The hacking started🎉

I have a question about the

raw

and

filtered

matrices for the hashing mode. Currently the user should provide 4 matrices: hto/rna and raw/filtered. Then for each tool uses can select if they want to use the raw/filtered for hto and the same for rna. This is a lot of parameters and I am not sure if this actually make sense. In my imagination, users would want to use the same combination of matrices for all tools. Thus, it might not be necessary that the users provide both raw and filtered matrices in the first place, but instead we could just have one

rna_matrix

and one

hto_matrix

as input, and we could just use whatever the user provides, no matter if these are then filtered or raw Am I missing something? @Lukas Heumos @Fabiola Curion

Day 2 🎉

Quick hackathon wrap-up: Modules: • 2 modules merged • 2 modules on the brink of being merged, some CI issues left to fix • 1 module left untouched, but Luis and Seo clearly got the hang in the end, so can probably be done quickly Pipeline: • Basic structure established • Implemented all modules that were available in #CJRH30T6V before the hackathon, new ones left to be done • What is missing: ◦ The newly added modules ◦ The final summarization and donor matching How we are planning to move on: • Luis volunteered to work on the remaining module (as it is R-based, and he mostly worked on R-based modules) • Seo will look into the CI issues of the two mentioned modules • I will spend a four hours per week adding the remaining modules to the pipeline I also talked to Luis and Seo about me joining your next bi-weekly meeting (23.06, 12:00) to talk about the hackathon in general and the next steps, @Lukas Heumos let me know if you think that makes sense

Current state of the pipeline • All merged modules are added to our pipeline (PR) ◦ added

htodemux

,

multiseq

, and

hasheddrops

to the pipeline ◦ added the preprocessing script for

htodemux

and

multiseq

in the local folder ◦ added a visualization script for

htodemux

in the local folder • Updated

htodemux

(PR),

multiseq

(PR),

hasheddrops

(PR), and

bff

(PR). I mainly fixed the data types so that they fit with the pipeline. • Due to the memory limit, we haven’t been able to merge bff. What can we do to finally merge this module? • What is the status of the remaining modules that haven’t been merged yet? (See progress table)

Hey <!subteam^S016E36N7TQ>, there is currently no branch for #C067K2P6GUV in #C02L5UB4Y9G and I can't create one due to repo permissions. Could someone create one for me?

Current state of hashing summary I have added all methods for which we already have nf-core modules to our hashing summary script (

htodemux

,

multiseq

,

demuxem

,

hasheddrops

and

gmmdemux

). We are currently still missing

bff

(PR) and

hashsolo

for hashing. @Nico Trummer, should I continue without these modules for now? Or do we have a solution for

bff

and

hashsolo

?

Nf-core questions @Nico Trummer, I have a basic question about

ext.args

inputs for nf-core, which may also be of interest to @Seo Kim .

What's next? So the hash summary part is done. We just need to merge it. Apart from that, what is still missing? Donor matching and the genetic summary? Is there anything else?

Update 🥘 or party cell Hey @Nico Trummer, I need one approving review from you for the updates to

souporcell

. Unfortunately, I cannot allow everyone to review it. I hope you find time to take a quick look at this. It's nothing major, and the tests are already running. This is the PR.

Gene summary and donor match PR The next steps to bring hadge to nf-core have been completed. However, I still need some help with the current PR: 1. A new nf-core version is available. When I run

nf-core pipelines sync

and then

git merge TEMPLATE

, I get several merge conflicts again. @Nico Trummer, last time you mentioned you could take care of that. Would you have time to do it again? If not, could you let me know who might be able to help, or should I give it a try myself? 2. I’ll also need someone to review my PR. @Lukas Heumos mentioned at the last meeting that he could take care of that. @Nico Trummer, would you also like (or need) to review it from a nf-core perspective? Thanks a lot! 🙏

Final steps 🏁 I'm currently adding the final features to hadge (see remaining issues with prio:high and prio:normal). As soon as I'm done with that, what are the steps to bring the pipeline to nf-core? @Nico Trummer, maybe you can help us with that?

Flexible Input Formats In our last meeting, Lukas and I discussed supporting different input formats for the count matrices. I researched how other pipelines handle this and checked the input requirements for our modules (see this issue). Except for hashsolo and demuxem (which doesn’t work anyway), all modules require 10X Genomics input. If we want to support other formats, I could write a module to convert AnnData or CSV into a 10X Genomics-compatible format.

Bring hadge to nf-core Thank you for the review, @Nico Trummer and @Lukas Heumos! I have incorporated your feedback, and all tests are still passing. So what's next?

Hi, I have been trying the nf-core/hadge pipeline on my data but I'm running into the following error in the last step:

ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_HADGE:HADGE:GENETIC_DEMULTIPLEXING:GENE_SUMMARY
(...)
Command executed [/home/lb2336/.nextflow/assets/nf-core/hadge/modules/local/gene_summary/templates/gene_summary.py]:
(...)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

any suggestions how to change this decoding error?

Generally, I found it would also be great to be able to skip some of the pre-processing steps (eg. BAM_QC, CELLSNP_MODEA) upon user choice and the memory requirements could probably be reduced

The process CREATE_ANNDATA_MUDATA seems to start even though I set:

--generate_mudata false --generate_anndata false

As well as CELLSNP_MODEA even though I didn't select CELLSNP as a tool - this was my command:

nextflow run nf-core/hadge -profile singularity -r dev -c test.config --input demux_sample_sheet_nfcore.csv --outdir test --mode genetic --genetic_tools demuxlet --match_donor false --generate_mudata false --generate_anndata false

Is CELLSNP maybe a new addition ? Its also not mentioned in the README overview image of the pipeline - would be great to know why its generally required if it is

Apologies for all the remarks - just wanted to give some feedback here

One more question - if I wanted to add another HTO multiplexing tool to the hadge toolbox for example "demuxmix" , would you be open to that ?| (https://academic.oup.com/bioinformatics/article/39/8/btad481/7234612)

Hi folks, just linking for potential to collaborate with @Kevin RUE

Release 🚀 @Nico Trummer, is there anything else that needs to be taken care of before we can release? If not, I'd be happy to start the final steps described here: nf-co.re/docs/developing/pipelines/release-procedure

✅ hadge/test_full completed successfully! 🎉 Run Name insane_kalman Duration 5h 25m 13s Status ✅ Success Tasks Completed: 28 Sep 28, 2026 at 3:18 AM

✅ hadge/test_full completed successfully! 🎉 Run Name prickly_fourier Duration 5h 29m 24s Status ✅ Success Tasks Completed: 28 Sep 28, 2026 at 11:54 AM

✅ hadge/test_full completed successfully! 🎉 Run Name thirsty_magritte Duration 4h 10m 56s Status ✅ Success Tasks Completed: 28 Sep 28, 2026 at 12:58 PM

@Luis Heinzlmeier just made release 1.0.0 Thanks everyone for contributing! Special thanks go to @Nico Trummer who made substantial contributions and guided @Luis Heinzlmeier where necessary.

❌ hadge/test_full failed 😿 Run Name golden_pare Duration 21.6s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/hadge>, projectDir: /.nextflow/assets/.repos/nf-core/hadge/clones/fedeeb3ef358fb7cf576eae6f20b97f95ef920d3, commitId: fedeeb3ef358fb7cf576eae6f20b97f95ef920d3, revision: dev, startTime: 2026-10-07T10:43:52.891922829Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/hadge>' -name golden_pare -params-file '<https://api.cloud.seqera.io/ephemeral/_MVWxxHlNm97P1HSB2Zgmw.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.6, build:12646, timestamp:09-07-2026 18:49 UTC, preview:nextflow.NextflowMeta$Preview@2778a7c3, enable:nextflow.NextflowMeta$Features@94ba90a, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/hadge/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/hadge>' -name golden_pare -params-file '<https://api.cloud.seqera.io/ephemeral/_MVWxxHlNm97P1HSB2Zgmw.json>' -with-tower -r dev -profile test_full

Oct 7, 2026 at 10:44 AM