# New RO-Crate

## Contents

- main
- bin/
- subworkflows/
- workflows/
- db/
- modules/
- envs/
- assets/
- conf/
- params.json
- README.md
- nextflow.config
- bin/gen_input.py
- bin/sortFasta.sh
- bin/combine.sh
- bin/extractFastaHeaders.sh
- subworkflows/FilterRepeat.nf
- subworkflows/ProcessRNAStar.nf
- subworkflows/PreprocessRNASeq.nf
- subworkflows/DenovoMaskingRepeatMasker.nf
- subworkflows/ProcessRNAMinimap.nf
- workflows/annotato.nf
- db/uniprot_sprot.noTEs.fasta.gz
- modules/local/
- modules/nf-core/
- modules/local/repeatmasker/
- modules/local/funannotate/
- modules/local/stringtie/
- modules/local/minimap2/
- modules/local/utils/
- modules/local/braker/
- modules/local/interproscan/
- modules/local/busco/
- modules/local/star/
- modules/local/protexcluder/
- modules/local/blast/
- modules/local/filterRepeat/
- modules/local/qc/
- modules/local/fastp/
- modules/local/repeatmasker/BuildDatabase.nf
- modules/local/repeatmasker/RepeatMasker.nf
- modules/local/repeatmasker/RepeatModeler.nf
- modules/local/funannotate/FunannotatePredict.nf
- modules/local/funannotate/FunannotateSort.nf
- modules/local/funannotate/FunannotateClean.nf
- modules/local/stringtie/Stringtie.nf
- modules/local/minimap2/AlignMinimap2.nf
- modules/local/minimap2/BuildMinimap2.nf
- modules/local/utils/Uncompress.nf
- modules/local/utils/CatAndSort.nf
- modules/local/utils/CombineFasta.nf
- modules/local/utils/MergeBam.nf
- modules/local/braker/Braker.nf
- modules/local/interproscan/Interproscan.nf
- modules/local/busco/Busco.nf
- modules/local/star/BuildSTAR.nf
- modules/local/star/AlignSTAR.nf
- modules/local/protexcluder/ProtExcluder.nf
- modules/local/blast/Blastx.nf
- modules/local/blast/MakeDB.nf
- modules/local/filterRepeat/Transposon.nf
- modules/local/filterRepeat/FilterProt.nf
- modules/local/qc/MultiQC.nf
- modules/local/qc/FastQC.nf
- modules/local/fastp/Fastp.nf
- modules/nf-core/custom/
- modules/nf-core/custom/dumpsoftwareversions/
- modules/nf-core/custom/dumpsoftwareversions/templates/
- modules/nf-core/custom/dumpsoftwareversions/meta.yml
- modules/nf-core/custom/dumpsoftwareversions/main.nf
- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
- envs/docker/
- envs/conda/
- envs/docker/gaas/
- envs/docker/protexcluder/
- envs/docker/transposon/
- envs/docker/gaas/environment.yml
- envs/docker/gaas/Dockerfile
- envs/docker/protexcluder/environment.yml
- envs/docker/protexcluder/Dockerfile
- envs/docker/transposon/environment.yml
- envs/docker/transposon/Dockerfile
- envs/conda/star.yml
- envs/conda/protexcluder.yml
- envs/conda/stringtie.yml
- envs/conda/unix.yml
- envs/conda/repeatmasker.yml
- envs/conda/multiqc.yml
- envs/conda/fastp.yml
- envs/conda/minimap2.yml
- envs/conda/busco.yml
- envs/conda/fastqc.yml
- envs/conda/transposonpsi.yml
- envs/conda/repeatmodeler.yml
- envs/conda/blast.yml
- envs/conda/funannotate.yml
- envs/conda/gaas.yml
- assets/images/
- assets/multiqc_config.yml
- assets/images/annotato-workflow.drawio.png
- assets/images/annotato-workflow.drawio.svg
- conf/container.config
- conf/base.config
- conf/conda.config
- conf/modules.config