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.yam
The initial production release, supporting RNA-seq, ChIP-seq, scRNA-seq (Cel-seq2), ATAC-seq and mor...
Bug fixes: multiQC in RNAseq allelic checks for successful sample identification in workflows where...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
snakePipes 2.4.2 Deeptools coverage RPKM in mRNA-seq and noncoding-RNA-seq worflows now respects bl...
Updated Bowtie2 parameters for the cut and tag data Updated multibamSummary in ChIPSeq pipeline for ...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
snakePipes 2.5.4 Fixed a number of minor GitHub issues: #791, #816, #807, #789, #783, #768, #827. ...
snakePipes 2.3.0 Deprecated mode Gruen in scRNAseq. scRNAseq mode Alevin now outputs spliced/unspli...
Updated citation for snakePipes Fixed replicate check for samples with trailing spaces in names Fixe...
snakePipes 2.2.1 Fix a bug in DAG for ChIPseq allelic with CSAW. Fixed deepTools qc DAG for ChIPseq...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were ...
snakePipes 2.4.0 Added support for multiple pairwise comparisons for DESeq2, sleuth, and rMats in t...
snakePipes 2.4.3 Fixed noncoding-RNA-seq workflow without sample sheet. Updated links to prebuilt i...
The initial production release, supporting RNA-seq, ChIP-seq, scRNA-seq (Cel-seq2), ATAC-seq and mor...
Bug fixes: multiQC in RNAseq allelic checks for successful sample identification in workflows where...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
snakePipes 2.4.2 Deeptools coverage RPKM in mRNA-seq and noncoding-RNA-seq worflows now respects bl...
Updated Bowtie2 parameters for the cut and tag data Updated multibamSummary in ChIPSeq pipeline for ...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
snakePipes 2.5.4 Fixed a number of minor GitHub issues: #791, #816, #807, #789, #783, #768, #827. ...
snakePipes 2.3.0 Deprecated mode Gruen in scRNAseq. scRNAseq mode Alevin now outputs spliced/unspli...
Updated citation for snakePipes Fixed replicate check for samples with trailing spaces in names Fixe...
snakePipes 2.2.1 Fix a bug in DAG for ChIPseq allelic with CSAW. Fixed deepTools qc DAG for ChIPseq...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were ...
snakePipes 2.4.0 Added support for multiple pairwise comparisons for DESeq2, sleuth, and rMats in t...
snakePipes 2.4.3 Fixed noncoding-RNA-seq workflow without sample sheet. Updated links to prebuilt i...
The initial production release, supporting RNA-seq, ChIP-seq, scRNA-seq (Cel-seq2), ATAC-seq and mor...
Bug fixes: multiQC in RNAseq allelic checks for successful sample identification in workflows where...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...