Bump version to v1.5

[ewels]

Bump to version 1.5. See #133 for details.

[ewels]

Maybe wait to resolve this merge conflict until the new docker image is built. Then we get to test the pipeline with the new software updates as a bonus.

Build is here: https://hub.docker.com/repository/registry-1.docker.io/nfcore/methylseq/builds/c31a7c6f-422b-4c82-9687-0caef2452da3

[ewels]

Build failed 😞

Package python-dateutil conflicts for:
bioconda::multiqc=1.8 -> click -> python-dateutil

I'll test locally and see if I can fix it.

[ewels]

ok, hopefully got the build working again by reverting the changes to Python, Samtools and Bowtie2. New docker image building here: https://hub.docker.com/repository/registry-1.docker.io/nfcore/methylseq/builds/3a7bbaf3-0e58-4620-b128-39415ee178ec

[ewels]

Build worked! ✅ Fixed the merge conflict - hopefully the tests will pass and we can go forward with the release...

[ewels]

Sigh. I should just not ever update anything.

    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/markdown/core.py", line 387, in markdown
      md = Markdown(**kwargs)
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/markdown/core.py", line 97, in __init__
      configs=kwargs.get('extension_configs', {}))
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/markdown/core.py", line 125, in registerExtensions
      ext._extendMarkdown(self)
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/markdown/extensions/__init__.py", line 77, in _extendMarkdown
      self.extendMarkdown(md)
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/pymdownx/extra.py", line 60, in extendMarkdown
      md.registerExtensions(extra_extensions, self.config)
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/markdown/core.py", line 125, in registerExtensions
      ext._extendMarkdown(self)
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/markdown/extensions/__init__.py", line 77, in _extendMarkdown
      self.extendMarkdown(md)
    File "/opt/conda/envs/nf-core-methylseq-1.4.1/lib/python3.7/site-packages/pymdownx/extrarawhtml.py", line 30, in extendMarkdown
      extra.MarkdownInHtmlProcessor(md.parser), 'markdown_block', 105
  AttributeError: module 'markdown.extensions.extra' has no attribute 'MarkdownInHtmlProcessor'

[ewels]

Ah, same bug is reported here: nf-core/tools#571

[ewels]

New build: https://hub.docker.com/repository/registry-1.docker.io/nfcore/methylseq/builds/b392523f-4817-4335-af62-7b3f2eb258cc

[phue]

I can't reproduce the latest error locally :(

[ewels]

I can't reproduce the latest error locally :(

Me either - so I figured it was something weird with the GitHub actions commands. I simplified them a little and now it's working 😄