Test with larger nf-core runners

[LuisHeinzlmeier]

• add larger nf-core runners

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 500e955

+| ✅ 359 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  11 tests had warnings |!
-| ❌   1 tests failed       |-

Details

❌ Test failures:

• rocrate_readme_sync - The RO-Crate descriptions do not match the README.md content. Use nf-core pipelines lint --fix rocrate_readme_sync to update.

❗ Test warnings:

• 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
• 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 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.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/CONTRIBUTING.md
• 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
• files_exist - File found: .github/actions/nf-test/action.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• 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-hadge_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/images/nf-core-hadge_logo_light.png
• files_exist - File found: docs/images/nf-core-hadge_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: tests/default.nf.test
• 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
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• 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-hadge_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/Utils.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/WorkflowHadge.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 manifest.version ends in dev: 1.0.0dev
• 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.mode= rescue
• nextflow_config - Config default value correct: params.hash_tools= gmm-demux
• nextflow_config - Config default value correct: params.genetic_tools= vireo
• nextflow_config - Config default value correct: params.bam_qc= true
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.match_donor= true
• nextflow_config - Config default value correct: params.find_variants= true
• nextflow_config - Config default value correct: params.subset_gt_donors= true
• nextflow_config - Config default value correct: params.variant_count= 10
• nextflow_config - Config default value correct: params.variant_pct= 0.9
• nextflow_config - Config default value correct: params.demuxem_generate_diagnostic_plots= true
• nextflow_config - Config default value correct: params.demuxem_alpha_on_samples= 0.0
• nextflow_config - Config default value correct: params.demuxem_min_num_genes= 100
• nextflow_config - Config default value correct: params.demuxem_min_num_umis= 100
• nextflow_config - Config default value correct: params.demuxem_min_signal_hashtag= 10.0
• nextflow_config - Config default value correct: params.demuxem_random_state= 0
• nextflow_config - Config default value correct: params.bff_methods= COMBINED
• nextflow_config - Config default value correct: params.bff_preprocessing= true
• nextflow_config - Config default value correct: params.bff_doHeatmap= true
• nextflow_config - Config default value correct: params.bff_chemistry= 10xV3
• nextflow_config - Config default value correct: params.gmmdemux_type_report= true
• nextflow_config - Config default value correct: params.gmmdemux_summary_report= true
• nextflow_config - Config default value correct: params.gmmdemux_threshold= 0.8
• nextflow_config - Config default value correct: params.gmmdemux_random_state= 0
• nextflow_config - Config default value correct: params.hashsolo_priors= 0.01,0.8,0.19
• nextflow_config - Config default value correct: params.hashsolo_round_digits= 10
• nextflow_config - Config default value correct: params.htodemux_quantile= 0.99
• nextflow_config - Config default value correct: params.htodemux_init= NULL
• nextflow_config - Config default value correct: params.htodemux_nstarts= 100
• nextflow_config - Config default value correct: params.htodemux_kfunc= clara
• nextflow_config - Config default value correct: params.htodemux_nsamples= 100
• nextflow_config - Config default value correct: params.htodemux_seed= 42
• nextflow_config - Config default value correct: params.htodemux_verbose= true
• nextflow_config - Config default value correct: params.htodemux_visualization_ridgePlot= true
• nextflow_config - Config default value correct: params.htodemux_visualization_ridgeNCol= 2
• nextflow_config - Config default value correct: params.htodemux_visualization_featureScatter= true
• nextflow_config - Config default value correct: params.htodemux_visualization_vlnPlot= true
• nextflow_config - Config default value correct: params.htodemux_visualization_vlnFeatures= nCount_RNA
• nextflow_config - Config default value correct: params.htodemux_visualization_vlnLog= true
• nextflow_config - Config default value correct: params.htodemux_visualization_tSNE= true
• nextflow_config - Config default value correct: params.htodemux_visualization_tSNEIdents= Negative
• nextflow_config - Config default value correct: params.htodemux_visualization_tSNEInvert= true
• nextflow_config - Config default value correct: params.htodemux_visualization_tSNEDimMax= 2
• nextflow_config - Config default value correct: params.htodemux_visualization_tSNEPerplexity= 100
• nextflow_config - Config default value correct: params.htodemux_visualization_heatMap= true
• nextflow_config - Config default value correct: params.htodemux_visualization_heatMapNcells= 500
• nextflow_config - Config default value correct: params.multiseqdemux_quantile= 0.7
• nextflow_config - Config default value correct: params.multiseqdemux_autoThresh= true
• nextflow_config - Config default value correct: params.multiseqdemux_maxiter= 5
• nextflow_config - Config default value correct: params.multiseqdemux_qrangeFrom= 0.1
• nextflow_config - Config default value correct: params.multiseqdemux_qrangeTo= 0.9
• nextflow_config - Config default value correct: params.multiseqdemux_qrangeBy= 0.05
• nextflow_config - Config default value correct: params.multiseqdemux_verbose= true
• nextflow_config - Config default value correct: params.hasheddrops_lower= 100
• nextflow_config - Config default value correct: params.hasheddrops_niters= 10000
• nextflow_config - Config default value correct: params.hasheddrops_testAmbient= true
• nextflow_config - Config default value correct: params.hasheddrops_round= true
• nextflow_config - Config default value correct: params.hasheddrops_isCellFDR= 0.01
• nextflow_config - Config default value correct: params.hasheddrops_gene_col= 2
• nextflow_config - Config default value correct: params.hasheddrops_ambient= true
• nextflow_config - Config default value correct: params.hasheddrops_minProp= 0.05
• nextflow_config - Config default value correct: params.hasheddrops_pseudoCount= 5
• nextflow_config - Config default value correct: params.hasheddrops_doubletNmads= 3
• nextflow_config - Config default value correct: params.hasheddrops_doubletMin= 2
• nextflow_config - Config default value correct: params.hasheddrops_confidentNmads= 3
• nextflow_config - Config default value correct: params.hasheddrops_confidentMin= 2
• nextflow_config - Config default value correct: params.preprocessing_sel_method= mean.var.plot
• nextflow_config - Config default value correct: params.preprocessing_ndelim= _
• nextflow_config - Config default value correct: params.preprocessing_n_features= 2000
• nextflow_config - Config default value correct: params.preprocessing_assay= HTO
• nextflow_config - Config default value correct: params.preprocessing_margin= 2
• nextflow_config - Config default value correct: params.preprocessing_norm_method= CLR
• nextflow_config - Config default value correct: params.preprocessing_gene_col= 2
• nextflow_config - Config default value correct: params.generate_anndata= true
• nextflow_config - Config default value correct: params.generate_mudata= true
• nextflow_config - Config default value correct: params.cellsnp_celltag= CB
• nextflow_config - Config default value correct: params.cellsnp_umitag= Auto
• nextflow_config - Config default value correct: params.cellsnp_mincount= 20
• nextflow_config - Config default value correct: params.cellsnp_minmaf= 0.0
• nextflow_config - Config default value correct: params.cellsnp_minlen= 30
• nextflow_config - Config default value correct: params.cellsnp_minmapq= 20
• nextflow_config - Config default value correct: params.cellsnp_maxdepth= 0
• nextflow_config - Config default value correct: params.vireo_genotag= GT
• nextflow_config - Config default value correct: params.vireo_n_init= 50
• nextflow_config - Config default value correct: params.vireo_extra_donor= 0
• nextflow_config - Config default value correct: params.vireo_extra_donor_mode= distance
• nextflow_config - Config default value correct: params.vireo_force_learn_gt= true
• nextflow_config - Config default value correct: params.vireo_rand_seed= 0
• nextflow_config - Config default value correct: params.vireo_cell_range= all
• nextflow_config - Config default value correct: params.dsc_pileup_tag_group= CB
• nextflow_config - Config default value correct: params.dsc_pileup_tag_umi= UB
• nextflow_config - Config default value correct: params.dsc_pileup_cap_bq= 40
• nextflow_config - Config default value correct: params.dsc_pileup_min_bq= 13
• nextflow_config - Config default value correct: params.dsc_pileup_min_mq= 20
• nextflow_config - Config default value correct: params.dsc_pileup_min_td= 0
• nextflow_config - Config default value correct: params.dsc_pileup_excl_flag= 3844
• nextflow_config - Config default value correct: params.dsc_pileup_min_total= 0
• nextflow_config - Config default value correct: params.dsc_pileup_min_uniq= 0
• nextflow_config - Config default value correct: params.dsc_pileup_min_snp= 0
• nextflow_config - Config default value correct: params.demuxlet_field= GT
• nextflow_config - Config default value correct: params.demuxlet_geno_error_offset= 0.1
• nextflow_config - Config default value correct: params.demuxlet_geno_error_coeff= 0.0
• nextflow_config - Config default value correct: params.demuxlet_r2_info= R2
• nextflow_config - Config default value correct: params.demuxlet_min_mac= 1
• nextflow_config - Config default value correct: params.demuxlet_min_callrate= 0.5
• nextflow_config - Config default value correct: params.demuxlet_alpha= 0.1,0.2,0.3,0.4,0.5
• nextflow_config - Config default value correct: params.demuxlet_doublet_prior= 0.5
• nextflow_config - Config default value correct: params.freemuxlet_doublet_prior= 0.5
• nextflow_config - Config default value correct: params.freemuxlet_geno_error= 0.1
• nextflow_config - Config default value correct: params.freemuxlet_bf_thres= 5.41
• nextflow_config - Config default value correct: params.freemuxlet_frac_init_clust= 1.0
• nextflow_config - Config default value correct: params.freemuxlet_iter_init= 10
• nextflow_config - Config default value correct: params.freemuxlet_seed= 0
• nextflow_config - Config default value correct: params.souporcell_ploidy= 2
• nextflow_config - Config default value correct: params.souporcell_min_alt= 10
• nextflow_config - Config default value correct: params.souporcell_min_ref= 10
• nextflow_config - Config default value correct: params.souporcell_max_loci= 2048
• nextflow_config - Config default value correct: params.souporcell_restarts= 100
• nextflow_config - Config default value correct: params.souporcell_skip_remap= false
• nextflow_config - Config default value correct: params.souporcell_ignore= false
• 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/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_donor_match.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_donor_match.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_donor_match.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_hashing.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_hashing.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_hashing.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_genetic.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_genetic.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_genetic.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/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.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/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-hadge_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-hadge_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-hadge_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: 25.04.0, Config: 25.04.0
• 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
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.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: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.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 - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
• modules_config - UMITOOLS_DEDUP found in conf/modules.config and Nextflow scripts.
• modules_config - EXTRACT_HASHES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_BAM found in conf/modules.config and Nextflow scripts.
• modules_config - DONOR_MATCH found in conf/modules.config and Nextflow scripts.
• modules_config - FIND_VARIANTS found in conf/modules.config and Nextflow scripts.
• modules_config - SUBSET_GT_DONORS found in conf/modules.config and Nextflow scripts.
• modules_config - JOIN_RESULTS_ASSIGNMENT found in conf/modules.config and Nextflow scripts.
• modules_config - JOIN_RESULTS_CLASSIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_ANNDATA_MUDATA found in conf/modules.config and Nextflow scripts.
• modules_config - CELLSNP_MODEA found in conf/modules.config and Nextflow scripts.
• modules_config - VIREO found in conf/modules.config and Nextflow scripts.
• modules_config - POPSCLE_DSCPILEUP found in conf/modules.config and Nextflow scripts.
• modules_config - POPSCLE_DEMUXLET found in conf/modules.config and Nextflow scripts.
• modules_config - POPSCLE_FREEMUXLET found in conf/modules.config and Nextflow scripts.
• modules_config - SOUPORCELL found in conf/modules.config and Nextflow scripts.
• modules_config - MTXCONVERT_RNA found in conf/modules.config and Nextflow scripts.
• modules_config - MTXCONVERT_HTO found in conf/modules.config and Nextflow scripts.
• modules_config - DEMUXEM found in conf/modules.config and Nextflow scripts.
• modules_config - BFF found in conf/modules.config and Nextflow scripts.
• modules_config - GMMDEMUX found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_RNA found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_HTO found in conf/modules.config and Nextflow scripts.
• modules_config - HTODEMUX found in conf/modules.config and Nextflow scripts.
• modules_config - HTODEMUX_VISUALIZATION found in conf/modules.config and Nextflow scripts.
• modules_config - MULTISEQDEMUX found in conf/modules.config and Nextflow scripts.
• modules_config - HASHEDDROPS found in conf/modules.config and Nextflow scripts.
• modules_config - HASH_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - GENE_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - PREPROCESSING_FOR_HTODEMUX_MULTISEQ found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - SCANPY_HASHSOLO 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: 3.4.1

Run details

• nf-core/tools version 3.4.1
• Run at 2026-02-20 11:51:17