├── .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 ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── chr_rename_add.txt ├── chr_rename_del.txt ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-phaseimpute_logo_light.png ├── panel.csv ├── regionsheet.csv ├── samplesheet.csv ├── schema_chunks.json ├── schema_input.json ├── schema_input_panel.json ├── schema_input_region.json ├── schema_map.json ├── schema_posfile.json ├── sendmail_template.txt └── slackreport.json ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── steps │ ├── chrcheck.config │ ├── imputation_beagle5.config │ ├── imputation_glimpse1.config │ ├── imputation_glimpse2.config │ ├── imputation_minimac4.config │ ├── imputation_quilt.config │ ├── imputation_stitch.config │ ├── initialisation.config │ ├── panel_prep.config │ ├── simulation.config │ └── validation.config ├── test.config ├── test_all.config ├── test_all_fullchr.config ├── test_batch.config ├── test_beagle5.config ├── test_dog.config ├── test_full.config ├── test_glimpse2.config ├── test_minimac4.config ├── test_panelprep.config ├── test_quilt.config ├── test_sim.config ├── test_stitch.config ├── test_validate.config └── test_vcf.config ├── docs ├── README.md ├── development.md ├── images │ ├── InputSoftware_compatibility.drawio │ ├── InputSoftware_compatibility.png │ ├── logo │ │ ├── nf-core-phaseimpute.svg │ │ ├── nf-core-phaseimpute_hexagonal_logo.png │ │ ├── nf-core-phaseimpute_logo_dark.png │ │ ├── nf-core-phaseimpute_logo_light.png │ │ ├── nf-core-phaseimpute_logo_only_dark.png │ │ └── nf-core-phaseimpute_logo_only_light.png │ ├── metro │ │ ├── Impute.png │ │ ├── MetroMap.png │ │ ├── MetroMap.svg │ │ ├── MetroMap.xml │ │ ├── MetroMap_animated.svg │ │ ├── MetroMap_animated_dark.svg │ │ ├── PanelPrep.png │ │ ├── Simulate.png │ │ ├── Validate.png │ │ ├── filtermetro.md │ │ ├── legend.png │ │ ├── metro.py │ │ ├── new.html │ │ └── pipeline_dag_2024-05-28_12-01-55.html │ ├── nf-core-phaseimpute_logo_dark.png │ └── nf-core-phaseimpute_logo_light.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── addcolumns │ │ ├── environment.yml │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── bamchrextract │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── listtofile │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── vcfchrextract │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap └── nf-core │ ├── bcftools │ ├── annotate │ │ ├── bcftools-annotate.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bcf.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── vcf.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── concat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── convert │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── merge │ │ ├── bcftools-merge.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bcf.config │ │ │ ├── bcf_gz.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow.gvcf.config │ │ │ ├── vcf.config │ │ │ ├── vcf_gz.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── mpileup │ │ ├── bcftools-mpileup.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── norm │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.bcf.config │ │ │ ├── nextflow.bcf_gz.config │ │ │ ├── nextflow.config │ │ │ ├── nextflow.vcf.config │ │ │ ├── nextflow.vcf_gz.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── pluginsplit │ │ ├── bcftools-pluginsplit.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── query │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── vcf_gz_index.config │ │ ├── vcf_gz_index_csi.config │ │ └── vcf_gz_index_tbi.config │ ├── beagle5 │ └── beagle │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bedtools │ └── makewindows │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── gawk │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── glimpse │ ├── chunk │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── ligate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── phase │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── glimpse2 │ ├── chunk │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── concordance │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── ligate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── phase │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── minimac4 │ ├── compressref │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── impute │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── quilt │ └── quilt │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── samtools │ ├── coverage │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-coverage.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── depth │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-depth.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── faidx │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow2.config │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-merge.diff │ │ └── tests │ │ │ ├── index.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── reheader │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-reheader.diff │ │ └── tests │ │ │ ├── chrdel.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── rgdel.config │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-view.diff │ │ └── tests │ │ ├── bam.config │ │ ├── bam_index.config │ │ ├── cram_index.config │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── shapeit5 │ ├── ligate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── phasecommon │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── shapeit5-phasecommon.diff │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── stitch │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── tabix │ ├── bgzip │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bgzip_compress.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── vcf_none.config │ └── tabix │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── tabix_bed.config │ │ ├── tabix_gff.config │ │ ├── tabix_vcf_csi.config │ │ └── tabix_vcf_tbi.config │ └── vcflib │ └── vcffixup │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ └── main.nf.test.snap ├── nextflow.config ├── nextflow_schema.json ├── nf-core-phaseimpute_logo_light.png ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── bam_chr_rename_samtools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bam_downsample_samtools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bam_extract_region_samtools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bam_gl_bcftools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bam_impute_quilt │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bam_impute_stitch │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── bam_vcf_impute_glimpse2 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── utils_nfcore_phaseimpute_pipeline │ │ ├── main.nf │ │ └── tests │ │ │ ├── function.nf.test │ │ │ ├── function.nf.test.snap │ │ │ ├── main.nf.test │ │ │ └── region.csv │ ├── vcf_chr_rename_bcftools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_chunk_glimpse │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_concatenate_bcftools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_concordance_glimpse2 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_impute_beagle5 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_impute_glimpse1 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_impute_minimac4 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_normalize_bcftools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_phase_shapeit5 │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── vcf_sites_extract_bcftools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── vcf_split_bcftools │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml └── 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 │ ├── 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 ├── .nftignore ├── config │ ├── env_nf.yml │ └── test_data.config ├── csv │ ├── chunks.csv │ ├── map_glimpse.csv │ ├── map_plink.csv │ ├── panel.csv │ ├── panel_dog.csv │ ├── 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