├── .gitattributes ├── .github └── workflows │ └── continuous_integration.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── assets └── multiqc_conf.yml ├── config ├── abinitio_training_modules.config ├── annotation_preprocessing_modules.config ├── functional_annotation_modules.config ├── modules.config ├── nf-core-defaults.config ├── test.config └── transcript_assembly_modules.config ├── main.nf ├── modules.json ├── modules ├── local │ ├── agat │ │ ├── extractsequences.nf │ │ ├── filterbyattribute.nf │ │ ├── filterbylocusdistance.nf │ │ ├── filterbymrnablastvalue.nf │ │ ├── filterincompletegenecodingmodels.nf │ │ ├── gff2zff.nf │ │ ├── keeplongestisoform.nf │ │ ├── managefunctionalannotation.nf │ │ └── separatebyrecord.nf │ ├── augustus │ │ ├── gbk2augustus.nf │ │ ├── gff2gbk.nf │ │ └── training.nf │ ├── blast │ │ └── blastp.nf │ ├── custom │ │ └── rankmodels.nf │ ├── gaas │ │ ├── fastapurify.nf │ │ └── fastastatistics.nf │ ├── hisat2 │ │ ├── align.nf │ │ └── build.nf │ ├── snap │ │ └── training.nf │ └── stringtie │ │ └── stringtie.nf └── nf-core │ ├── blast │ └── makeblastdb │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── busco │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── interproscan │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ └── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── tags.yml ├── nextflow.config └── subworkflows ├── abinitio_training ├── README.md └── main.nf ├── annotation_preprocessing ├── README.md └── main.nf ├── functional_annotation ├── README.md └── main.nf └── transcript_assembly ├── README.md └── main.nf /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NBISweden/pipelines-nextflow/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/continuous_integration.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NBISweden/pipelines-nextflow/HEAD/.github/workflows/continuous_integration.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .nextflow* 2 | results/ 3 | work/ 4 | 5 | .DS_Store 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