Cellranger gtf space incompatibility by nictru · Pull Request #554 · nf-core/scrnaseq

nictru · 2026-05-28T22:52:54Z

This causes failure in the megatests, and generally it is not optimal if the genomes we provide are not fully compatible with the pipeline. This issue occurs only with the GRCh38 genome, which is probably the one used most often. While I was at it, I also created a dedicated subworkflow for genome preparation, to reduce the complexity of the main workflow.

Install the nf-core/gawk module from nf-core/modules for use in the pipeline.

Add PREPARE_GENOME to prepare references and run GTF_SOURCE_FIX (gawk) when iGenomes marks the GTF source column as having spaces and a Cell Ranger aligner is selected.

github-actions · 2026-05-28T22:54:38Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 38362a6

+| ✅ 245 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 4.2.0
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!
pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
schema_description - No description provided in schema for parameter: skip_emptydrops

❔ Tests ignored:

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

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
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
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
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files_exist - File found: .github/workflows/linting_comment.yml
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files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-scrnaseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-scrnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-scrnaseq_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
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files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-scrnaseq_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowScrnaseq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 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= simpleaf
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_umi_resolution= cr-like
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.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/
nf_test_content - 'tests/main_pipeline_kallisto.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_simpleaf.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_simpleaf.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_simpleaf.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangerarc.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellrangerarc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangerarc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellranger.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellranger.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellranger.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_star.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-scrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scrnaseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.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: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awstest.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/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 - ANNDATA_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 - GTF_SOURCE_FIX 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.
modules_config - CELLRANGERARC_MKGTF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGERARC_MKREF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGERARC_COUNT 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 - QCATCH 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 - KALLISTOBUSTOOLS_REF found in conf/modules.config and Nextflow scripts.
modules_config - KALLISTOBUSTOOLS_COUNT found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MULTI found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP 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: 4.0.2
rocrate_readme_sync - RO-Crate description matches the README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.0.2
Run at 2026-06-06 10:08:13

Add usage guidance and runtime warning for GRCh38 GTF source-column compatibility, mirroring the legacy STAR iGenomes documentation in #552.

nictru added 2 commits May 29, 2026 00:48

Add nf-core/gawk module

53f4fd8

Install the nf-core/gawk module from nf-core/modules for use in the pipeline.

Fix Cell Ranger mkref GTF source column for GRCh38

746a439

Add PREPARE_GENOME to prepare references and run GTF_SOURCE_FIX (gawk) when iGenomes marks the GTF source column as having spaces and a Cell Ranger aligner is selected.

Update pipeline test snapshots

7427111

nictru force-pushed the cellranger-gtf-space-incompatibility branch from f117d68 to 7427111 Compare May 29, 2026 08:52

nictru marked this pull request as draft May 29, 2026 09:00

nictru added 4 commits May 29, 2026 11:02

Merge branch 'dev' into cellranger-gtf-space-incompatibility

a024869

Merge origin/dev into cellranger-gtf-space-incompatibility

ed178c7

Merge origin/dev into cellranger-gtf-space-incompatibility

bf63d88

Document Cell Ranger iGenomes GTF source fix

38362a6

Add usage guidance and runtime warning for GRCh38 GTF source-column compatibility, mirroring the legacy STAR iGenomes documentation in #552.

nictru marked this pull request as ready for review June 6, 2026 10:18

nictru requested a review from fmalmeida June 6, 2026 10:18

fmalmeida approved these changes Jun 9, 2026

View reviewed changes

nictru merged commit 2c72754 into dev Jun 9, 2026
21 checks passed

nictru deleted the cellranger-gtf-space-incompatibility branch June 9, 2026 13:15

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Cellranger gtf space incompatibility#554

Cellranger gtf space incompatibility#554
nictru merged 7 commits into
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cellranger-gtf-space-incompatibility

nictru commented May 28, 2026

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nictru commented May 28, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️