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