home.md

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