Pore-c-py

Added
- Stdout options for annotate and digest sub commands.
Changed
- Simplified logging for easier parsing.
- Rewrote CLI, removing utils and keeping only those programs which are used.
- Parse bam subcommand renamed annotate.
Removed
- A lot of code and dependencies.

Fixed
- bamindex fetch error when running more than one sample and `--chunk_size` is greater than 0.

Fixed
- `--bed` parameter will now output BED file using the paired_end BAM file.
- Reduce memory usage of BED file creation and sorting.
- Increased memory allocation for `prepare_hic` and `merge_mcool` processes.
- If sample sheet provided and cutter column not present the workflow will instead use `--cutter` parameter.
Changed
- Bump pore-c-py to v2.1.4 to prevent issues with modified base tags and strip minimap2 tags from inputs.
Added
- Reduce peak memory usage of minimap2 by adding `--cap-kalloc 100m --cap-sw-mem 50m` to the minimap2 command in the `digest_align_annotate` process.

Added
- `--bed` parameter which if set to true will output a BED file that is compatible with downstream tools including the scaffolder [Yahs](https://github.com/c-zhou/yahs).
- `--pairtools_chunksize` parameter which exposes pairtools dedup chunksize parameter, in case peak memory usage of hi_c process needs to be reduced.
- `digest_align_annotate` process uses dedicated pore_c_py container.
- `--max_monomers` parameter, which is set to 250 by default, will filter out any reads that have more than this number of monomers. These reads will not be included in the analysis.
- Output a `filtered_out/{alias}.bam` with any reads that are filtered out due to the max_monomers parameter.

Changed
- Tidy up for release as a conda package in the EPI2MELabs channel

Fixed
- digest: don't strip mod base tags by default