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Minor fixes spotted in v1.7 template #425

Merged
merged 11 commits into from
Oct 16, 2019
Merged

Minor fixes spotted in v1.7 template #425

merged 11 commits into from
Oct 16, 2019

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drpatelh
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@drpatelh drpatelh commented Oct 14, 2019 •
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Many thanks to contributing to nf-core/tools!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

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!
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md

  • See CHANGELOG.
  • May need to discuss igenomes.config...

@drpatelh drpatelh requested a review from a team October 14, 2019 15:03
apeltzer
apeltzer approved these changes Oct 14, 2019
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Looking good :-)

@drpatelh drpatelh mentioned this pull request Oct 14, 2019
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ewels
ewels approved these changes Oct 14, 2019
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Couple of minor things, otherwise LGTM!

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md Outdated Show resolved Hide resolved
nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md Show resolved Hide resolved
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@apeltzer @ewels Are you both happy with igenomes.config? I included blacklist too even though it is currently shipped with the pipelines, and so wont exist in most pipelines. Wont matter though unless its used in the pipeline in which case the files can just be copied to the same location until they are added to AWS iGenomes. Can then just update this file in the template.

Also, for bwa I have used index_dir/genome.fa and for the others I have used just index_dir/. We implemented the former as a simple fix to use custom reference file names as input. Havent really looked at how other pipelines are using the other indices, however, if possible it would be good to be consistent.

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Dammit! I forgot this PR was still open. Just pushed another commit to fix #349 ! Would you mind having a look at the changes Dockerfile please?

drpatelh
drpatelh commented Oct 15, 2019
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nf_core/pipeline-template/{{cookiecutter.name_noslash}}/Dockerfile
@@ -5,3 +5,4 @@ LABEL authors="{{ cookiecutter.author }}" \
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/{{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}/bin:$PATH
RUN conda env export --name {{ cookiecutter.name_noslash }}-{{ cookiecutter.version }} > {{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}.yml
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Tested this with the atacseq and chipseq Singularity images and it seems to be working fine.

@ewels ewels merged commit f5c4442 into nf-core:dev Oct 16, 2019
@drpatelh drpatelh mentioned this pull request Jan 17, 2020
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@drpatelh @ewels @apeltzer