Standardize conversion workflow

[fmalmeida]

Summary

Hi,
This work relates to #310 and discussion that is happening in slack.

Currently, the implementation as been done only for Star aligner so I am opening the PR so we can have a proper discussion and alignment over what the code should look like, before I can apply the same for the other aligners.

PoC overview

• Only Star aligner
• Moved mtx_to_h5ad module to aligner sub-workflow so it is aligner specific and avoid having a gigantic module with multiple conditions
• added a copy of cellbender subworkflow from scdownstream to perform a more straightforward empty drops filter that keeps format of h5ad input
  • Thus, not requiring further work after filter, since it will keep the format of its input, which should be the standardized h5ad
• Moved h5ad to Rds conversion to use anndataR package so to keep it simple

TODOs summary

• Define where (and what) h5ad format standardization should happen
  • Should it happen directly in the alinger-specific module (would be the most straightforward) or should it be in a separate (maybe the anndataR conversion) module that will perform the standardization and generate a new h5ad for all aligners?
• Create the anndataR docker container within nf-core (currently is using my personal repo)
  • e.g. if done in the anndataR module, it would generate as output a h5ad and a rds file.
• Define what is the desired standardization for h5ad
  • which commands should be executed?
• After defined, should be implemented for other aligners
• Cleanup repo (remove old modules currently as backup, documentation, etc.)

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7c304cc

+| ✅ 205 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

• files_exist - File is ignored: lib/Utils.groovy
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• template_strings - template_strings
• schema_params - schema_params

✅ Tests passed:

• files_exist - File found: .gitattributes
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• files_exist - File found: CHANGELOG.md
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• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
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• files_exist - File found: .github/.dockstore.yml
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• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
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• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
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• files_exist - File found: conf/modules.config
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• nextflow_config - Config variable (correctly) not found: params.nf_required_version
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• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 2.8.0dev
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.aligner= alevin
• nextflow_config - Config default value correct: params.protocol= auto
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.simpleaf_rlen= 91
• nextflow_config - Config default value correct: params.star_feature= Gene
• nextflow_config - Config default value correct: params.kb_workflow= standard
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
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• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
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• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
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• files_unchanged - assets/email_template.html matches the template
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• files_unchanged - assets/nf-core-scrnaseq_logo_light.png matches the template
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• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_name_conventions - Name adheres to nf-core convention
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - CELLBENDER_REMOVEBACKGROUND found in conf/modules.config and Nextflow scripts.
• modules_config - ADATA_BARCODES found in conf/modules.config and Nextflow scripts.
• modules_config - MTX_TO_H5AD found in conf/modules.config and Nextflow scripts.
• modules_config - GTF_GENE_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - CELLRANGER_MKGTF found in conf/modules.config and Nextflow scripts.
• modules_config - CELLRANGER_MKREF found in conf/modules.config and Nextflow scripts.
• modules_config - CELLRANGER_COUNT found in conf/modules.config and Nextflow scripts.
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• modules_config - CELLRANGERARC_COUNT found in conf/modules.config and Nextflow scripts.
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• modules_config - CELLRANGER_MKREF found in conf/modules.config and Nextflow scripts.
• modules_config - UNIVERSC found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD_TXP2GENE found in conf/modules.config and Nextflow scripts.
• modules_config - SIMPLEAF_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SIMPLEAF_QUANT found in conf/modules.config and Nextflow scripts.
• modules_config - ALEVINQC found in conf/modules.config and Nextflow scripts.
• modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
• modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - KALLISTOBUSTOOLS_REF found in conf/modules.config and Nextflow scripts.
• modules_config - KALLISTOBUSTOOLS_COUNT found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_SCRNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
• modules_config - CELLRANGER_MKGTF found in conf/modules.config and Nextflow scripts.
• modules_config - CELLRANGER_MKREF found in conf/modules.config and Nextflow scripts.
• modules_config - CELLRANGER_MKVDJREF found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-09-16 08:48:11