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Updated bigstream invert paramaters #3

Merged
merged 8 commits into from
Feb 13, 2025
Merged

Updated bigstream invert paramaters #3

merged 8 commits into from
Feb 13, 2025

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cgoina
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@cgoina cgoina commented Feb 13, 2025

Updated parameters for generated the invert displacement vector.

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @cgoina,

It looks like this pull-request is has been made against the JaneliaSciComp/easifish main branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the JaneliaSciComp/easifish dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@cgoina
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cgoina commented Feb 13, 2025

@krokicki

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github-actions bot commented Feb 13, 2025 •
edited
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit e5ce4c1

+| ✅ 214 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗  23 tests had warnings |!
-| ❌  32 tests failed       |-

❌ Test failures:

  • files_exist - File not found: assets/nf-core-easifish_logo_light.png
  • files_exist - File not found: docs/images/nf-core-easifish_logo_light.png
  • files_exist - File not found: docs/images/nf-core-easifish_logo_dark.png
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Plugin 'nf-validation' does not have a pinned version
  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • nextflow_config - Config default value incorrect: params.bigstream_config is set as ${projectDir}/conf/bigstream_config.yml in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/bigstream_config.yml in nextflow.config.
  • nextflow_config - Config default value incorrect: params.dask_config is set as ${projectDir}/conf/dask_config.yml in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/dask_config.yml in nextflow.config.
  • nextflow_config - Config default value incorrect: params.local_align_worker_cpus is set as 3 in nextflow_schema.json but is 1 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.bigstream_inv_use_root is set as true in nextflow_schema.json but is false in nextflow.config.
  • nextflow_config - Config default value incorrect: params.multiscale_spark_workers is set as 1 in nextflow_schema.json but is 0 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.multiscale_spark_worker_cores is set as 3 in nextflow_schema.json but is 0 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.multiscale_spark_driver_mem_gb is set as 1 in nextflow_schema.json but is 0 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.cellpose_log_config is set as ${projectDir}/conf/cellpose_logging_config.ini in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/cellpose_logging_config.ini in nextflow.config.
  • nextflow_config - Config default value incorrect: params.cellpose_dask_config is set as ${projectDir}/conf/dask_config.yml in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/dask_config.yml in nextflow.config.
  • nextflow_config - Config default value incorrect: params.cellpose_dask_workers is set as 10 in nextflow_schema.json but is 8 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.user_id is set as 0 in nextflow_schema.json but is 1001 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.group_id is set as 0 in nextflow_schema.json but is 118 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.singularity_cache_dir is set as $HOME/.singularity_cache in nextflow_schema.json but is /home/runner/.singularity_cache in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'
  • schema_params - Default value for param bigstream_inv_use_root invalid: Schema default (True) does not match the config default (false)
  • modules_json - Your modules.json file is outdated. It will be automatically generated by running any module command.
  • multiqc_config - assets/multiqc_config.yml not found.

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: assets/nf-core-easifish_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-easifish_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-easifish_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/easifish/easifish/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-02-13 19:47:46

moved cellpose properties under segmentation
e5ce4c1 
tried to cleanup some lint errors
@cgoina cgoina merged commit 222a87a into main Feb 13, 2025
0 of 9 checks passed
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@cgoina