Closed gq1 closed 8 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 473ee9f
+| ✅ 127 tests passed |+
#| ❔ 17 tests were ignored |#
!| ❗ 7 tests had warnings |!
@yumisims @DLBPointon
Do we have the following step in the rapid test before? I remember the rapid test can pass when using the Github default runner.
RAPID:SANGERTOL_TREEVAL_RAPID:TREEVAL_RAPID:HIC_MAPPING:JUICER_TOOLS_PRE
There is java process asking for 36G memory directly. Can we try java -Xms1g -Xmx36g
?
Hi Guoying, sorry for taking my time getting back to you. I've been on holiday.
@yumisims @DLBPointon Do we have the following step in the rapid test before? I remember the rapid test can pass when using the Github default runner.
RAPID:SANGERTOL_TREEVAL_RAPID:TREEVAL_RAPID:HIC_MAPPING:JUICER_TOOLS_PRE
The process was in there. However, it was coded to not run on the GitHub runner due to the sheer amount of resources the process needs. I thought the runner was to still get the tiny test working properly and then a large run on the farm. If not then I can add the full test back in, but Tiny will also need the custom runner.
There is java process asking for 36G memory directly. Can we try
java -Xms1g -Xmx36g
?
We can indeed try this.
Hi Guoying, sorry for taking my time getting back to you. I've been on holiday.
@yumisims @DLBPointon Do we have the following step in the rapid test before? I remember the rapid test can pass when using the Github default runner.
RAPID:SANGERTOL_TREEVAL_RAPID:TREEVAL_RAPID:HIC_MAPPING:JUICER_TOOLS_PRE
The process was in there. However, it was coded to not run on the GitHub runner due to the sheer amount of resources the process needs. I thought the runner was to still get the tiny test working properly and then a large run on the farm. If not then I can add the full test back in, but Tiny will also need the custom runner.
There is java process asking for 36G memory directly. Can we try
java -Xms1g -Xmx36g
?We can indeed try this.
@DLBPointon need Will @weaglesBio to update the juicer part first. then we could minimize the heap, I am thinking to optimise the other resource a bit, these should resolve the testing problem.
@DLBPointon need Will @weaglesBio to update the juicer part first. then we could minimize the heap, I am thinking to optimise the other resource a bit, these should resolve the testing problem.
Sure ok.
I'll get some decent graphs going.
change to the default runner for now.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).