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<!channel> I will soon release a security patch re...
# pipeline-maintainers
m
<!channel> I will soon release a security patch release (nf-core/tools 4.0.3), that patches a possible exploit through PR comments triggered through GitHub Actions (see advisory: https://nf-co.re/advisories/pr-comment-workflow-vulnerability) The fix unfortunately needs to be merged into the default branch to work. We will open a patch PR from 
patch
to the default branch to fix this issue. We will try to do that on as many pipelines as possible, feel free to do merge them yourself when you see them. Since this is just related to CI, the changes in `main`/`master` do not require a new release.
s
Please help by doing this yourself if possible!
i
I only see a normal template PR, is the special one incoming as well?
m
yes, patch PR is incoming (i first needed to update the template branch via sync)
this is an example of how the patch PR looks like https://github.com/nf-core/rnaseq/pull/1895/changes For clarification: there will actually be two patch PRs, first to the default branch and then to 
dev
(if it is a released pipeline), so the changes will not get lost in a merge from 
dev
to `main`/`master`. that second one is only triggered once the default branch has been updated.
r
I am going to merge without waiting for the tests https://github.com/nf-core/bamtofastq
👍 1
m
thanks. kicked it off for 10 pipelines and already had 5 edge cases (why do we keep renaming files in the template 😁)
s
Yeah, I think we don't need to wait for nf-test for these
r
just to cliarfy: the template sync is nice but not necessary, correct?
m
Correct
r
@Stephen Watts
f
Merged the template updates for #C08P26ZAZM4 and #C05AJBTJXDY salute. Cellpainting default is 
dev
but molkart has a release so its 
master
. Are the patches to master still incoming?
s
I’ve merged the security patch for #C04CQ1LK7U1 in both the 
master
and 
dev
branches
(as an aside, is there a documented process to switch from 
master
to 
main
for the default branch that anyone can point me to)
r
m
Hi, I want to do the security patch myself as soon as possible on sammyseq but before that we need to update the default branch (dev) with the latest development in this PR before applying the patch because it is a huge work and it would be a nightmare to rebase afterwards... Can anyone help with this PR please? there are two pending tests but I am not sure what are they waiting for
s
@Margherita Mutarelli, I don't know why they were stuck, but I retriggered them manually.
thankyou 1
r
I don't think we got the patch PR yet for sarek/master. Are they still rolling out or do I need to do anything to trigger it
i
Patch also still missing in #C06R4FC4C1E
m
yes, these are not simple/straight-forward cases will tackle them today
✔️ 1
m
@Simon Pearce thank you also for the weird changes catch! We'll revert them and work on make linting pass
m
patch backmerge PRs rolling out now (updating the 
dev
branch with the fix to have the same shared ancestor as the default branch (if != dev) to avoid weird git issues and keeping the history clean)
this one is not urgent to be merged, the fix is already in for all. but it should be merged before a new release.
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