Adding ONT functionality to RAW and CLEAN #133
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simonleandergrimm
changed the base branch from
master
to
single-read-raw-clean
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@harmonbhasin Can you take an initial look and let me know if you see obvious flaws? Here is what the output of the MultiQC output for ONT data looks like: https://data.securebio.org/simons-notebook/posts/2024-12-08-mgs-ont-raw-eval/ |
simonleandergrimm
changed the title
harmonbhasin
approved these changes
Dec 19, 2024
harmonbhasin
requested changes
Dec 19, 2024
Fixed |
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@harmonbhasin This is the error I get when nf-test is run on github. nf-test works locally. Can you let me know if you see what might be wrong here? Otherwise I adopted your suggestions. Once the nf-test thing is resolved this is good for review by Will. |
@simonleandergrimm specific docker images from sequera (and even dockerhub for that matter) have given me trouble on Github Actions in the past, and my guess is that you're having a similar issue, although I have not run into this specific issue before. As of right now, the best way I know of fixing issues with docker images issues related to Github Actions is trial-and-error. The first thing I would do is try a different distribution of tidyverse, this might be a good place to start, https://hub.docker.com/r/rocker/tidyverse. |
harmonbhasin
requested changes
Jan 7, 2025
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@harmonbhasin The run works now (updated tidyverse container from 4.4.1 to 4.4.2). Index run now fails, but probably due to timing out as has happened previously? If this seems fine, please assign to Will and ping for re-review. |
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Also @harmonbhasin can you "assign" the PR to me when I'm blocking it? This makes it easier to know in which court the PR is! |
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@willbradshaw Can you review? Once done, I will create a Changelog. |
harmonbhasin
approved these changes
Jan 10, 2025
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@simonleandergrimm I'll try to add you as PR in the future when the ball is in your court, thanks for fixing this!
| @@ -55,7 +55,7 @@ process { | |||
| container = "securebio/nao-pypkg" | |||
| } | |||
| withLabel: tidyverse { | |||
| container = "rocker/tidyverse:4.4.1" | |||
| container = "rocker/tidyverse:4.4.2" | |||
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Turns out my test ran fine with the old version of the docker container, #138, so this was probably just a temporary error. However, all we're doing is updating the docker container, which I have no issue with so this looks good to me.
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@simonleandergrimm I was trying to run the BLAST workflow ( Also, make sure to update the tests with any new import statements you add so that we don't run into these problems in the future. I'll be sure to look out for these things in the future as well! |
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This issue was in |
harmonbhasin
previously approved these changes
Jan 10, 2025
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Thanks for fixing the issue, this is good for you to look at @willbradshaw.
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@simonleandergrimm based on our discussion yesterday, are you planning on adding any tests before we merge this? |
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@willbradshaw I likely do not have time for this in the next few days (maybe even not until I leave for the holiday, due to Zephyr and P2RA manuscript demands). |
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OK, let's drop that here then. I do want my comment on configs/read_type.config to be addressed before I merge this, though. |
…arameter for data being ONT. Added adapters to the ONT file so it doesn't break.
I dropped the ont param from read_type.config, and added the following bit to the run config files. Let me know if the wording looks good. Still waiting for checks to run to completion. |
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Ah looks like the ONT test files can't get fetched due to being on restricted. Will fix shortly. |
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