Open drpatelh opened 5 years ago
As it stands bioconda::idr
and bioconda::macs2
wont build in the same environment because they are built with Python 3 and Python 2, respectively.
https://anaconda.org/bioconda/idr/files
https://anaconda.org/bioconda/macs2/files
Need a workaround for this.
MACS2 Python3 support is hopefully coming... https://github.com/taoliu/MACS/issues/242#issuecomment-432829877 (though there have been threads around this since 2017, so not sure when..)
Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines: https://github.com/kundajelab/atac-seq-pipeline https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit
Another implementation in NF: https://github.com/DoaneAS/atacflow
ENCODE ATAC-seq Guidelines: https://www.encodeproject.org/atac-seq/
Amongst other things, this will probably also involve creating pseudo-replicates by merging and equally sampling alignments across replicates.