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FASTQ / .GZ Fix (Issue #44) #57
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…abstracted out the retrieval of fasta sample names used in metadata validation + created a static function for configuring file permissions when opening them (including other meta properties)
…res in the script
…utility script, as a method under the MainUtility class, which is now being imported within the script as well
…nput for the input fasta, and it is now testing .fq.gz file
… file and zipped them + changed the delimiter of > used in a .fasta file to the @ symbol instead
…ual command for two of the tests
kyleoconnell
approved these changes
Jul 13, 2023
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Consider using biopython for fasta parsing. May also be some functions in biopython for handling fasta .gz
Meant fastq.gz |
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Description
Please Describe the Bug(s) Fixed and/or the Feature(s) Added:
Checklist
Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed
General Checks
Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?
For each relevant configuration:
Have you conducted proper linting procedures?
Have you updated existing documentation (README.md, etc.) or created new ones within docs?
CDC Checks
Are additional approvals needed for this change? If so, please mention them below:
No
Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below:
No