├── .dockstore.yml ├── .github └── workflows │ ├── galaxy.yml │ ├── nextflow.yml │ ├── scipipe.yml │ └── snakemake.yml ├── LICENSE ├── README.md ├── bpipe ├── README.md ├── bpipe.config └── quantify_rna.groovy ├── docs └── imgs │ ├── review_poc.png │ ├── workflow_online_description.png │ └── workflow_online_description_small.png ├── galaxy ├── README.md ├── salmon-workflow-tests.yml └── salmon-workflow.ga ├── genpipes ├── README.md └── readset.txt ├── nextflow ├── README.md └── example.nf ├── scipipe ├── README.md ├── example.go ├── go.mod ├── go.sum └── run.sh ├── snakemake ├── README.md ├── config │ └── config.yaml └── workflow │ ├── Snakefile │ ├── envs │ ├── fastqc.yaml │ ├── salmon.yaml │ └── stats.yaml │ ├── notebooks │ └── plot-tpm.py.ipynb │ └── rules │ └── common.smk ├── template └── README.md ├── test_data ├── README.md ├── reads_1.fq.gz ├── reads_2.fq.gz ├── transcriptome.fa └── truth.tsv ├── toil ├── README.md ├── cwl │ ├── cwl_input.yaml │ ├── example.cwl │ ├── fastqc.cwl │ ├── salmonIndex.cwl │ └── salmonQuant.cwl ├── python │ └── draft.py └── wdl │ ├── example.wdl │ └── wdl_input.json └── wdl ├── README.md ├── example.wdl ├── options.json └── wdl_input.json /.dockstore.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GoekeLab/bioinformatics-workflows/HEAD/.dockstore.yml -------------------------------------------------------------------------------- /.github/workflows/galaxy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GoekeLab/bioinformatics-workflows/HEAD/.github/workflows/galaxy.yml -------------------------------------------------------------------------------- /.github/workflows/nextflow.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GoekeLab/bioinformatics-workflows/HEAD/.github/workflows/nextflow.yml 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