Patch 2.0.1

[jkh00]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/methylong branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

This patch release is meant to address some bugs.

• fix caching issue
• when --all-contexts is set, the default dmr analysis is by modkit because DSS only process CpG island.
• remove --combine-strands in modkit pileup
• all output, if possible should be compressed
• update modkit versions
• update modkit pileup module
• replace --motif A 0 with --modified-bases 6mA in modkit pileup, because version v0.6.0 will give this error otherwise Error! single base motifs not supported, use --modified-bases.
• update output structures and documentation
• update affected subworkflows, where the modkit pileup module now directly output bgzf-compressed bedmethyl
• inspect modkit pileup output
• migrate versions to topic

[jkh00]

@nf-core-bot fix linting

[YiJin-Xiong]

@jkh00 Hiii, I noticed you mentioned there was still something to be done, and I was just wondering if you have any idea when it might be finished?😊

[jkh00]

Hii, I will try to implement some of them next week. But right now I have some other priorities, so it might be going in a slower pace.. you are more than welcome to contribute too! 😊 i think the compressing part should be easy to implement

[YiJin-Xiong]

Sure! I'll try to handle them these two days!

[jkh00]

@YiJin-Xiong thanks alot for the help! I will get my hands on in the next two days :))

[jkh00]

@nf-core-bot fix linting

[jkh00]

@nf-core-bot fix linting

[jkh00]

@YiJin-Xiong Hi! sorry i was away for the past months, but now I have updated the modkit modules and also updated versions output for most nf-core modules. from my side the updates are completed. if you agree with the changes, then its ready to merge :)

[YiJin-Xiong]

@jkh00 Glad you're back!! I noticed the versions output has changed a lot, and I've reviewed all the updates, they look great to me. Just some tiny issues.

[jkh00]

@YiJin-Xiong thank you again for the assistants and feedbacks!! always a pleasure to work with you :) glad to be improving the pipeline with you.
I have also received your email, will reply to you shortly!

[YiJin-Xiong]

@jkh00 Thanks so much for your kind words, I really appreciate it!! It's truly a pleasure working with you as well, and I've learned a lot through our collaboration. 🫶🫶