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add --cut_dada_ref_taxonomy #283

Merged
merged 2 commits into from Jun 23, 2021
Merged

add --cut_dada_ref_taxonomy #283

merged 2 commits into from Jun 23, 2021

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d4straub
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@d4straub d4straub commented Jun 23, 2021 •
edited

This should solve #259

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/ampliseq 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 23, 2021 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 48a0760

+| ✅ 125 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  60 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.pacbio
  • params_used - Config variable not found in main.nf: params.iontorrent
  • params_used - Config variable not found in main.nf: params.FW_primer
  • params_used - Config variable not found in main.nf: params.RV_primer
  • params_used - Config variable not found in main.nf: params.classifier
  • params_used - Config variable not found in main.nf: params.metadata
  • params_used - Config variable not found in main.nf: params.extension
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • params_used - Config variable not found in main.nf: params.trunc_qmin
  • params_used - Config variable not found in main.nf: params.trunc_rmin
  • params_used - Config variable not found in main.nf: params.trunclenf
  • params_used - Config variable not found in main.nf: params.trunclenr
  • params_used - Config variable not found in main.nf: params.max_ee
  • params_used - Config variable not found in main.nf: params.max_len
  • params_used - Config variable not found in main.nf: params.min_len
  • params_used - Config variable not found in main.nf: params.metadata_category
  • params_used - Config variable not found in main.nf: params.double_primer
  • params_used - Config variable not found in main.nf: params.retain_untrimmed
  • params_used - Config variable not found in main.nf: params.exclude_taxa
  • params_used - Config variable not found in main.nf: params.min_frequency
  • params_used - Config variable not found in main.nf: params.min_samples
  • params_used - Config variable not found in main.nf: params.multiple_sequencing_runs
  • params_used - Config variable not found in main.nf: params.single_end
  • params_used - Config variable not found in main.nf: params.sample_inference
  • params_used - Config variable not found in main.nf: params.illumina_pe_its
  • params_used - Config variable not found in main.nf: params.concatenate_reads
  • params_used - Config variable not found in main.nf: params.cut_its
  • params_used - Config variable not found in main.nf: params.skip_qiime
  • params_used - Config variable not found in main.nf: params.skip_fastqc
  • params_used - Config variable not found in main.nf: params.skip_alpha_rarefaction
  • params_used - Config variable not found in main.nf: params.skip_abundance_tables
  • params_used - Config variable not found in main.nf: params.skip_barplot
  • params_used - Config variable not found in main.nf: params.skip_taxonomy
  • params_used - Config variable not found in main.nf: params.skip_diversity_indices
  • params_used - Config variable not found in main.nf: params.skip_ancom
  • params_used - Config variable not found in main.nf: params.skip_multiqc
  • params_used - Config variable not found in main.nf: params.dada_ref_taxonomy
  • params_used - Config variable not found in main.nf: params.cut_dada_ref_taxonomy
  • params_used - Config variable not found in main.nf: params.qiime_ref_taxonomy
  • params_used - Config variable not found in main.nf: params.outdir
  • 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.email
  • params_used - Config variable not found in main.nf: params.email_on_fail
  • params_used - Config variable not found in main.nf: params.max_multiqc_email_size
  • params_used - Config variable not found in main.nf: params.plaintext_email
  • params_used - Config variable not found in main.nf: params.tracedir
  • 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.singularity_pull_docker_container
  • 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.

❔ Tests ignored:

  • 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 2021-06-23 14:45:43

erikrikarddaniel
erikrikarddaniel approved these changes Jun 23, 2021
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Looks fine.

@d4straub
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Thanks!

@d4straub d4straub merged commit 5bae632 into nf-core:dev Jun 23, 2021
@d4straub d4straub deleted the cut-dada2-ref-taxonomy branch June 23, 2021 15:09
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@d4straub @erikrikarddaniel