Good news, <1.2.0> is ready to go! I’ve scheduled ...
# riboseqi
Ira Iosub
12/02/2025, 12:30 PMGood news, 1.2.0 is ready to go! I’ve scheduled the release for Thu, 04.12.2025, and I plan to follow the remaining nf-core release steps that morning.
If we prefer to publish earlier, we can also make the release today. I’d just need a quick approval on a PR updating the release date in the changelog. Happy either way, let me know.
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Felix Krueger
12/02/2025, 1:48 PMGreat stuff! If you feel that you could manage the release today - I’d say go for it. Happy to approve a date change.
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Ira Iosub
12/03/2025, 12:31 PMHey Felix, I added you as a reviewer yesterday
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Felix Krueger
12/03/2025, 12:58 PMAh I missed that (nf-core emails go into a special folder….). 106 Files changed!?!
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Ira Iosub
12/03/2025, 12:59 PMwait a sec, let me give you the link
Ira Iosub
12/03/2025, 12:59 PMIra Iosub
12/03/2025, 12:59 PMjust 1 change, in the changelog
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Felix Krueger
12/03/2025, 1:01 PMthat was easy 🙂 merged
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Ira Iosub
12/03/2025, 1:02 PMthanks! i'll go ahead with the release today! That should give us a clean starting point for all the exciting changes coming up
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Felix Krueger
12/03/2025, 1:03 PMoh yeah! thanks! shipit parrot
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Ira Iosub
12/03/2025, 4:00 PM👏 5
nf core 3
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Felix Krueger
12/03/2025, 4:19 PMand it is running!
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Felix Krueger
12/03/2025, 5:49 PMHmm, it fails because of iGenomes…:
Copy code
The following invalid input values have been detected:
* --igenomes_base (<s3://ngi-igenomes/igenomes/>): could not validate file format of '<s3://ngi-igenomes/igenomes/>': Access Denied (Service: Amazon S3; Status Code: 403; Error Code: AccessDenied; Request ID: Q78X84VJFAPASRFV; S3 Extended Request ID: 5jKX4kPlOISuYsb3bWNbFN46zYJDvcPvFZ2fuFSzUyM7/UXeJiG+rG2gQVQwK/qWJYJ8ENCOM80=; Proxy: null)
-- Check script '.nextflow/assets/nf-core/riboseq/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 68 or see 'nf-2anmojs1JoVJki.log' file for more detailsFelix Krueger
12/03/2025, 5:49 PMsetting
ignore_igenomes Copy code
The following invalid input values have been detected:
* --igenomes_base (<s3://ngi-igenomes/igenomes/>): could not validate file format of '<s3://ngi-igenomes/igenomes/>': Access Denied (Service: S3, Status Code: 403, Request ID: 79NXP3K21ZBSZQAB, Extended Request ID: pprLYrAElXGfRcef86PuTg/2ledBD0BXp2aItCKwy8G8Sn0QOnDxcUCuVpK3jOPX+c9Je6hJNnnkvIylsamcDcZVzDw3/h4j) (SDK Attempt Count: 1)Felix Krueger
12/03/2025, 5:51 PMdeleting the igenomes_base entry seems to finally pass the first check!
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Felix Krueger
12/04/2025, 1:25 PMQuick follow-up: The job completed fine, including the Ribowaltz! 🎉
One odd thing: The workflow no longer seems to pick up FastQC results in the MultiQC report?
Felix Krueger
12/04/2025, 1:29 PMone suggestion: the output has a folder called
riboseq_qc Copy code
riboseq_qc/
├── ribotish
│ ├── ...
└── ribotricer
├── ...ribowaltz_qcribowaltzi
Ira Iosub
12/04/2025, 1:32 PMi have a full_test run from before the 3.5.1 template update - and that contains the FastQC in the report. I'll set up a new run full test with v1.2.0 and see if i run into the same thing
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Ira Iosub
12/04/2025, 1:34 PMfor ribowaltz qc results paths, would you mind opening an issue so we can track it for the next release?
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Felix Krueger
12/04/2025, 1:34 PMi
Ira Iosub
12/04/2025, 2:20 PMthis is what i get with the small test, fastqc is there
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Felix Krueger
12/04/2025, 2:22 PMthis is very odd….
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Ira Iosub
12/04/2025, 2:23 PMi do notice that only 6 samples included though, it seems just the ones that are riboseq - i will open an issue for this
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Felix Krueger
12/04/2025, 9:09 PMJust had a funny thought. For some reason, the 2 samples I dealt with yesterday had been sequenced as paired-end data. Is there a chance that paired-end samples (Ribo or RNA-seq) do not end up as FastQC results in the MultiQC report? Should know by tomorrow…