... | ... | @@ -56,6 +56,7 @@ |
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* size of the input that needs to be provided
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* type: Accessions - repositories / Fastq files
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* automated inferences: type of sample preparation, adaptors
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* custom genomes and annotations possible?
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* Output
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* sample quality metrics
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* complexity
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... | ... | @@ -73,5 +74,55 @@ |
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* inference
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* novel isoforms: splicing/polyadenylation
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* SNPs/mutations
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* Number/type of supported platforms
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* Desktop application/needs cluster |
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* Workflow engine
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* Modern (CWL, WDL, Snakemake, Galaxy, Nextflow)
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* Legacy (anything else that's not homegrown)
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* Custom
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* User interface
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* Browser app
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* Desktop app
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* Mobile app
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* Command line interface (programmable)
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* HTTP/"REST" API available (programmable)
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* Supported platforms
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* Cloud (AWS, GCP, Azure, ...)
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* Kubernetes / OpenShift
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* HPC (Slurm, SGE/OGE/UGA, ...)
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* Desktop/laptop
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* Installation
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* Type
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* VM
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* Containerized
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* Virtual env cross-language (conda)
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* Virtual env single language (e.g., virtualenv)
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* Package manager without virtualization (e.g., pip, Bioconductor)
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* Manual install
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* Instructions & auxiliary scripts available for supported platforms
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* Openness
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* License
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* Open source development encouraged?
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* Contribution instructions available?
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* Contact options
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* Issue tracker
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* Q/A forum (e.g., Biostars)
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* Chat (e.g., Slack or Gitter channel)
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* Email
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* Maintenance
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* Actively developed?
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* number of contributors
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* last update
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* frequency of commits
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* Tests available
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* Test code coverage published?
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* Usability
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* Clean, well-documented, programmable, easy-to-use, intuitive API for input and outputs?
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* Workflow can be started quickly for one sample (incl. preparation of configs)
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* Workflow can be started quickly for multiple samples (incl. preparation of configs)
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* Supports local data
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* Supports uploading data
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* Supports cloud data (e.g., Amazon S3)
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* Interfacing with SRA and/or other relevant data repos
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* Interfacing with Ensembl and/or other genome resource repos
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* Tooling available to filter genome resources or compile custom ones?
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