├── .devcontainer └── devcontainer.json ├── .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 ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── 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 ├── multiqc_config_hybrid.yml ├── multiqc_config_long.yml ├── multiqc_config_short.yml ├── nf-core-bacass_logo_light.png ├── samplesheet.tsv ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json └── test_config_dfast.py ├── bin ├── csv_to_yaml.py ├── download_reference.py ├── find_common_reference.py ├── kmerfinder_summary.py └── multiqc_to_custom_csv.py ├── conf ├── base.config ├── modules.config ├── test.config ├── test_dfast.config ├── test_full.config ├── test_hybrid.config ├── test_hybrid_dragonflye.config ├── test_liftoff.config ├── test_long.config ├── test_long_dragonflye.config ├── test_long_miniasm.config └── test_long_miniasm_prokka.config ├── docs ├── README.md ├── images │ ├── bandage.png │ ├── fastqc.png │ ├── icarus.png │ ├── kraken2.png │ ├── nanoplot.png │ ├── nf-core-bacass_logo_dark.png │ ├── nf-core-bacass_logo_light.png │ ├── prokka.png │ ├── quast.png │ └── toulligqc.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── custom │ │ └── multiqc │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── dfast │ │ ├── environment.yml │ │ └── main.nf │ ├── kmerfinder │ │ ├── download_reference │ │ │ ├── environment.yml │ │ │ └── main.nf │ │ ├── kmerfinder │ │ │ ├── environment.yml │ │ │ └── main.nf │ │ └── summary │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── kraken2 │ │ └── db_preparation │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── medaka │ │ ├── environment.yml │ │ └── main.nf │ ├── nanopolish │ │ ├── environment.yml │ │ └── main.nf │ └── pycoqc │ │ ├── environment.yml │ │ └── main.nf └── nf-core │ ├── bakta │ ├── bakta │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── baktadbdownload │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── busco │ └── busco │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── canu │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── custom │ └── dumpsoftwareversions │ │ └── templates │ │ └── dumpsoftwareversions.py │ ├── dragonflye │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.interleaved.config │ │ └── nextflow.save_failed.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── filtlong │ ├── 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 │ │ └── tags.yml │ ├── kraken2 │ └── kraken2 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── liftoff │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── miniasm │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── minimap2 │ └── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── multiqc │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── nanoplot │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── nanoplot.diff │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yaml │ ├── porechop │ └── porechop │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── prokka │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── quast │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── racon │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── racon.diff │ ├── samtools │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── toulligqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── unicycler │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ └── untar │ ├── 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 │ ├── bakta_dbdownload_run │ │ └── main.nf │ ├── kmerfinder_summary_download │ │ └── main.nf │ ├── qc_nanoplot_toulliqc │ │ └── main.nf │ └── utils_nfcore_bacass_pipeline │ │ └── main.nf └── nf-core │ ├── fastq_trim_fastp_fastqc │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── 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 │ │ └── 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 │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tests ├── .nftignore ├── .nftignore_files_entirely ├── default.nf.test ├── default.nf.test.snap ├── dfast.nf.test ├── dfast.nf.test.snap ├── hybrid.nf.test ├── hybrid.nf.test.snap ├── hybrid_dragonflye.nf.test ├── hybrid_dragonflye.nf.test.snap ├── long.nf.test ├── long.nf.test.snap ├── long_dragonflye.nf.test ├── long_dragonflye.nf.test.snap ├── long_liftoff.nf.test ├── long_liftoff.nf.test.snap ├── long_miniasm.nf.test ├── long_miniasm.nf.test.snap ├── long_miniasm_prokka.nf.test ├── long_miniasm_prokka.nf.test.snap └── nextflow.config ├── tower.yml └── workflows └── bacass.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/.dockstore.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/.dockstore.yml -------------------------------------------------------------------------------- /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/CONTRIBUTING.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/ISSUE_TEMPLATE/bug_report.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/ISSUE_TEMPLATE/config.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/ISSUE_TEMPLATE/feature_request.yml -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/PULL_REQUEST_TEMPLATE.md -------------------------------------------------------------------------------- /.github/actions/get-shards/action.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/actions/get-shards/action.yml -------------------------------------------------------------------------------- /.github/actions/nf-test/action.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/actions/nf-test/action.yml -------------------------------------------------------------------------------- /.github/workflows/awsfulltest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/awsfulltest.yml -------------------------------------------------------------------------------- /.github/workflows/awstest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/awstest.yml -------------------------------------------------------------------------------- /.github/workflows/branch.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/branch.yml -------------------------------------------------------------------------------- /.github/workflows/clean-up.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/clean-up.yml -------------------------------------------------------------------------------- /.github/workflows/download_pipeline.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/download_pipeline.yml -------------------------------------------------------------------------------- /.github/workflows/fix_linting.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/fix_linting.yml -------------------------------------------------------------------------------- /.github/workflows/linting.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/linting.yml -------------------------------------------------------------------------------- /.github/workflows/linting_comment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/linting_comment.yml -------------------------------------------------------------------------------- /.github/workflows/nf-test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/nf-test.yml -------------------------------------------------------------------------------- /.github/workflows/release-announcements.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/release-announcements.yml -------------------------------------------------------------------------------- /.github/workflows/template-version-comment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.github/workflows/template-version-comment.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitpod.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.gitpod.yml -------------------------------------------------------------------------------- /.nf-core.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.nf-core.yml -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.prettierignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.prettierignore -------------------------------------------------------------------------------- /.prettierrc.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/.prettierrc.yml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATIONS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/CITATIONS.md -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/README.md -------------------------------------------------------------------------------- /assets/adaptivecard.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/adaptivecard.json -------------------------------------------------------------------------------- /assets/email_template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/email_template.html -------------------------------------------------------------------------------- /assets/email_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/email_template.txt -------------------------------------------------------------------------------- /assets/methods_description_template.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/methods_description_template.yml -------------------------------------------------------------------------------- /assets/multiqc_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/multiqc_config.yml -------------------------------------------------------------------------------- /assets/multiqc_config_hybrid.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/multiqc_config_hybrid.yml -------------------------------------------------------------------------------- /assets/multiqc_config_long.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/multiqc_config_long.yml -------------------------------------------------------------------------------- /assets/multiqc_config_short.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/multiqc_config_short.yml -------------------------------------------------------------------------------- /assets/nf-core-bacass_logo_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/nf-core-bacass_logo_light.png -------------------------------------------------------------------------------- /assets/samplesheet.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/samplesheet.tsv -------------------------------------------------------------------------------- /assets/schema_input.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/schema_input.json -------------------------------------------------------------------------------- /assets/sendmail_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/sendmail_template.txt -------------------------------------------------------------------------------- /assets/slackreport.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/slackreport.json -------------------------------------------------------------------------------- /assets/test_config_dfast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/assets/test_config_dfast.py -------------------------------------------------------------------------------- /bin/csv_to_yaml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/bin/csv_to_yaml.py -------------------------------------------------------------------------------- /bin/download_reference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/bin/download_reference.py -------------------------------------------------------------------------------- /bin/find_common_reference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/bin/find_common_reference.py -------------------------------------------------------------------------------- /bin/kmerfinder_summary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/bin/kmerfinder_summary.py -------------------------------------------------------------------------------- /bin/multiqc_to_custom_csv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/bin/multiqc_to_custom_csv.py -------------------------------------------------------------------------------- /conf/base.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/base.config -------------------------------------------------------------------------------- /conf/modules.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/modules.config -------------------------------------------------------------------------------- /conf/test.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test.config -------------------------------------------------------------------------------- /conf/test_dfast.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_dfast.config -------------------------------------------------------------------------------- /conf/test_full.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_full.config -------------------------------------------------------------------------------- /conf/test_hybrid.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_hybrid.config -------------------------------------------------------------------------------- /conf/test_hybrid_dragonflye.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_hybrid_dragonflye.config -------------------------------------------------------------------------------- /conf/test_liftoff.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_liftoff.config -------------------------------------------------------------------------------- /conf/test_long.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_long.config -------------------------------------------------------------------------------- /conf/test_long_dragonflye.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_long_dragonflye.config -------------------------------------------------------------------------------- /conf/test_long_miniasm.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_long_miniasm.config -------------------------------------------------------------------------------- /conf/test_long_miniasm_prokka.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/conf/test_long_miniasm_prokka.config -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/images/bandage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/bandage.png -------------------------------------------------------------------------------- /docs/images/fastqc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/fastqc.png -------------------------------------------------------------------------------- /docs/images/icarus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/icarus.png -------------------------------------------------------------------------------- /docs/images/kraken2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/kraken2.png -------------------------------------------------------------------------------- /docs/images/nanoplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/nanoplot.png -------------------------------------------------------------------------------- /docs/images/nf-core-bacass_logo_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/nf-core-bacass_logo_dark.png -------------------------------------------------------------------------------- /docs/images/nf-core-bacass_logo_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/nf-core-bacass_logo_light.png -------------------------------------------------------------------------------- /docs/images/prokka.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/prokka.png -------------------------------------------------------------------------------- /docs/images/quast.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/quast.png -------------------------------------------------------------------------------- /docs/images/toulligqc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/images/toulligqc.png -------------------------------------------------------------------------------- /docs/output.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/output.md -------------------------------------------------------------------------------- /docs/usage.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/docs/usage.md -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/main.nf -------------------------------------------------------------------------------- /modules.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules.json -------------------------------------------------------------------------------- /modules/local/custom/multiqc/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/custom/multiqc/environment.yml -------------------------------------------------------------------------------- /modules/local/custom/multiqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/custom/multiqc/main.nf -------------------------------------------------------------------------------- /modules/local/dfast/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/dfast/environment.yml -------------------------------------------------------------------------------- /modules/local/dfast/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/dfast/main.nf -------------------------------------------------------------------------------- /modules/local/kmerfinder/download_reference/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kmerfinder/download_reference/environment.yml -------------------------------------------------------------------------------- /modules/local/kmerfinder/download_reference/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kmerfinder/download_reference/main.nf -------------------------------------------------------------------------------- /modules/local/kmerfinder/kmerfinder/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kmerfinder/kmerfinder/environment.yml -------------------------------------------------------------------------------- /modules/local/kmerfinder/kmerfinder/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kmerfinder/kmerfinder/main.nf -------------------------------------------------------------------------------- /modules/local/kmerfinder/summary/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kmerfinder/summary/environment.yml -------------------------------------------------------------------------------- /modules/local/kmerfinder/summary/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kmerfinder/summary/main.nf -------------------------------------------------------------------------------- /modules/local/kraken2/db_preparation/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kraken2/db_preparation/environment.yml -------------------------------------------------------------------------------- /modules/local/kraken2/db_preparation/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/kraken2/db_preparation/main.nf -------------------------------------------------------------------------------- /modules/local/medaka/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/medaka/environment.yml -------------------------------------------------------------------------------- /modules/local/medaka/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/medaka/main.nf -------------------------------------------------------------------------------- /modules/local/nanopolish/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/nanopolish/environment.yml -------------------------------------------------------------------------------- /modules/local/nanopolish/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/nanopolish/main.nf -------------------------------------------------------------------------------- /modules/local/pycoqc/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/pycoqc/environment.yml -------------------------------------------------------------------------------- /modules/local/pycoqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/local/pycoqc/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/bakta/bakta/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/bakta/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/bakta/baktadbdownload/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/bakta/baktadbdownload/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/busco/busco/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/busco/busco/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/busco/busco/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/busco/busco/main.nf -------------------------------------------------------------------------------- /modules/nf-core/busco/busco/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/busco/busco/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/busco/busco/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/busco/busco/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/busco/busco/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/busco/busco/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/busco/busco/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/busco/busco/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/canu/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/canu/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/canu/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/canu/main.nf -------------------------------------------------------------------------------- /modules/nf-core/canu/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/canu/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/cat/fastq/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/cat/fastq/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/cat/fastq/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/cat/fastq/main.nf -------------------------------------------------------------------------------- /modules/nf-core/cat/fastq/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/cat/fastq/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/cat/fastq/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/cat/fastq/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/cat/fastq/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/cat/fastq/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/cat/fastq/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/cat/fastq/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -------------------------------------------------------------------------------- /modules/nf-core/dragonflye/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/dragonflye/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/dragonflye/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/dragonflye/main.nf -------------------------------------------------------------------------------- /modules/nf-core/dragonflye/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/dragonflye/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/dragonflye/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/dragonflye/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/dragonflye/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/dragonflye/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/dragonflye/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/dragonflye/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/fastp/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/fastp/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/main.nf -------------------------------------------------------------------------------- /modules/nf-core/fastp/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/nextflow.interleaved.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/tests/nextflow.interleaved.config -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/nextflow.save_failed.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastp/tests/nextflow.save_failed.config -------------------------------------------------------------------------------- /modules/nf-core/fastqc/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastqc/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/fastqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastqc/main.nf -------------------------------------------------------------------------------- /modules/nf-core/fastqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastqc/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/fastqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastqc/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/fastqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/fastqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/filtlong/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/filtlong/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/filtlong/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/filtlong/main.nf -------------------------------------------------------------------------------- /modules/nf-core/filtlong/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/filtlong/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/filtlong/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/filtlong/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/filtlong/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/filtlong/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/filtlong/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/filtlong/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/gunzip/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/gunzip/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/gunzip/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/gunzip/main.nf -------------------------------------------------------------------------------- /modules/nf-core/gunzip/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/gunzip/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/gunzip/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/gunzip/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/gunzip/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/gunzip/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/gunzip/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/gunzip/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/kraken2/kraken2/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/kraken2/kraken2/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/kraken2/kraken2/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/kraken2/kraken2/main.nf -------------------------------------------------------------------------------- /modules/nf-core/kraken2/kraken2/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/kraken2/kraken2/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/kraken2/kraken2/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/kraken2/kraken2/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/kraken2/kraken2/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/kraken2/kraken2/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/liftoff/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/liftoff/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/liftoff/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/liftoff/main.nf -------------------------------------------------------------------------------- /modules/nf-core/liftoff/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/liftoff/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/liftoff/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/liftoff/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/liftoff/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/liftoff/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/liftoff/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/liftoff/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/miniasm/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/miniasm/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/miniasm/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/miniasm/main.nf -------------------------------------------------------------------------------- /modules/nf-core/miniasm/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/miniasm/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/minimap2/align/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/minimap2/align/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/minimap2/align/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/minimap2/align/main.nf -------------------------------------------------------------------------------- /modules/nf-core/minimap2/align/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/minimap2/align/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/minimap2/align/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/minimap2/align/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/minimap2/align/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/minimap2/align/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/minimap2/align/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/minimap2/align/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/multiqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/multiqc/main.nf -------------------------------------------------------------------------------- /modules/nf-core/multiqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/multiqc/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/multiqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/multiqc/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/multiqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/multiqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/multiqc/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/multiqc/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/main.nf -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/nanoplot.diff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/nanoplot.diff -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/nanoplot/tests/tags.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/nanoplot/tests/tags.yaml -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/main.nf -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/porechop/porechop/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/porechop/porechop/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/prokka/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/prokka/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/prokka/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/prokka/main.nf -------------------------------------------------------------------------------- /modules/nf-core/prokka/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/prokka/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/prokka/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/prokka/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/prokka/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/prokka/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/prokka/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/prokka/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/quast/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/quast/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/quast/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/quast/main.nf -------------------------------------------------------------------------------- /modules/nf-core/quast/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/quast/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/racon/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/racon/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/racon/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/racon/main.nf -------------------------------------------------------------------------------- /modules/nf-core/racon/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/racon/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/racon/racon.diff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/racon/racon.diff -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/csi.nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/tests/csi.nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/index/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/samtools/sort/tests/tags.yml -------------------------------------------------------------------------------- /modules/nf-core/toulligqc/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/toulligqc/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/toulligqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/toulligqc/main.nf -------------------------------------------------------------------------------- /modules/nf-core/toulligqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/toulligqc/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/toulligqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/toulligqc/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/toulligqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/toulligqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/toulligqc/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/toulligqc/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/unicycler/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/unicycler/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/unicycler/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/unicycler/main.nf -------------------------------------------------------------------------------- /modules/nf-core/unicycler/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/unicycler/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/unicycler/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/unicycler/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/unicycler/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/unicycler/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/untar/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/untar/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/untar/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/untar/main.nf -------------------------------------------------------------------------------- /modules/nf-core/untar/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/untar/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/untar/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/untar/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/untar/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/modules/nf-core/untar/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/untar/tests/tags.yml: -------------------------------------------------------------------------------- 1 | untar: 2 | - modules/nf-core/untar/** 3 | -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/nextflow.config -------------------------------------------------------------------------------- /nextflow_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/nextflow_schema.json -------------------------------------------------------------------------------- /nf-test.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/nf-test.config -------------------------------------------------------------------------------- /ro-crate-metadata.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/ro-crate-metadata.json -------------------------------------------------------------------------------- /subworkflows/local/bakta_dbdownload_run/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/local/bakta_dbdownload_run/main.nf -------------------------------------------------------------------------------- /subworkflows/local/kmerfinder_summary_download/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/local/kmerfinder_summary_download/main.nf -------------------------------------------------------------------------------- /subworkflows/local/qc_nanoplot_toulliqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/local/qc_nanoplot_toulliqc/main.nf -------------------------------------------------------------------------------- /subworkflows/local/utils_nfcore_bacass_pipeline/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfschema_plugin/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfschema_plugin/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json -------------------------------------------------------------------------------- /tests/.nftignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/.nftignore -------------------------------------------------------------------------------- /tests/.nftignore_files_entirely: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/.nftignore_files_entirely -------------------------------------------------------------------------------- /tests/default.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/default.nf.test -------------------------------------------------------------------------------- /tests/default.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/default.nf.test.snap -------------------------------------------------------------------------------- /tests/dfast.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/dfast.nf.test -------------------------------------------------------------------------------- /tests/dfast.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/dfast.nf.test.snap -------------------------------------------------------------------------------- /tests/hybrid.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/hybrid.nf.test -------------------------------------------------------------------------------- /tests/hybrid.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/hybrid.nf.test.snap -------------------------------------------------------------------------------- /tests/hybrid_dragonflye.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/hybrid_dragonflye.nf.test -------------------------------------------------------------------------------- /tests/hybrid_dragonflye.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/hybrid_dragonflye.nf.test.snap -------------------------------------------------------------------------------- /tests/long.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long.nf.test -------------------------------------------------------------------------------- /tests/long.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long.nf.test.snap -------------------------------------------------------------------------------- /tests/long_dragonflye.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_dragonflye.nf.test -------------------------------------------------------------------------------- /tests/long_dragonflye.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_dragonflye.nf.test.snap -------------------------------------------------------------------------------- /tests/long_liftoff.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_liftoff.nf.test -------------------------------------------------------------------------------- /tests/long_liftoff.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_liftoff.nf.test.snap -------------------------------------------------------------------------------- /tests/long_miniasm.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_miniasm.nf.test -------------------------------------------------------------------------------- /tests/long_miniasm.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_miniasm.nf.test.snap -------------------------------------------------------------------------------- /tests/long_miniasm_prokka.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_miniasm_prokka.nf.test -------------------------------------------------------------------------------- /tests/long_miniasm_prokka.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/long_miniasm_prokka.nf.test.snap -------------------------------------------------------------------------------- /tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tests/nextflow.config -------------------------------------------------------------------------------- /tower.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/tower.yml -------------------------------------------------------------------------------- /workflows/bacass.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/bacass/HEAD/workflows/bacass.nf --------------------------------------------------------------------------------