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Fix Kraken2 database handling #194

Merged
merged 4 commits into from
May 25, 2021
Merged

Fix Kraken2 database handling #194

merged 4 commits into from
May 25, 2021

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skrakau
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@skrakau skrakau commented May 21, 2021 •
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Fix Kraken2 database handling: allow different folder structures containing *.k2d files.

Addresses #187.

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
  • 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).

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github-actions bot commented May 21, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ad16ae8

+| ✅ 123 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  75 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.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.mean_quality
  • params_used - Config variable not found in main.nf: params.trimming_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
  • schema_description - No description provided in schema for parameter: skip_multiqc

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.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 2021-05-25 10:26:25

@skrakau skrakau requested a review from d4straub May 21, 2021 14:52
d4straub
d4straub reviewed May 25, 2021
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I think it would be good to explain the expected data structure also in the parameter documentation.

@skrakau skrakau mentioned this pull request May 25, 2021
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@skrakau skrakau requested a review from d4straub May 25, 2021 12:01
d4straub
d4straub approved these changes May 25, 2021
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LGTM!

@skrakau
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skrakau commented May 25, 2021

Thanks @d4straub !

@skrakau skrakau merged commit a43f50f into nf-core:dev May 25, 2021
@skrakau skrakau deleted the fix_kraken2_db_handling branch May 31, 2021 13:38
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@skrakau @d4straub