Added options to customise cpu and memory used per multicore for bismark align

[ewels]

Closes #124

Note that this PR will hopefully build with the new docker image created in PR #123. This should be considered when checking the CI tests..

[ewels]

Sigh, the docker build failed: https://cloud.docker.com/u/nfcore/repository/docker/nfcore/methylseq/builds/dce2a365-d736-4d56-a467-399b8e15ac36

UnsatisfiableError: The following specifications were found to be in conflict:
- bioconda::hisat2=2.1.0 -> python[version='>=2.7,<2.8.0a0']
- python=3.7
Use "conda search <package> --info" to see the dependencies for each package.

[ewels]

https://bioconda.github.io/contributor/guidelines.html states that:

hisat2 runs 2to3 to make it Python 3 compatible, and copies over individual scripts to the bin dir

Sure enough, the build recipe does this: https://github.com/bioconda/bioconda-recipes/blob/90620569f00fa786b85d272507445a229748272d/recipes/hisat2/build.sh#L5-L20

However, the meta file then skips python 3k builds: https://github.com/bioconda/bioconda-recipes/blob/90620569f00fa786b85d272507445a229748272d/recipes/hisat2/meta.yaml#L13 🤦‍♂

[ewels]

x-ref: bioconda/bioconda-recipes#18911

[ewels]

Reverted MultiQC back to version 1.7 and removed the Python 3 dependency. Hopefully everything will start working again then 🤞

Still need to come back to the Python 3 thing at a later date, as future versions of MultiQC will drop py2k support. But we need to release soon to fix the iGenomes bug, so that can wait.

[ewels]

Again, needs to be merged and a new PR opened to test that the reverted MultiQC build works..

[alneberg]

Only some slight comment on the docs. Personally I find the bismark parameters impossible to understand and I wouldn't possibly try to mixture with them, but I guess someone out there might be able to.

[alneberg]

Does this mean 3 if either of the two first and 5 if --non_directional is specified? It's a bit ambiguous the way it's currently written

[ewels]

3 unless any of those three are specified..

[ewels]

But yes I agree, this was not clear 👍 Hopefully improved now..

[alneberg]

Yes, much better.

[ewels]

Tests look fine apart from MultiQC breaking..