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Add core detection test data to config #3199

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merged 1 commit into from
Mar 30, 2023

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adamjtaylor
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This PR contributes to nf-core/test-datasets#822 by exposing test data sets for TMA core detection modules in the test_data.config file

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

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@FloWuenne FloWuenne left a comment

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LGTM! test-datasets have already been merged for this!

@adamjtaylor adamjtaylor added this pull request to the merge queue Mar 29, 2023
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I think this is looking good once the test dataset is switched over

@adamjtaylor adamjtaylor mentioned this pull request Mar 29, 2023
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@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to no response for status checks Mar 29, 2023
@FloWuenne FloWuenne added this pull request to the merge queue Mar 29, 2023
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to no response for status checks Mar 29, 2023
@adamjtaylor adamjtaylor added this pull request to the merge queue Mar 29, 2023
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to no response for status checks Mar 29, 2023
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FYI @FloWuenne this is still getting chucked out of the merge queue. I'm going to give it a day or two for the post hackathon madness to cool down before trying again.

@adamjtaylor adamjtaylor added this pull request to the merge queue Mar 29, 2023
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to no response for status checks Mar 29, 2023
@adamjtaylor adamjtaylor added this pull request to the merge queue Mar 30, 2023
Merged via the queue into master with commit 51ec1b3 Mar 30, 2023
@adamjtaylor adamjtaylor deleted the add_coredetection_test_data branch March 30, 2023 07:26
jvfe added a commit to jvfe/modules that referenced this pull request Mar 30, 2023
* master:
  Ngscheckmate (nf-core#3094)
  New module Mindagap (nf-core#2860)
  Coreograph Module (nf-core#3201)
  new module wisecondorx/newref (nf-core#3212)
  Add core detection test data to config (nf-core#3199)
  Collectinsertsizemetrics (nf-core#3179)
  update appropriate label for freyja boot (nf-core#3215)
  Emit files from uncompression utilities (nf-core#3144)
  new tool: art_illumina (nf-core#3162)
  Addition of new module: Issue nf-core#3113 Survivor/filter (nf-core#3168)
  Removed -1 in CPU size specification for samtools in BWA module (nf-core#3205)
  nf-test Transition CI (nf-core#3191)
  new module: sourmash/index (nf-core#3163)
  Chopper (nf-core#3174)
  Update mapdage2 module (nf-core#3185)
  Add imaging test data in config (nf-core#3190)
  New subworkflow: Fastq_fastp_trim_fastqc (nf-core#3146)
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2 participants