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For the coming PRs, when we merge (except for a release PR), could we pay attention and choose to

squash and merge

instead of the regular

Merge pull request

? Just need to click on the arrow at the right hand side of the green button, and select

Squash and merge

in the drop down menu

I thought this was the default now?

I thought too actually, but it might be just on my side, I will look at it next week, too late for that today anyway

okidoki

thanks for pointing it out

Final wrap up for me: Merged another modules update: https://github.com/nf-core/seqinspector/pull/215 For https://github.com/nf-core/seqinspector/pull/209 I think we just need to rethink the logic to get to the decision. We cannot access the results before the pipeline has ended. But there are ways to make this work, I'll work on it on Monday. For https://github.com/nf-core/seqinspector/pull/212 I think it's just a question of properly rerunning the tests. I'll work on it on Monday too.

Update on MULTIQC_SAV PR, I have branched out from the initial https://github.com/nf-core/seqinspector/pull/209 PR in https://github.com/nf-core/seqinspector/pull/216, due to some heavy refactoring. I think we can save ourselves a lot of duplicate code by always using MULTIQC SAV in lieu of MULTIQC_GLOBAL, and just not providing the rundir when we don't want to use them. That being said, I really liked the ideas in this PR, and I am not rewriting it all for the sake of it. I actually just ended up reusing most of the logic in it, and it's all still in the git history, which is for me the most important I am still working on it, but just wanted to update you on this. And I discovered an issue with the Multiqc sav modules, that somehow doesn't seem to produce any images 😱. But thanks to this investigation we now have amazingly complete tests for #C05663US2B0 -> https://github.com/nf-core/modules/pull/10935 I apoligize for inconvenience, as this will delay the release. but I really hope that we will fix all that ASAP.

Trying to update the subway map before the coming release. Nitpicking welcome cc @James Fellows Yates

could be of interest for us here

Taking over the old PRs: • Done: https://github.com/nf-core/seqinspector/pull/59 • WIP: https://github.com/nf-core/seqinspector/pull/236

More modular and easy control on which tool should run on subsampled data: https://github.com/nf-core/seqinspector/pull/243 @Pontus Höjer I will continue working on the multiQC report to make this more prominent

I am thinking about the “FASTQ files” and “BAM files” labeling, I would like to enable unaligned BAM input at some point so then this labeling would be a bit confussing. How about: “”FASTQ files” --> “Raw sequence QC”/“Sequence QC”, “BAM files” --> “Reference mapped QC”/“Mapped QC”

Other then that it looks great! 🌟

✅ seqinspector/test_full completed successfully! 🎉 Run Name desperate_lamarr Duration 11m 25s Status ✅ Success Tasks Completed: 265 Jul 14, 2026 at 10:43 AM

✅ seqinspector/test_full completed successfully! 🎉 Run Name serene_roentgen Duration 10m 55s Status ✅ Success Tasks Completed: 265 Jul 14, 2026 at 12:27 PM

✅ seqinspector/test_full completed successfully! 🎉 Run Name happy_engelbart Duration 10m 35s Status ✅ Success Tasks Completed: 265 Jul 14, 2026 at 2:36 PM

NEW RELEASE: 1.1.0 aka Veronica Mars marsbar: • https://github.com/nf-core/seqinspector/releases/tag/1.1.0 New tools: • FASTQE (added by @Adam Talbot) • Fastp (added by @Agrima Bhatt) • fq/lint (added by @Adam Talbot assisted by @Agrima Bhatt) • toulligqc (added by @Thomas Adams) • Kraken2 (added by @Cris Tuñí assisted by @Agrima Bhatt) • CheckQC (added by @Matilda Åslin) • MultiQCSAV (added by @Nelly Nkonge) • sequali (added by @Pontus Höjer) • Seqkit (added by @Sarah Griffiths) • bbmap (added by @Erkut Ilaslan) • Riker (added by @Maxime Garcia) Refactored and updated documentation + new metro map, thanks to @Franziska Bonath @mashehu @James Fellows Yates @Jonathan Manning and @Pontus Höjer. Improved and simplified tools usage via tools_bundle, and other code/tests improvements/refactoring. Thanks to reviewers @Matthias De Smet and @mashehu Full CHANGELOG in: https://github.com/nf-core/seqinspector/blob/master/CHANGELOG.md

❌ seqinspector/test_full failed 😿 Run Name lonely_moriondo Duration 6m 8s Status ❌ Failed Error Message

The following invalid input values have been detected:

* --input (<https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/full_tests/SampleSheet.csv>): Validation of file failed:
	-> Entry 2: Error for field 'fastq_1' (<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_...stq/Bpacificus-ATCC10987-rep2-sWGS-MiSeqi100-241111_S2_L001_R1_001.fastq.gz>): the file or directory '<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_PairedEnd/Fastq/Bpacificus-ATCC10987-rep2-sWGS-MiSeqi100-241111_S2_L001_R1_001.fastq.gz>' does not exist (FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz')
	-> Entry 2: Error for field 'fastq_2' (<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_...stq/Bpacificus-ATCC10987-rep2-sWGS-MiSeqi100-241111_S2_L001_R2_001.fastq.gz>): the file or directory '<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_PairedEnd/Fastq/Bpacificus-ATCC10987-rep2-sWGS-MiSeqi100-241111_S2_L001_R2_001.fastq.gz>' does not exist (FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz')
	-> Entry 7: Error for field 'fastq_1' (<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_...stq/Bpacificus-ATCC10987-rep7-sWGS-MiSeqi100-241111_S7_L001_R1_001.fastq.gz>): the file or directory '<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_PairedEnd/Fastq/Bpacificus-ATCC10987-rep7-sWGS-MiSeqi100-241111_S7_L001_R1_001.fastq.gz>' does not exist (FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz')
	-> Entry 17: Error for field 'fastq_1' (<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSeq_.../Rsphaeroides-ATCC17023-rep1-sWGS-MiSeqi100-241111_S17_L001_R1_001.fastq.gz>): the file or directory '<https://github.com/nf-core/test-datasets/raw/seqinspector/full_tests/MiSe>...

Command Line

nextflow run '<https://github.com/nf-core/seqinspector>' -name lonely_moriondo -params-file '<https://api.cloud.seqera.io/ephemeral/xHdCs8g3q8E9ueQ8hu4oxg.json>' -with-tower -r dev -profile test_full

Jul 24, 2026 at 4:23 PM

✅ seqinspector/test_full completed successfully! 🎉 Run Name voluminous_kimura Duration 9m 53s Status ✅ Success Tasks Completed: 265 Aug 12, 2026 at 12:47 PM

✅ seqinspector/test_full completed successfully! 🎉 Run Name high_hoover Duration 8m 19s Status ✅ Success Tasks Completed: 265 Aug 12, 2026 at 2:41 PM

We just released https://github.com/nf-core/seqinspector/releases/tag/1.1.1 cattyping Minor release, mainly TEMPLATE update blob np Which had some security updates for GHAs, so nothing to concern for any end user, just us on the nf-core side, read more here: https://nf-co.re/advisories/pr-comment-workflow-vulnerability 😱 • chelae/trim as an alternative trimming tool ✂️ • output multiqc directory structure fixed 🐛

✅ seqinspector/test_full completed successfully! 🎉 Run Name nauseous_lamport Duration 10m 6s Status ✅ Success Tasks Completed: 265 Aug 19, 2026 at 12:14 PM

@Agrima Bhatt made her first release: https://github.com/nf-core/seqinspector/releases/tag/1.1.2 Very minor release, mainly TEMPLATE update blob np

✅ seqinspector/test_full completed successfully! 🎉 Run Name gloomy_meucci Duration 9m 18s Status ✅ Success Tasks Completed: 265 Aug 19, 2026 at 12:31 PM

Removing checkqc from the group reports because it bleeds info from the runfolder otherwise: https://github.com/nf-core/seqinspector/pull/279

<!here> I have submitted (meaning @Maxime Garcia has submitted for me) a project for the upcoming hackathon in Barcelona. If you have specific topics or issues you would like us to work on, please add them here. My current suggestions are as follows: • review and optimize tool bundles (make sure they make sense!) • optimize MultiQC outputs (order, what is displayed etc) • write a module for ONT runfolder parsing • add PacBio support (Bam file input, will soon also be required for ONT) • improve and update the metro map (we will at some point need a way to have a metromap that will not display all possible tools and that is still useful!)

Also, please let me know if you intend to join the hackathon and work on seqinspector 🙂

I opened a PR to add riker RNA files for metrics collection and am looking for a review; let me know if you have questions!