Allocate more RAM to the process running MACS2

[jinmingda]

Many thanks to contributing to nf-core/atacseq!

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• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
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Description

The memory footprint of macs2 is largely based on the size of the input BAM file. The label process_long used in "merge_library_macs" and "merge_replicate_macs" can only assign 2GB to the processes, which is hardly enough for many real human samples.

[drpatelh]

Perfect 👍 Can you update CHANGELOG too please. Thanks.

[drpatelh]

Would you mind also adding a separate PR (or you can do it here if you like) increasing the resource requirements for all of the annotatePeaks processes? After we have merged all of the changes it would be good if you are able to test the dev version of the pipeline using the -r dev parameter. Hopefully, it finishes without errors this time!

[drpatelh]

Added in BED download functionality from AWS iGenomes in the PR below along with some other minor changes:
#49

[jinmingda]

Hi @drpatelh, sorry I couldn't reply back to you asap since I wasn't at home yesterday. I will take a look at your review and work on the code later today.

[drpatelh]

Hi @jinmingda . No worries! Ive incorporated all the changes you suggested now. Can you check the open PR to see ive missed anything please and I'll add it in 👍 Thanks again.

[jinmingda]

@drpatelh I think your PR has incorporated everything I've found. However, it seems the description of using the staged blacklist file in makeGenomeFilter is not included in the CHANGELOG.

[drpatelh]

Good point. I'll add it in tomorrow. Thanks.

[drpatelh]

If there are any other improvements that you think that the pipeline would benefit from then let me know and I'll try and add them in. Probably going to do a minor release over the next couple of weeks to get the pipeline running on AWS without issue.

[jinmingda]

@drpatelh Sure! I will keep you informed if I find any bugs or things that can improve the pipeline.