snakePipes 2.5.4

snakePipes 2.5.4

• Fixed a number of minor GitHub issues: #791, #816, #807, #789, #783, #768, #827.

• Fixed misleading rule name for bamcoverage in atac-seq.

• Fixed conda env building on microsoft azure.

• Fixed CSAW report for ChIP-seq.

snakePipes 2.5.3

• Switched to mamba by default at createEnvs function.

2.5.2

• snakemake version >= 6.2.1
• python version >= 3.7
• added snakeMake in readme
• bug fix 777, 781
• multiqc version = 1.10.1 to be able to report qc fir hic pipeline
• added snakemake catalog yaml

2.5.1

• Updated Bowtie2 parameters for the cut and tag data
• Updated multibamSummary in ChIPSeq pipeline for data with spike-in
• Uncommented the BamCompare for ChIPseq pipeline with spike-in
• set a max thread for each rule
• External PR #764: always check for >0 when generating heatmap for the differential analysis done by deseq2

2.5.0

• Added tbb = 2020.2 to dna_mapping, creatIndices and rnae_seq yaml file
• Added cut and tag parameters to macs2 and bowtei2. The parameters have been used in Kaya-Okur et al. 2019 and can be called by using --cut_n_tag.
• Updated azure tests. python37 create envs constantly failing due its long run time. This test is now split into smaller chunks. set_macos is removed since it was completely redundant with the set.yaml

Release_2.4.3

snakePipes 2.4.3

• Fixed noncoding-RNA-seq workflow without sample sheet.
• Updated links to prebuilt indices on zenodo.
• Fixed read length estimation for rMats.
• Cutadapt is set as default read trimming program for both noncoding-RNA-seq and mRNA-seq workflows.

Release_2.4.2

snakePipes 2.4.2

• Deeptools coverage RPKM in mRNA-seq and noncoding-RNA-seq worflows now respects blacklist and ingoreForNorm arguments.
• In mRNA-seq and noncoding-RNA-seq workflow, deeptools qc will now also output DESeq2 size factor-normalized bigwig files.
• Fixed conda env for WGBS.
• Fixed control group ordering in split sample sheets in mRNA-seq and other workflows.
• Removed rule moving bams from allelic mRNA-seq and DNA-mapping workflows.

Release_2.4.1

snakePipes 2.4.1

• Fixed sampleSheet splitting for multiple pairwise comparisons when group "All" is not listed.

Release_2.4.0

snakePipes 2.4.0

• Added support for multiple pairwise comparisons for DESeq2, sleuth, and rMats in the mRNA-seq workflow, as well as for DESeq2 in the noncoding-RNA-seq workflow.
• Loompy from conda is now used in mode STARsolo in scRNA-seq workflow.
• Added bamExt to mRNA-seq and noncoding-RNA-seq commandline arguments.
• Added multi-thread support to rMats in mRNA-seq workflow.
• Fixed deepTools GC bias command with SE reads.
• Bumped HiC explorer version.
• Fixed STARsoloCoords for Custom kit.

Release_2.3.1

snakePipes 2.3.1

• Fixed aligner options for bwa in DNA-mapping.
• Fixed allelic mode for single end reads .
• Bumped hiC explorer version in HiC.