v3.1.0

What's Changed

• Dev ks by @katsikora in #1042
• Dev ks by @katsikora in #1043
• Fix CI test by @katsikora in #1046
• fix 1023 by @katsikora in #1047
• fix 1025 by @katsikora in #1052
• Fix 1049 and 1009 by @katsikora in #1054
• docs by @katsikora in #1055
• drop log as omitted by profile by @WardDeb in #1059
• Pairtools merge by @WardDeb in #1067
• Create indices orgyamls by @WardDeb in #1072
• 3.1.0 by @WardDeb in #1073

Full Changelog: v3.0.0...v3.1.0

v3.0.0

• base python version 3.11 or newer is now required
• With toml transition, all '-' in workflows have been removed (mRNA-seq -> mRNAseq).
• makePairs workflow has been initiated
• pytest / lint have been moved to a [actions] optional dependency
• docs requirements have been moved to a [docs] optional dependency
• version is no longer set in init, but in toml file
• mamba requirement is dropped, tests ported to conda
• cluster.yaml is deprecated in favor of profiles, condaEnvDir is now specified to be set in the profile rather then in another yaml file.
• dependency pins dropped, snakemake >= 8 required.
• createEnvs has changed, autoDetectCondaDir has been removed (as it needs to be set in snakemake profile).
• all rule-specific log redirectives have been removed, let profile capture and save to specific files.
• DAG plotting has been made dependent on graphviz, if graphviz is not available as a library (happens if installed via conda) or if dot is not available in path, the DAG is printed out in ASCII format to a txt file
• regex changes in createIndices changed to match lines starting with >, spikeinExt is appended at the end.
• regex change in threeprimeseq mode that simplifies the wildcard constraint (though should have the same functionality).
• default adapter trimming for Illumina stranded library prep (CTGTCTCTTATACACATCT) instead of TruSeq adapter (AGATCGGAAGAGC)
• commented out temped sortedByName bam files under SNPsplit rules, as they don't seem to be generated (perhaps this was some older version's default)
• createEnvs has some basic profile checks (wether conda-frontend is set, if a prefix is set, etc.)

2.8.1

What's Changed

• fix thefuzz dep by @katsikora in #976
• Develop by @katsikora in #977
• bugfix 2.8.0 by @WardDeb in #978
• bugfix 2.8.0 by @WardDeb in #980
• Vboost by @WardDeb in #981
• dunder 2.8.1 by @WardDeb in #982
• update version in conda recipe, include a more sensible default conda… by @WardDeb in #984
• recipe version, condaenvdir default version by @WardDeb in #985
• include news for 281 by @WardDeb in #986
• Include the news for 2.8.1 by @WardDeb in #987

Full Changelog: 2.8.0...2.8.1

• Boosted versions on shared_env, as python 3.7 and multiqc no longer work together.
• WGBS doesn't draw a PCA on datasets with one or two samples.
• HiCExplorer version boosted in HiC mode

snakePipes 2.8.0

snakePipes 2.8.0

• Moved SalmonIndex creation from mRNAseq and scRNAseq to createIndices.
• Changed the behaviour of snakePipes createEnvs - it is no longer possible to set condaEnvDir with this function. It is required to set it with snakePipes config beforhand, instead. To ingore what's in the defaults.yaml and overwrite the condaEnvDir value with default system conda prefix, use '--autodetectCondaEnvDir'.
• Snakemake options in the defaults.yaml are now an empty string. The required arguments '--use-conda --conda-prefix' have been directly added to the command string. condaEnvDir is parsed from defaults.yaml, requiring running snakePipes config first.
• Added a 'three-prime-seq' mode to mRNAseq (David Koppstein and Katarzyna Sikora).
• Added DESeq2 run on PAS clusters to the 'three-prime-seq' mode of mRNAseq.
• Added support for multiple comparison groups to ChIPseq and ATAC-seq.
• Added SEACR as an optional peak caller to ChIPseq.
• Fixes #819
• Fixes #947
• Fixes #945
• Fixes #941
• Fixes #951
• fastq files are checked for validity
• an 'on success' file is touched in the output directory when a workflow is finished successfully
• fuzzywuzzy deprecated in favor for thefuzz

snakePipes 2.7.3

• Fixes #884 by creating an additional conda env for DSS. Build tests are now run with strict channel priority.

snakePipes 2.7.2

snakePipes 2.7.2

• STAR version has been updated to 2.7.10b. 2.7.10a was returning segmentation fault on MAC.

• STAR command has been updated. Now, STAR itself offers a command line option for processing input files.

• Put a cap on python version for the deeptools env. The current version of deeptools is not supporting the newer python versions and some tools fail.

• Update default condaDir.

• The filter_gtf function has become a bit more versatile. GTF files that include delimiters (';') in e.g. a description field are now allowed. Gene names are also allowed to have symbols now. Lastly, GTF files that have xRNA instead of transcript as a feature in column 3 can also be parsed.

What's Changed

• capped snakemake version by @katsikora in #864
• bumped minor version by @katsikora in #865
• Develop by @katsikora in #866
• Release 2.7.1 by @katsikora in #868
• mm10 organism yaml blacklist by @katsikora in #867
• changes in STAR command and version by @LeilyR in #873
• updated the news.rst file by @LeilyR in #875
• Config ks by @katsikora in #876
• Filtergtf by @WardDeb in #869
• Develop by @katsikora in #879
• bumped bugfix version by @katsikora in #882

Full Changelog: 2.7.0...2.7.2

snakePipes 2.7.1

Merge pull request #866 from maxplanck-ie/develop

Develop

snakePipes 2.7.0

• Added the allelic version of Salmon-based transcript quantitation to mRNA-seq workflow. Will be run if both 'allelic-mapping' and 'alignment-free' modes are specified. An allelic version of sleuth will be run, if sample sheet is provided, as well as DESeq2 on allelic Salmon counts.
• Fixes #836

snakePipes 2.6.1

• Capped tabulate version as 0.9.0 breaks snakemake

snakePipes 2.6.0

• Added apeglm2 logFC shrinkage to allelic DESeq2 results.
• Added bwa-mem2 as an optional aligner to DNA-mapping and HiC, as well as as an additional tool to createIndices.
• Added bwameth2 as an optional tool to createIndices - this will create a bwameth index with bwa-mem2.
• Added bwameth2 as an optional aligner to WGBS - this will run bwameth with bwa-mem2 underneath.
• Updated software versions in environment yamls.
• Updated organism yamls.
• Updated CSAW output.
• Fixed a couple of issues in the ATAC-seq workflow after sofware versions update.
• Fixes #837
• Fixes #834
• Fixes #833
• Fixes #832
• Fixes #820
• Fixes #817