├── .devcontainer ├── devcontainer.json └── setup.sh ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ ├── release-announcements.yml │ └── template-version-comment.yml ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .ruff.toml ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── EMPTY ├── adaptivecard.json ├── cellranger_barcodes_samplesheet.csv ├── cellranger_barcodes_samplesheet_rat.csv ├── cellrangerarc_samplesheet.csv ├── cellrangermulti_samplesheet.csv ├── cellrangermulti_samplesheet_rat.csv ├── email_template.html ├── email_template.txt ├── fb_reference.csv ├── frna_probeset_subset.csv ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-scrnaseq_logo_light.png ├── protocols.json ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json └── whitelist │ ├── 10x_V1_barcode_whitelist.txt.gz │ ├── 10x_V2_barcode_whitelist.txt.gz │ ├── 10x_V3_barcode_whitelist.txt.gz │ └── 10x_V4_barcode_whitelist.txt.gz ├── bin ├── alevin_qc.r ├── check_cellrangermulti.py ├── filter_gtf_for_genes_in_genome.py ├── generate_lib_csv.py ├── postprocessing.r └── t2g.py ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── test.config ├── test_cellranger_multi.config └── test_full.config ├── docs ├── README.md ├── images │ ├── nf-core-scrnaseq_logo_dark.png │ ├── nf-core-scrnaseq_logo_light.png │ ├── scrnaseq_pipeline_V3.0-metro_clean.png │ └── scrnaseq_pipeline_V3.0-metro_clean.svg ├── output.md └── usage.md ├── lib └── Utils.groovy ├── main.nf ├── modules.json ├── modules ├── local │ ├── alevinqc.nf │ ├── anndatar_convert.nf │ ├── concat_h5ad.nf │ ├── gffread_transcriptome.nf │ ├── gtf_gene_filter.nf │ ├── mtx_to_h5ad.nf │ ├── parse_cellrangermulti_samplesheet.nf │ ├── star_align.nf │ └── templates │ │ ├── anndatar_convert.R │ │ ├── concat_h5ad.py │ │ ├── mtx_to_h5ad_cellranger.py │ │ ├── mtx_to_h5ad_kallisto.py │ │ ├── mtx_to_h5ad_simpleaf.py │ │ └── mtx_to_h5ad_star.py └── nf-core │ ├── anndata │ └── barcodes │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── barcodes.py │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── cellbender │ └── removebackground │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── epochs.config │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── cellranger │ ├── count │ │ ├── README.md │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ │ └── cellranger_count.py │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── mkgtf │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── mkref │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── mkvdjref │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── multi │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── cellranger_multi.py │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── cellrangerarc │ ├── Dockerfile │ ├── README.md │ ├── count │ │ ├── main.nf │ │ └── meta.yml │ ├── mkgtf │ │ ├── main.nf │ │ └── meta.yml │ └── mkref │ │ ├── main.nf │ │ └── meta.yml │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gffread │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow-gff3.config │ │ ├── nextflow.config │ │ └── tags.yml │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── kallistobustools │ ├── count │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── ref │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── simpleaf │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── quant │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── star │ └── genomegenerate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ └── unzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── align_cellranger.nf │ ├── align_cellrangerarc.nf │ ├── align_cellrangermulti.nf │ ├── fastqc.nf │ ├── h5ad_conversion.nf │ ├── kallisto_bustools.nf │ ├── simpleaf.nf │ ├── starsolo.nf │ └── utils_nfcore_scrnaseq_pipeline │ │ └── main.nf └── nf-core │ ├── h5ad_removebackground_barcodes_cellbender_anndata │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── epochs.config │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ └── nextflow.config │ ├── utils_nfcore_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── main.workflow.nf.test.snap │ │ └── nextflow.config │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tests ├── .nf-test.log ├── .nftignore ├── main_pipeline_cellranger.nf.test ├── main_pipeline_cellranger.nf.test.snap ├── main_pipeline_cellrangerarc.nf.test ├── main_pipeline_cellrangerarc.nf.test.snap ├── main_pipeline_cellrangermulti.nf.test ├── main_pipeline_cellrangermulti.nf.test.snap ├── main_pipeline_kallisto.nf.test ├── main_pipeline_kallisto.nf.test.snap 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