olgabot/sourmash sig merge

[olgabot]

nf-core/kmermaid pull request

Many thanks for contributing to nf-core/kmermaid!

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!
• [ ] If necessary, also make a PR on the nf-core/kmermaid branch on the nf-core/test-datasets repo
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
• [ ] Make sure your code lints (nf-core lint .).
• [ ] Documentation in docs is updated
• [ ] CHANGELOG.md is updated
• [ ] README.md is updated

Learn more about contributing: CONTRIBUTING.md

[github-actions[bot]]

nf-core lint overall result: Failed :x:

Posted for pipeline commit c4f9521

+| ✅ 18 tests passed       |+
!| ❗  2 tests had warnings |!
-| ❌  1 tests failed       |-

### :x: Test failures: * [Test #1](https://nf-co.re/errors#1) - File must be removed: `bin/markdown_to_html.r` ### :heavy_exclamation_mark: Test warnings: * [Test #1](https://nf-co.re/errors#1) - File not found: `.github/workflows/awstest.yml` * [Test #1](https://nf-co.re/errors#1) - File not found: `.github/workflows/awsfulltest.yml` ### :white_check_mark: Tests passed: * [Test #1](https://nf-co.re/errors#1) - File found: `nextflow.config` * [Test #1](https://nf-co.re/errors#1) - File found: `nextflow_schema.json` * [Test #1](https://nf-co.re/errors#1) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [Test #1](https://nf-co.re/errors#1) - File found: `README.md` * [Test #1](https://nf-co.re/errors#1) - File found: `CHANGELOG.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/README.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/output.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/usage.md` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/branch.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/ci.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/linting.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `main.nf` * [Test #1](https://nf-co.re/errors#1) - File found: `environment.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `Dockerfile` * [Test #1](https://nf-co.re/errors#1) - File found: `conf/base.config` * [Test #1](https://nf-co.re/errors#1) - File not found check: `Singularity` * [Test #1](https://nf-co.re/errors#1) - File not found check: `parameters.settings.json` * [Test #1](https://nf-co.re/errors#1) - File not found check: `.travis.yml` ### Run details: * nf-core/tools version 1.11 * Run at `2020-10-28 16:08:07`

[pranathivemuri]

Will review once the tests are fixed

[olgabot]

Addresses https://github.com/nf-core/kmermaid/issues/108

[pranathivemuri]

looks like the index and merge PRS test fail with similar errors

----------------------------------------------------
[9d/f0ba5a] Submitted process > get_software_versions
Channel `sourmash_sketches_nucleotide` has been used as an input by more than a process or an operator

 -- Check script 'main.nf' at line: 1499 or see '.nextflow.log' file for more details

[olgabot]

I'm going to be bad and merge this in with failing tests because I need some of this functionality in https://github.com/nf-core/kmermaid/pull/131