├── .github └── workflows │ └── nextflow-test.yml ├── .gitignore ├── LICENSE ├── README.md ├── assets ├── ens_species_mapping.tsv ├── multiqc_config.yaml ├── multiqc_config_no_smr.yaml └── regionReport_DESeq2Exploration_custom.Rmd ├── bin ├── deseq2.R ├── improve_deseq_table.rb ├── piano.R ├── refactor_reportingtools_table.rb └── webgestalt.R ├── citations.md ├── configs ├── conda.config ├── container.config ├── local.config └── nodes.config ├── envs ├── basic_tools.yaml ├── busco.yaml ├── dammit.yaml ├── deseq2.yaml ├── fastp.yaml ├── fastqc.yaml ├── hisat2.yaml ├── minimap2.yaml ├── multiqc.yaml ├── nanoplot.yaml ├── python3.yaml ├── sortmerna.yaml ├── stringtie.yaml ├── subread.yaml ├── trinity.yaml └── webgestalt.yaml ├── figures ├── chart.png ├── logo.png ├── tower.png └── workflow.jpg ├── main.nf ├── modules ├── annotationGet.nf ├── busco.nf ├── buscoGetDB.nf ├── containerGet.nf ├── dammit.nf ├── dammitGetDB.nf ├── deseq2.nf ├── fastp.nf ├── fastqc.nf ├── featurecounts.nf ├── format_read_name.nf ├── get_test_data.nf ├── hisat2.nf ├── minimap2.nf ├── multiqc.nf ├── nanoplot.nf ├── piano.nf ├── prepare_annotation.nf ├── rattle.nf ├── referenceGet.nf ├── sortmerna.nf ├── sortmernaGet.nf ├── stringtie.nf ├── tpm_filter.nf ├── trinity.nf ├── utils.nf └── webgestalt.nf ├── nextflow.config └── test-data ├── execution_report.html ├── hsa ├── README.md ├── SRR3670977_sub.fastq.gz ├── SRR3670978_sub.fastq.gz ├── SRR3670985_sub.fastq.gz └── SRR3670986_sub.fastq.gz └── input.se.hsa_small.csv /.github/workflows/nextflow-test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/.github/workflows/nextflow-test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/README.md -------------------------------------------------------------------------------- /assets/ens_species_mapping.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/assets/ens_species_mapping.tsv -------------------------------------------------------------------------------- /assets/multiqc_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/assets/multiqc_config.yaml -------------------------------------------------------------------------------- /assets/multiqc_config_no_smr.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/assets/multiqc_config_no_smr.yaml -------------------------------------------------------------------------------- /assets/regionReport_DESeq2Exploration_custom.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/assets/regionReport_DESeq2Exploration_custom.Rmd -------------------------------------------------------------------------------- /bin/deseq2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/bin/deseq2.R -------------------------------------------------------------------------------- /bin/improve_deseq_table.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/bin/improve_deseq_table.rb -------------------------------------------------------------------------------- /bin/piano.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/bin/piano.R -------------------------------------------------------------------------------- /bin/refactor_reportingtools_table.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/bin/refactor_reportingtools_table.rb -------------------------------------------------------------------------------- /bin/webgestalt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/bin/webgestalt.R -------------------------------------------------------------------------------- /citations.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/citations.md -------------------------------------------------------------------------------- /configs/conda.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/configs/conda.config -------------------------------------------------------------------------------- /configs/container.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/configs/container.config -------------------------------------------------------------------------------- /configs/local.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/configs/local.config -------------------------------------------------------------------------------- /configs/nodes.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/configs/nodes.config -------------------------------------------------------------------------------- /envs/basic_tools.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/basic_tools.yaml -------------------------------------------------------------------------------- /envs/busco.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/busco.yaml -------------------------------------------------------------------------------- /envs/dammit.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/dammit.yaml -------------------------------------------------------------------------------- /envs/deseq2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/deseq2.yaml -------------------------------------------------------------------------------- /envs/fastp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/fastp.yaml -------------------------------------------------------------------------------- /envs/fastqc.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/fastqc.yaml -------------------------------------------------------------------------------- /envs/hisat2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/hisat2.yaml -------------------------------------------------------------------------------- /envs/minimap2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/minimap2.yaml -------------------------------------------------------------------------------- /envs/multiqc.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/multiqc.yaml -------------------------------------------------------------------------------- /envs/nanoplot.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/nanoplot.yaml -------------------------------------------------------------------------------- /envs/python3.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/python3.yaml -------------------------------------------------------------------------------- /envs/sortmerna.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/sortmerna.yaml -------------------------------------------------------------------------------- /envs/stringtie.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/stringtie.yaml -------------------------------------------------------------------------------- /envs/subread.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/subread.yaml -------------------------------------------------------------------------------- /envs/trinity.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/trinity.yaml -------------------------------------------------------------------------------- /envs/webgestalt.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/envs/webgestalt.yaml -------------------------------------------------------------------------------- /figures/chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/figures/chart.png -------------------------------------------------------------------------------- /figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/figures/logo.png -------------------------------------------------------------------------------- /figures/tower.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/figures/tower.png -------------------------------------------------------------------------------- /figures/workflow.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/figures/workflow.jpg -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/main.nf -------------------------------------------------------------------------------- /modules/annotationGet.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/annotationGet.nf -------------------------------------------------------------------------------- /modules/busco.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/busco.nf -------------------------------------------------------------------------------- /modules/buscoGetDB.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/buscoGetDB.nf -------------------------------------------------------------------------------- /modules/containerGet.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/containerGet.nf -------------------------------------------------------------------------------- /modules/dammit.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/dammit.nf -------------------------------------------------------------------------------- /modules/dammitGetDB.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/dammitGetDB.nf -------------------------------------------------------------------------------- /modules/deseq2.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/deseq2.nf -------------------------------------------------------------------------------- /modules/fastp.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/fastp.nf -------------------------------------------------------------------------------- /modules/fastqc.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/fastqc.nf -------------------------------------------------------------------------------- /modules/featurecounts.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/featurecounts.nf -------------------------------------------------------------------------------- /modules/format_read_name.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/format_read_name.nf -------------------------------------------------------------------------------- /modules/get_test_data.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/get_test_data.nf -------------------------------------------------------------------------------- /modules/hisat2.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/hisat2.nf -------------------------------------------------------------------------------- /modules/minimap2.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/minimap2.nf -------------------------------------------------------------------------------- /modules/multiqc.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/multiqc.nf -------------------------------------------------------------------------------- /modules/nanoplot.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/nanoplot.nf -------------------------------------------------------------------------------- /modules/piano.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/piano.nf -------------------------------------------------------------------------------- /modules/prepare_annotation.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/prepare_annotation.nf -------------------------------------------------------------------------------- /modules/rattle.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/rattle.nf -------------------------------------------------------------------------------- /modules/referenceGet.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/referenceGet.nf -------------------------------------------------------------------------------- /modules/sortmerna.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/sortmerna.nf -------------------------------------------------------------------------------- /modules/sortmernaGet.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/sortmernaGet.nf -------------------------------------------------------------------------------- /modules/stringtie.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/stringtie.nf -------------------------------------------------------------------------------- /modules/tpm_filter.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/tpm_filter.nf -------------------------------------------------------------------------------- /modules/trinity.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/trinity.nf -------------------------------------------------------------------------------- /modules/utils.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/utils.nf -------------------------------------------------------------------------------- /modules/webgestalt.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/modules/webgestalt.nf -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/nextflow.config -------------------------------------------------------------------------------- /test-data/execution_report.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/execution_report.html -------------------------------------------------------------------------------- /test-data/hsa/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/hsa/README.md -------------------------------------------------------------------------------- /test-data/hsa/SRR3670977_sub.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/hsa/SRR3670977_sub.fastq.gz -------------------------------------------------------------------------------- /test-data/hsa/SRR3670978_sub.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/hsa/SRR3670978_sub.fastq.gz -------------------------------------------------------------------------------- /test-data/hsa/SRR3670985_sub.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/hsa/SRR3670985_sub.fastq.gz -------------------------------------------------------------------------------- /test-data/hsa/SRR3670986_sub.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/hsa/SRR3670986_sub.fastq.gz -------------------------------------------------------------------------------- /test-data/input.se.hsa_small.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hoelzer-lab/rnaflow/HEAD/test-data/input.se.hsa_small.csv --------------------------------------------------------------------------------