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Add CAT summary into the global bin_summary #562

Merged
merged 12 commits into from
Feb 1, 2024
Merged

Add CAT summary into the global bin_summary #562

merged 12 commits into from
Feb 1, 2024

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maxibor
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@maxibor maxibor commented Jan 26, 2024 •
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PR checklist

This PR adds the merging of the CAT summary into the global bin_summary table of nf-core/mag

To merge after #548

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • CHANGELOG.md is updated.

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github-actions bot commented Jan 26, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 212d079

+| ✅ 197 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌  16 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.igenomes_base is set as s3://ngi-igenomes/igenomes in nextflow_schema.json but is s3://ngi-igenomes/igenomes/ in nextflow.config.
  • nextflow_config - Config default value incorrect: params.phix_reference is set as ${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz in nextflow_schema.json but is /home/runner/work/mag/mag/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz in nextflow.config.
  • nextflow_config - Config default value incorrect: params.lambda_reference is set as ${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz in nextflow_schema.json but is /home/runner/work/mag/mag/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz in nextflow.config.
  • nextflow_config - Config default value incorrect: params.gtdbtk_min_perc_aa is set as 10.0 in nextflow_schema.json but is 10 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.gtdbtk_pplacer_cpus is set as 1.0 in nextflow_schema.json but is 1 in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-mag_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-mag_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-mag_logo_dark.png does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-30 14:20:38

@maxibor
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maxibor commented Jan 26, 2024

Will close #535

@maxibor maxibor linked an issue Jan 26, 2024 that may be closed by this pull request
CAT is not included in the the BIN_SUMMARY #535
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@maxibor maxibor requested a review from jfy133 January 26, 2024 15:16
@jfy133 jfy133 merged commit 15650d8 into nf-core:dev Feb 1, 2024
14 of 15 checks passed
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@jfy133 jfy133 jfy133 approved these changes

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CAT is not included in the the BIN_SUMMARY
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@maxibor @jfy133 @nf-core-bot