Beta Testing
Thank you for your willingness to be a PHoeNIx beta tester! The team appreciates the time and effort in helping to improve the pipeline. As you go through each of these tests if you come across a bug submit and issue on this github repo following the guidelines of what to include. Any feedback you have on typos, wording, points of confusion etc. and the requested documents to be returned can be provided via email to [email protected] with the subject line "Beta tester feedback". Just one email after all tests are run is sufficient, no need to write one per test.
Make sure you are in the 1.0.0-dev tag:
The goal of this first test is to determine if the instructions provided are sufficient for correct install. Please follow the instructions on the Dependencies and install page and test your install with:
nextflow run $PATH_TO_CLONED_DIR/phoenix/main.nf -profile test,<singularity/docker/custom>This command will run the pipeline on preloaded data. If all goes well you should see some output that looks like this:
Please provide any feedback on wording, points of confusion or errors that you run into while going through this process.
Download the following samples from SRA and run them through the pipeline following the instructions for using --input to pass a samplesheet to PHoeNIx. For this section, after running the samples through the pipeline please provide feedback on the following:
- The process getting PHoeNIx to run (What was your user experience?)
- Feedback on install/configure process. How long did it take to download database files?
- Thoughts on the output looks like and are there other metrics/files you would like included?
- Return
Phoenix_Output_Report.tsvfor the runs. - Return nextflow reports that are found in the
pipeline_infodirectory.
- SRR17084768
- SRR16492550
- SRR8668707
- SRR13183128
- SRR15503286
- SRR15167040
- SRR12352255
- SRR13965548
- SRR16820311
- SRR11594646
- SRR17250615
SRA samples can be downloaded with the SRAtoolkit
You can get SRA data one at a time with
prefetch SRR11953697
cd SRR11953697/Or you can download many SRAs at once by creating a file with one SRA on each line then run the following
prefetch --option-file SRRs_to_Fetch.txtOnce the files are downloaded you will need to convert the .sra to fastq forward and reverse files.
fastq-dump SRR11953697.sra --split-filesNo, seriously run whatever HAI sequences you have laying around through PHoeNIx and see if it 💥.
After we receive your email/issues we will take some time (~week) to review the information before we ask for a meeting to debrief and discuss any questions/concerns/comments/affirmations you might have. Thanks again for participating and working to make public health better 💪!