├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── ci_immcantation.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── release-announcements.yml │ └── template_version_comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-airrflow_logo_light.png ├── nf-core-airrflow_logo_reports.png ├── nf-core_style.css ├── repertoire_comparison.Rmd ├── reveal │ └── mapping_MiAIRR_BioSample_v1.3.1.tsv ├── schema_input.json ├── sendmail_template.txt ├── single_cell_tutorial │ ├── airrflow.sh │ └── samplesheet.tsv └── slackreport.json ├── bin ├── add_metadata.R ├── check_samplesheet.py ├── clean_imgtdb.py ├── execute_report.R ├── fetch_databases.sh ├── fetch_igblastdb.sh ├── fetch_imgt.sh ├── imgt2igblast.sh ├── log_parsing.py ├── log_parsing_no-umi.py ├── merge_R1_umi.py ├── merge_graphs.sh ├── reveal_add_metadata.R ├── reveal_collapseDuplicates.R ├── reveal_filter_quality.R └── reveal_mod_3_junction.R ├── conf ├── base.config ├── clontech_umi_bcr.config ├── clontech_umi_tcr.config ├── igenomes_ignored.config ├── modules.config ├── nebnext_umi_bcr.config ├── nebnext_umi_tcr.config ├── test.config ├── test_10x_sc.config ├── test_assembled_hs.config ├── test_assembled_immcantation_devel_hs.config ├── test_assembled_immcantation_devel_mm.config ├── test_assembled_mm.config ├── test_clontech_umi.config ├── test_embeddings_H.config ├── test_embeddings_HL.config ├── test_fetchimgt.config ├── test_full.config ├── test_maskprimers_align.config ├── test_maskprimers_extract.config ├── test_nebnext_umi.config ├── test_no_umi.config ├── test_nocluster.config ├── test_raw_immcantation_devel.config ├── test_rnaseq_bulk.config ├── test_rnaseq_sc.config └── test_tcr.config ├── docs ├── README.md ├── images │ ├── Primers_R1_UMI_C.png │ ├── Primers_R1_UMI_V.png │ ├── Primers_R1_V.png │ ├── TAKARA_RACE_BCR.png │ ├── TAKARA_RACE_TCR.png │ ├── airrflow_workflow_overview.ai │ ├── airrflow_workflow_overview.pdf │ ├── airrflow_workflow_overview.png │ ├── metro-map-airrflow.ai │ ├── metro-map-airrflow.pdf │ ├── metro-map-airrflow.png │ ├── metro-map-airrflow.svg │ ├── nf-core-airrflow_logo_dark.png │ └── nf-core-airrflow_logo_light.png ├── output.md ├── usage.md └── usage │ ├── FAQ.md │ ├── bulk_tutorial.md │ ├── bulk_tutorial │ └── bulk_sample_code │ │ ├── airrflow_bulk_b_fastq.sh │ │ ├── metadata_pcr_umi_airr_300.tsv │ │ └── resource.config │ ├── single_cell_tutorial.md │ └── single_cell_tutorial │ └── sample_data_code │ ├── 10x_sc_raw.tsv │ ├── airrflow_sc_from_assembled.sh │ ├── airrflow_sc_from_fastq.sh │ ├── assembled_samplesheet.tsv │ ├── assembled_samplesheet_missing_sex.tsv │ └── resource.config ├── main.nf ├── modules.json ├── modules ├── local │ ├── airrflow_report │ │ └── airrflow_report.nf │ ├── changeo │ │ ├── changeo_assigngenes.nf │ │ ├── changeo_convertdb_fasta.nf │ │ ├── changeo_creategermlines.nf │ │ ├── changeo_makedb.nf │ │ ├── changeo_parsedb_select_locus.nf │ │ └── changeo_parsedb_split.nf │ ├── enchantr │ │ ├── collapse_duplicates.nf │ │ ├── define_clones.nf │ │ ├── detect_contamination.nf │ │ ├── dowser_lineages.nf │ │ ├── find_threshold.nf │ │ ├── remove_chimeric.nf │ │ ├── report_file_size.nf │ │ ├── single_cell_qc.nf │ │ └── validate_input.nf │ ├── fastqc_postassembly.nf │ ├── fetch_databases.nf │ ├── gunzip.nf │ ├── merge_UMI.nf │ ├── parse_logs.nf │ ├── prepare_trust4_reference.nf │ ├── presto │ │ ├── presto_assemblepairs.nf │ │ ├── presto_assemblepairs_sequential.nf │ │ ├── presto_buildconsensus.nf │ │ ├── presto_clustersets.nf │ │ ├── presto_collapseseq.nf │ │ ├── presto_filterseq.nf │ │ ├── presto_filterseq_postassembly.nf │ │ ├── presto_maskprimers.nf │ │ ├── presto_maskprimers_align.nf │ │ ├── presto_maskprimers_extract.nf │ │ ├── presto_maskprimers_postassembly.nf │ │ ├── presto_maskprimers_score.nf │ │ ├── presto_pairseq.nf │ │ ├── presto_parse_cluster.nf │ │ ├── presto_parseheaders.nf │ │ ├── presto_parseheaders_metadata.nf │ │ ├── presto_parseheaders_primers.nf │ │ ├── presto_postconsensus_pairseq.nf │ │ └── presto_splitseq.nf │ ├── rename_fastq.nf │ ├── rename_file.nf │ ├── reveal │ │ ├── add_meta_to_tab.nf │ │ ├── filter_junction_mod3.nf │ │ └── filter_quality.nf │ ├── samplesheet_check.nf │ ├── unzip_cellrangerdb.nf │ └── unzip_db.nf └── nf-core │ ├── amulety │ ├── antiberta2 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── gpu.nf.test │ │ │ ├── gpu.nf.test.snap │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── antiberty │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── gpu.nf.test │ │ │ ├── gpu.nf.test.snap │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── balmpaired │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── gpu.nf.test │ │ │ ├── gpu.nf.test.snap │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── esm2 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── gpu.nf.test │ │ │ ├── gpu.nf.test.snap │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── translate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── cellranger │ ├── mkvdjref │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── vdj │ │ ├── main.nf │ │ └── meta.yml │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ └── trust4 │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── assembled_input_check.nf │ ├── bulk_qc_and_filter.nf │ ├── clonal_analysis.nf │ ├── databases.nf │ ├── fastq_input_check.nf │ ├── presto_sans_umi.nf │ ├── presto_umi.nf │ ├── repertoire_analysis_reporting.nf │ ├── rnaseq_input.nf │ ├── sc_raw_input.nf │ ├── sequence_assembly.nf │ ├── single_cell_qc_and_filtering.nf │ ├── translate_embed.nf │ ├── utils_nfcore_airrflow_pipeline │ │ └── main.nf │ └── vdj_annotation.nf └── nf-core │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── nextflow.config │ │ └── tags.yml │ ├── 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 │ │ └── tags.yml │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tower.yml └── workflows └── airrflow.nf 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