8000 Adjust release date for v2.0.0 by skrakau · Pull Request #209 · nf-core/mag · GitHub
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Adjust release date for v2.0.0 #209

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Merged
merged 2 commits into from
Jun 1, 2021
Merged

Adjust release date for v2.0.0 #209

merged 2 commits into from
Jun 1, 2021

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skrakau
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@skrakau skrakau commented Jun 1, 2021

Adjust release date for v2.0.0

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 you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/mag 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).

@skrakau skrakau requested review from d4straub and ggabernet June 1, 2021 08:04
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github-actions bot commented Jun 1, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e4be427

+| ✅ 121 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  77 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
  • nextflow_config - Config manifest.version should end in dev: '2.0.0'
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.single_end
  • params_used - Config variable not found in main.nf: params.save_trimmed_fail
  • params_used - Config variable not found in main.nf: params.fastp_qualified_quality
  • params_used - Config variable not found in main.nf: params.fastp_cut_mean_quality
  • params_used - Config variable not found in main.nf: params.keep_phix
  • params_used - Config variable not found in main.nf: params.phix_reference
  • params_used - Config variable not found in main.nf: params.host_fasta
  • params_used - Config variable not found in main.nf: params.host_genome
  • params_used - Config variable not found in main.nf: params.host_removal_verysensitive
  • params_used - Config variable not found in main.nf: params.host_removal_save_ids
  • params_used - Config variable not found in main.nf: params.binning_map_mode
  • params_used - Config variable not found in main.nf: params.skip_binning
  • params_used - Config variable not found in main.nf: params.min_contig_size
  • params_used - Config variable not found in main.nf: params.min_length_unbinned_contigs
  • params_used - Config variable not found in main.nf: params.max_unbinned_contigs
  • params_used - Config variable not found in main.nf: params.coassemble_group
  • params_used - Config variable not found in main.nf: params.spades_options
  • params_used - Config variable not found in main.nf: params.megahit_options
  • params_used - Config variable not found in main.nf: params.skip_spades
  • params_used - Config variable not found in main.nf: params.skip_spadeshybrid
  • params_used - Config variable not found in main.nf: params.skip_megahit
  • params_used - Config variable not found in main.nf: params.skip_quast
  • params_used - Config variable not found in main.nf: params.centrifuge_db
  • params_used - Config variable not found in main.nf: params.kraken2_db
  • params_used - Config variable not found in main.nf: params.skip_krona
  • params_used - Config variable not found in main.nf: params.cat_db
  • params_used - Config variable not found in main.nf: params.cat_db_generate
  • params_used - Config variable not found in main.nf: params.save_cat_db
  • params_used - Config variable not found in main.nf: params.gtdb
  • params_used - Config variable not found in main.nf: params.gtdbtk_min_completeness
  • params_used - Config variable not found in main.nf: params.gtdbtk_max_contamination
  • params_used - Config variable not found in main.nf: params.gtdbtk_min_perc_aa
  • params_used - Config variable not found in main.nf: params.gtdbtk_min_af
  • params_used - Config variable not found in main.nf: params.gtdbtk_pplacer_cpus
  • params_used - Config variable not found in main.nf: params.gtdbtk_pplacer_scratch
  • params_used - Config variable not found in main.nf: params.skip_adapter_trimming
  • params_used - Config variable not found in main.nf: params.keep_lambda
  • params_used - Config variable not found in main.nf: params.longreads_min_length
  • params_used - Config variable not found in main.nf: params.longreads_keep_percent
  • params_used - Config variable not found in main.nf: params.longreads_length_weight
  • params_used - Config variable not found in main.nf: params.lambda_reference
  • params_used - Config variable not found in main.nf: params.skip_busco
  • params_used - Config variable not found in main.nf: params.busco_reference
  • params_used - Config variable not found in main.nf: params.busco_download_path
  • params_used - Config variable not found in main.nf: params.busco_auto_lineage_prok
  • params_used - Config variable not found in main.nf: params.save_busco_reference
  • params_used - Config variable not found in main.nf: params.megahit_fix_cpu_1
  • params_used - Config variable not found in main.nf: params.spades_fix_cpus
  • params_used - Config variable not found in main.nf: params.spadeshybrid_fix_cpus
  • params_used - Config variable not found in main.nf: params.metabat_rng_seed
  • 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.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.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.enable_conda
  • params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
  • params_used - Config variable not found in main.nf: params.validate_params
  • 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.
  • schema_description - No description provided in schema for parameter: skip_multiqc

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreSc 8000 hema.groovy
  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
  • conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
  • conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-01 08:04:27

@skrakau skrakau merged commit 0b4f0ef into master Jun 1, 2021
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Reviewers

@d4straub d4straub Awaiting requested review from d4straub

@ggabernet ggabernet Awaiting requested review from ggabernet

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