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Fixes #39

Merged
merged 8 commits into from
Jun 15, 2021
Merged

Fixes #39

merged 8 commits into from
Jun 15, 2021

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antunderwood
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PR checklist

Small changes to address comments from @drpatelh

  • 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/bactmap branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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).

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Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --fix
    • Manually resolve anything left from markdownlint .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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github-actions bot commented Jun 11, 2021 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7276abe

+| ✅ 110 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗  42 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: environment.yml
  • files_exist - File not found: Dockerfile
  • nextflow_config - Config variable not found: process.container
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.reference
  • params_used - Config variable not found in main.nf: params.trim
  • params_used - Config variable not found in main.nf: params.save_trimmed_fail
  • params_used - Config variable not found in main.nf: params.adapter_file
  • params_used - Config variable not found in main.nf: params.subsampling_off
  • params_used - Config variable not found in main.nf: params.subsampling_depth_cutoff
  • params_used - Config variable not found in main.nf: params.genome_size
  • params_used - Config variable not found in main.nf: params.remove_recombination
  • params_used - Config variable not found in main.nf: params.non_GATC_threshold
  • params_used - Config variable not found in main.nf: params.rapidnj
  • params_used - Config variable not found in main.nf: params.fasttree
  • params_used - Config variable not found in main.nf: params.iqtree
  • params_used - Config variable not found in main.nf: params.raxmlng
  • params_used - Config variable not found in main.nf: params.multiqc_config
  • params_used - Config variable not found in main.nf: params.multiqc_title
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.tracedir
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • params_used - Config variable not found in main.nf: params.email
  • params_used - Config variable not found in main.nf: params.email_on_fail
  • params_used - Config variable not found in main.nf: params.plaintext_email
  • params_used - Config variable not found in main.nf: params.max_multiqc_email_size
  • params_used - Config variable not found in main.nf: params.skip_multiqc
  • params_used - Config variable not found in main.nf: params.enable_conda
  • params_used - Config variable not found in main.nf: params.validate_params
  • params_used - Config variable not found in main.nf: params.monochrome_logs
  • params_used - Config variable not found in main.nf: params.help
  • params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
  • params_used - Config variable not found in main.nf: params.hostnames
  • params_used - Config variable not found in main.nf: params.config_profile_description
  • params_used - Config variable not found in main.nf: params.config_profile_contact
  • params_used - Config variable not found in main.nf: params.config_profile_url
  • params_used - Config variable not found in main.nf: params.max_memory
  • params_used - Config variable not found in main.nf: params.max_cpus
  • params_used - Config variable not found in main.nf: params.max_time
  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below, update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-15 07:02:51

@antunderwood antunderwood mentioned this pull request Jun 11, 2021
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@drpatelh
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drpatelh commented Jun 15, 2021 •
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Need to move this line up and out of the workflow section too @aunderwo . See this issue nf-core/viralrecon#201. Ok, I done it for you.

drpatelh
drpatelh reviewed Jun 15, 2021
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subworkflows/sub_sampling.nf
@@ -20,7 +19,7 @@ workflow SUB_SAMPLING {
MASH_SKETCH (
reads
)
genome_size = MASH_SKETCH.out.stats.map { meta, file -> [meta, find_genome_size(file.text)]}
genome_size = MASH_SKETCH.out.stats.map { meta, file -> [meta, WorkflowBactmap.find_genome_size(file.text)]}
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Nice!!

drpatelh
drpatelh approved these changes Jun 15, 2021
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LGTM! Now just need to create a PR from dev -> master for the release, bump versions to 1.0, change release info in CHANGELOG and we are good to go from my side!

@drpatelh drpatelh merged commit fa18945 into dev Jun 15, 2021
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@drpatelh drpatelh drpatelh approved these changes

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@antunderwood @drpatelh