twere

bug fix cutadapt rule that affected fwd_1 settings: primers weren't properly translated to RC. This may have left to primers that were read into at the end of the sequence not being cut properly, which may affect ASV richness if primer or the bit behind it wasn't anyway removed by truncating/QC in a later step.

isaroseisarose

a couple fixes for starting from an old data set

daffordeal

dadasnake v0.11!

Major changes:

• ASVs are now called ASVs! sorry for the confusion, but it should be possible to run dadasnake v0.11 on top of old runs and it will internally deal with the naming. File names stay the same.
• Clustering of ASVs into OTUs: dadasnake will still make DADA2 ASVs, but can now also cluster these (using VSEARCH or R's DECIPHER) at a user-specified similarity cut-off. All downstream processing can be done with these clusters instead of or in addition to the ASVs: taxonomic annotation, ITSx annotation or filtering, blasting, filtering on length and/or taxonomy, matching with funguild or fungalTraits. Exceptions is the functional predictions with PICRUSt2 which is done at ASV level. The results of the clustering step are to be found in the 'clusteredTables' folder. Post-clustering can be turned on by requesting that taxonomy steps are run on 'cluster' in addition to 'ASV' or by setting post_clustering to true. Post-processing (funguild etc) of the clustered data is still found in the post directory.
• PICRUST2: since tax4fun2 is no longer maintained (it seems), PICRUSt2 has been integrated.
• Error models for Novaseq have been added to the code base and can (like all error models) be selected by name in the config. It is recommended to use them for Novaseq data.

Minor changes:

• README was adjusted to the new steps. The default and example config files were adjusted and they have a better structure and commenting now.
• the works for the major changes necessitated some changes that should be invisible for the user.
• a few bugs got fixed along the way, so more lenient use of the config file might be possible.

score

fixed dada2_env by removing bioconductor-genomeinfodbdata=1.2.3 which isn't needed anymore

bowl

Bug fix for cutadapt step to allow datasets with different directions

oh canache!

version 0.10.3 features:

you can use multiple databases for taxonomic classification (unchanged from 0.10.1)
blast results are added to the OTU table using BASTA (unchanged from 0.10.1)
tax4fun2 can be run with user databases (as in 0.10.0)
you can specify the ITSx models (as in 0.10.0)
fastqc and multiQC output (fixed zip problem from in 0.10.1)
behaviour for cluster submission is now more flexible (see readme and FAQ)
VARIABLE_CONFIG can have spaces in the variable values now

oh... canache!

version 0.10.2 features:

• you can use multiple databases for taxonomic classification (unchanged from 0.10.1)
• blast results are added to the OTU table using BASTA (unchanged from 0.10.1)
• tax4fun2 can be run with user databases (as in 0.10.0)
• you can specify the ITSx models (as in 0.10.0)
• fastqc and multiQC output (unchanged from in 0.10.1)
• bug fix: number of reads in raw files were sometimes shown as NA in earlier versions and should now always be there.

oh! canache

version 0.10.1 features:

you can use multiple databases for taxonomic classification (some bugs fixed over 0.10.0 - they would have resulted in not running)
blast results are added to the OTU table using BASTA (nicer formatting over 0.10.0 - the repeated names are easy to spot in the old version)
tax4fun2 can be run with user databases (as in 0.10.0)
you can specify the ITSx models (as in 0.10.0)
fastqc and multiQC output (now implemented in all workflows)

oh canache

version 0.10.0 features:

• you can use multiple databases for taxonomic classification
• blast results are added to the OTU table using BASTA
• tax4fun2 can be run with user databases
• you can specify the ITSx models
• fastqc and multiQC output

waffle of content

bug fix in config.default.yaml