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Add support for providing pre-annotated files #298

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Add support for providing pre-annotated files #298

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jfy133
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@jfy133 jfy133 commented Jul 26, 2023

closes #254

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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/funcscan 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 --outdir <OUTDIR>).
  • 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).

@jfy133 jfy133 marked this pull request as draft July 26, 2023 11:27
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github-actions bot commented Jul 26, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 40600c5

+| ✅ 205 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌  15 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.annotation_prokka_evalue is set as 1e-06 in nextflow_schema.json but is 0.000001 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.amp_ampcombi_cutoff is set as 0.4 in nextflow_schema.json but is 0 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.arg_amrfinderplus_identmin is set as -1.0 in nextflow_schema.json but is -1 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.arg_deeparg_alignmentevalue is set as 1e-10 in nextflow_schema.json but is 1E-10 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.bgc_gecco_pfilter is set as 1e-09 in nextflow_schema.json but is 1E-9 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-funcscan_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-funcscan_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-funcscan_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-31 13:51:43

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jfy133 commented Jul 26, 2023

Current status:

  • Have the problem where pre-annotated channel cannot be joined back to the without annotation channel, as the latter has BIOAWK length meta, whereas pre-annotated does not.
    • I guess pre-annotated also needs to go through bioawk... problem is joining the two back at the other end... possible consider further patching bioawk module to also export the other two channels (if we can force NXF to emit as output the input...)

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jfy133 commented Feb 7, 2024

Nope, was being silly: do the thiseas shuffle, prior joining of channels, move bioawk meta out of the main meta, join, then add meta back in

@jfy133 jfy133 closed this Feb 14, 2024
@jasmezz jasmezz deleted the presupplied-orfs-new branch July 8, 2024 13:10
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