1.0.0-beta2

Various bug fixes, adds the --notemp option to all pipelines. Most importantly, we no longer need to modify snakemake to handle permission issues.

1.0.0-beta1

This prerelease finally includes a createIndices workflow. That should drastically streamline index creation.

1.0.0-alpha6

• Documentation updates
• A few minor bug fixes, such as a multiQC input in the HiC pipeline

1.0.0-alpha5

Merge pull request #217 from maxplanck-ie/Fix_awk_QC

Fix peak QC awk command in ChIP and ATAC workflows

1.0.0-alpha4

make PCA plot wider, set --plotWidth 10 as default (#211)

1.0.0-alpha3

Merge pull request #203 from maxplanck-ie/update_conda

Update the conda recipe

1.0.0-alpha2

A second alpha release. This has various bug fixes and now modifies snakemake so that temporary files are always written in the working directory.

First alpha release

This is the first alpha release going toward version 1.0. The workflows seem to all work, but we still need more documentation and further internal testing.

0.7.1

• Fixed issue #57 again, this time via pull request #79. This issue prevented processing of single-end ChIPseq data.

Green Mamba

Major changes:

• Adds a HiC workflow
• Full integration with read the docs

Other changes:

• Better python3 support (#55)
• Fixed a minor issue with the documentation of the ChIPseq workflow (#57)