, add check for percent identity max to prevent unclear error messages downstream
+* Add the option to bypass quality control to the wmgx_wmtx workflow
+* Fix warning message for mismatch of file pairs
+* Add database name reduction to qc vis to fit in tables
+* Update strainphlan tasks to allow for identification at a strain level instead of species
+* Increase sample2makers time
+* Make the find of the metaphlan pkl file version agnostic
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 ## v3.2 (TBD) ###
 
 * Update the DADA2 Silva databases to the latest versions

diff --git a/setup.py b/setup.py
@@ -14,7 +14,7 @@
 
 from glob import glob    
 
-VERSION = "3.1"
+VERSION = "4.0.0a1"
 
 AUTHOR = "bioBakery workflows development team"
 AUTHOR_EMAIL = "biobakery-users@googlegroups.com"