Closed priyanka-surana closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 444e34d
+| ✅ 115 tests passed |+
#| ❔ 25 tests were ignored |#
!| ❗ 10 tests had warnings |!
It partially works for me. I can see the files being created, but the processes typically hang.
I have a workaround that involves wrapping the command with timeout
, but it's not 100% bullet-proof.
How did you test this ?
It partially works for me. I can see the files being created, but the processes typically hang. I have a workaround that involves wrapping the command with
timeout
, but it's not 100% bullet-proof.How did you test this ?
Same if thetimeout
parameter is increased to 60 seconds in conf/modules.config
:
withName: "BLOBTOOLKIT_IMAGES" {
ext.args = "--format png --timeout 60"
publishDir = [
path: { "${params.outdir}/${blobdir.name}/" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
]
}
The files are created without errors or retries but it might not work for other datasets, so it would be helpful to find a way to check that the files are generated and exported to the results folder.
The issue most probably comes from the firefox_driver based on what I read. I have flagged this to Rich and waiting for his response.
The issue most probably comes from the firefox_driver based on what I read. I have flagged this to Rich and waiting for his response.
@alxndrdiaz Replace the view
command with blobtk plot
for snail
only. Skip the rest.
For snail plots (and almost for the basic blob) there is a
blobtk plot -v snail -d /path/to/blobdir
command available in the container as i'm working towards getting rid of the firefox dependency, but it needs more work to replace all the plot generation.
The issue most probably comes from the firefox_driver based on what I read. I have flagged this to Rich and waiting for his response.
@alxndrdiaz Replace the
view
command withblobtk plot
forsnail
only. Skip the rest.For snail plots (and almost for the basic blob) there is a
blobtk plot -v snail -d /path/to/blobdir
command available in the container as i'm working towards getting rid of the firefox dependency, but it needs more work to replace all the plot generation.
Done, the snail plot can be generated with this command:
The issue most probably comes from the firefox_driver based on what I read. I have flagged this to Rich and waiting for his response.
@alxndrdiaz Replace the
view
command withblobtk plot
forsnail
only. Skip the rest.For snail plots (and almost for the basic blob) there is a
blobtk plot -v snail -d /path/to/blobdir
command available in the container as i'm working towards getting rid of the firefox dependency, but it needs more work to replace all the plot generation.
Done, the snail plot can be generated with the command you suggested:
blobtk plot \\
-v snail \\
-o ${prefix}.snail.png \\
-d ${blobdir} \\
$args
@muffato Can we get a final approval to merge this PR? I have the next one to get release ready from the branch template_merge
.
Some tests still running but there seems to be a spurious test.png
in the resulting blobdir
Some tests still running but there seems to be a spurious
test.png
in the resulting blobdir
Yes I saw that too and flagged to Rich. Waiting for his response.
@muffato What else is needed to merge this PR?
This PR has the combined code from @priyanka-surana (summary) and @alxndrdiaz (images). This is also the last subworkflow for v1.0.0 release 🎉