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Define conda and container directives otuside of process scope#4

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Define conda and container directives otuside of process scope#4
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@vinisalazar

@vinisalazar vinisalazar commented Mar 3, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4dc620a

+| ✅ 205 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  48 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
  • pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
  • pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in main.nf: input:Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
  • pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in main.nf: If the module doesn't use arguments ($args), you SHOULD remove:
  • pipeline_todos - TODO string in environment.yml: List required Conda package(s).
  • pipeline_todos - TODO string in meta.yml: # Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
  • pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
  • pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
  • pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - concatall.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-funcprofiler_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-03 08:20:10

@vinisalazar vinisalazar closed this Mar 3, 2026
@vinisalazar vinisalazar deleted the dev-tests branch March 3, 2026 09:40
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