Quality Assessment not using alternate samples specified

[ChaochihL]

Type of issue

• [x] Bug
• [ ] Feature request

---

Bugs

Have you looked at the wiki?

The wiki is located here

• [x] Yes
• [ ] No

Which handler are you having trouble with?

Quality Assessment

Describe your problem

When I provide an alternate sample list (i.e. sample list for trimmed fastq files) for the ALTERNATE_SAMPLES variable, sequence handling calls on the RAW_SAMPLES variable.

What is the error message being generated?

There is no error message, Quality Assessment runs and finishes without errors, but runs Quality Assessment on the RAW_SAMPLES instead of the ALTERNATE_SAMPLES.

# Put your error message here

Copy the part of the config file used by this handler

#   Shared values go here

#   Handler-specific values go here
#   Config file Line 9
RAW_SAMPLES=
#   Config file Line 77
ALTERNATE_SAMPLES=

#   In sequence_handling script
#   Line 58 only checks for sample list under RAW_SAMPLES not ALTERNATE_SAMPLES
checkSamples "${RAW_SAMPLES}" # Check to see if samples and sample list exists

#   Line 61 only sources Quality_Assessment for RAW_SAMPLES not ALTERNATE_SAMPLES
echo "source ${CONFIG} && source ${SEQUENCE_HANDLING}/Handlers/Quality_Assessment.sh && Quality_Assessment ${RAW_SAMPLES} ${OUT_DIR} ${PROJECT}" | qsub -l "${QA_QSUB}" -e "${ERROR}" -o "${ERROR}" -m abe -M "${EMAIL}" -N "${PROJECT}"_Quality_Assessment

#   Dependency definitions go here

Has anyone else been able to replicate your error?

• [ ] Yes
• [ ] No

---

Feature requests

What new thing is being added?

• [ ] New handler
• [ ] Modification to handler

Describe the changes made

Where does this fit in with the existing pipeline?

List any dependencies that will be needed for this change, providing links to the source code as needed

Do you have a script for this change? Please note that we can implement your code faster if you write everything as BASH functions.

• [ ] Yes
• [ ] No

If yes, please make sure the code is posted online and link to it below:

name of code exerpt

Good hosting sites are GitHub and GitHub Gist.

Thank you for your help improving sequence_handling!

[Aerin13]

The latest commit should fix this issue, but I haven't done extensive testing. Could you please pull the latest version and re-try Quality_Assessment? Please let me know if there are still bugs.

[ChaochihL]

Thanks! I've only tested it on one set of samples, but it worked.