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Preparing for release #40

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Merged
avantonder merged 5 commits into from
Jun 16, 2021
Merged

Preparing for release #40

avantonder merged 5 commits into from
Jun 16, 2021

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@antunderwood
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@antunderwood antunderwood commented Jun 16, 2021

PR checklist

tweaks for release

  • 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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github-actions bot commented Jun 16, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 852830c

+| ✅ 106 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  43 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: environment.yml
  • files_exist - File not found: Dockerfile
  • nextflow_config - Config variable not found: process.container
  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • 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 2021-06-16 18:27:47

@antunderwood antunderwood requested a review from avantonder June 16, 2021 19:22
@avantonder avantonder merged commit 717a052 into dev Jun 16, 2021
@ewels ewels deleted the preparing_for_release branch March 13, 2025 14:44
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@avantonder avantonder avantonder approved these changes

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@antunderwood @avantonder