# Weekly helpdesk internal notes

_Please keep anonymous except for hosts as a rule, however links to direct PRs on public repositories etc. are OK_

## 2025-10-09 (10 AM CEST)

Holst: Júlia

3 people:

- Question about data staging in workdir
- Question regarding Google Cloud and error strategy
- Coffee break discussing tools release and teaching Nextflow

## 2025-09-11 (10 AM CEST)

Hosts: James, Maxime

4 people:

- VEP input/output problems
- Unit vs continuious integration pros- and cons (testing patched modules)
- Module template and bump-versioning questions
- Should I push patched changes in local module to official nf-core?

## 2025-06-19 (10 AM CEST)

Hosts: James

2 people

- Rubberducking nf-test issues with testing functions
- Troubleshooting HPC configuration

## 2025-06-05 (10 AM CEST)

Hosts: James, Maxime

3 (+ Rike, Jonas, Simon of maintainers) people joined

- Multiple pipeline devs asked questions on how to port custom nf-test to pipeline-level nf-test snapshots (identified suboptimal command in blog post, now fixed!)
- Sammyseq dev add some question on how to implement a step solution à la sarek
- Oncoanalyzer dev add a question about how to solve a process not being run
- Maxime and Simon discussed at lenght about the alt file for the last subworkflow to port from pytest and how to properly deal with it

graph TD;
  conf/test.config --is defined in-->  nextflow.config
  
  nextflow.config --gets picked up by--> .nf.test

  conf/test.config -.can be specified via the profile option.-> .nf.test

## 2025-05-22 (10 AM CEST)

Hosts: Maxime, Mahesh

1 person joined

- Debugging why a process wasn't running.

## 2025-05-15 (10 AM CEST)

Hosts: James, Matthias

4 people joined

- mitodetect x metnanext collaboration
- Best practise for exporting a large subworkflow to to it's own pipeline
- Advice on custom variant calling pipeline and differences to nf-test (Rubber ducking) (based on sarek)

## 2025-04-24 (10 AM CEST)

Hosts: Mahesh, @JoseEspinosa

1 people joined

- Question about running pipeline with Docker in GCP and files being staged as root and giving an error because then the file is not readable by Nextflow.

## 2025-04-17 (10 AM ET)

Hosts: Matthias, Maxime

4 people joined

- Question about linting error with a patched module => probably a [nf-core/tools bug](https://github.com/nf-core/tools/issues/3540)
- Question about pipeline level nf-test, and maintaining a forked pipeline
- Discussion about workflow/pipeline design
- Question about samplesheet handling

## 2025-04-10 (10 AM ET)

Hosts: Mahesh, Maxime

2 people joined

- Question about rscript and functions
- Answered with some solutions and directed to https://community.seqera.io/t/source-another-r-script-in-the-bin-directory/1059
- The hosts asked a question for once, and we know now more about what the sammyseq pipeline is actually doing
- Questions about modules imported by subworkflows but not actually used in the pipeline
- Question about best practice for Rscripts, whether to keep in bin, or with the module
- Question about debugging java in a container for a specific user.
- Question how to split inputs to distribute process over chromosome and region windows / using intervals and spread/gather strategy

## 2025-03-20 (10AM ET)

Hosts: Mahesh, @JoseEspinosa

- 3 people joined
- Question regarding an error related to input samplesheet and nf-schema validation for nf-core/evexplorer.
- Question about how the IGV modules work.
- nf-core/sammyseq hackathon task to add trimgalore so that there are two trimming tools on the pipeline. The task was not finished and there was an error on how the output was retrieved

## 2025-04-02 (3PM EAPACT)

Hosts : Arthur, Chirs H

- 3 members joined hosts :fire:
- Discussions about not being able to find things in documentation
- Discussions about balance between documenting how modules work and the burden of maintaining that documentation
- Discussions about nf-test and frustrations about pipeline level tests that pick up configs
- Discussions about converting dualseq from DSL1 > DSL2
- Discussions about how to contribute to nf-core modules, Chris to collate resources and send to user who will attend next week to discuss.

## 2025-04-01 (2PM ET)

Hosts : @FloWuenne , @emiller

Slack thread: https://nfcore.slack.com/archives/C06KSS9L8M7/p1743530413058119
- 2 members joined hosts Florian and Edmund
- proteinannotator: We went over some troubleshooting of potential Fusion and container issues for #proteinannotator
- Modules configs: We discussed #modules configurations and how to apply different configs at pipeline vs module repo level.
- Boston Summit: We discussed some activities and networking opportunities when attending Boston summit.

## 2025-03-20 (10AM ET)

Hosts: Maxime

- 2 people joined
- Question about handling meta information in a samplesheet with nf-schema
- Question about institutional configs and how to deal with pipeline level configs
- Discussion about references

## 2025-03-13 (10AM ET)

Hosts: James, Maxime

- 3 people joined
- Follow up question regarding high-level testing on oncoanalyser
- Questions regarding how to handle references
- Question about what types of project tasks are good for the upcoming hackathon
- Question about which order to add nf-tests (local modules -> subworkflows -> pipelines, or in reverse)
- Spring cleaning live demo: Maxime cleaned up 20 branches from sammyseq

## 2025-03-11 (10AM ET)

Hosts: @emiller

- 1 Person joined: Ken Youens-Clark
- Helped with basic Nextflow learning and discussed the language
- Had trouble with the new output syntax but wanted to use it instead of `outputDir`

## 2025-03-06 (10AM ET)

Hosts: Jose, Júlia

- 5 people joined
- question regarding adding a subworkflow to a pipeline, adapting the one from atacseq
- downloading DB from an HPC connected to internet through a proxi. There's an error "unreachable".
- question about involving students in the hackathon
- how to implement high-level testing for oncoanalyser(workflow and subworkflow). Question regarding how to pass parameters to the test.
- issue with the size of runners for CI (15Gb)

## 2025-03-04 (2PM ET)

Hosts: Florian, Lorena, Edmund

- Slack thread for all discussions of the huddle:
https://nfcore.slack.com/archives/C06KSS9L8M7/p1741114765482879
- sSqinspector discussions
- Devs are thinking of enabling users to subsample fastq files and run pipeline with this subsampled fastq files and/or the full sizes fastqs
- Some tools can run with subsampled data and others can't and so will need to be able to have tool specific configs to enable using subsampled fastq or not
- Discussions around resource configuration defaults in nf-core pipelines and modules
- `test_full` are using quite wasteful resource configurations even though we know EXACTLY how much resources this will need everyime
- In general, we are buying quite broad with modules cpu and memory settings by using these larger labels : `process_single`, `process_low`,`process_medium`,`process_high`
- Some previous discussions around this can be found in these issues
- https://github.com/nf-core/modules/issues/6629
- https://github.com/nf-core/modules/pull/6628/files
- Institutional configs exist but serve largely a different purpose
- https://github.com/nf-core/configs
- General discussion about regulatory
- General discussion around design of modules with pinning containers versus defining run environments more closely to conda environments for provenance
- [Wave and conda lock files](https://seqera.io/blog/ensuring-consistent-behavior-across-conda-and-docker-environments-with-wave/) together with nf-core modules like libraries can almost fulfill this purpose completely

## 2025-02-27 (10 CET)

Hosts: Maxime, Jose, Simon

- One person + colleague with params questions, related to species, so we advised to have a go with modifying the igenomes.config, with example from atacseq and sarek
- same persons had a wave question about building a complex container and Simon came to a rescue with this: https://www.linkedin.com/feed/update/urn:li:activity:7292567517745569793/
- Jose and I decided to promote Simon to co-host
- we also discussed on how to validate samples in sammyseq by checking that snps are the same bw. samples. Simon has experience and claimed that in many steps samples can get mislabelled
- a returning member came to ask questions about schema and input validation, and parsing args in R as done in diffab
- 2 persons were just lurking and no questions were asked
- Discussion about the [fgbio subworkflow](https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf) being broken after fgbio tools modules were updated by Simon, the subworkflow is not used in any pipeline. Might be that at some point the subworkflow was used in Sarek.

## 2025-02-25 (2PM ET)

Hosts: Edmund, Lorena?

- One person with Sarek feedback and questions on using nf-core in industry
- One person with questions about adopting nf-core and contributing back
- Started a region-boston and submitted two potential interest groups.

## 2025-02-20 (10 CET)

Hosts: Matthias

- One person with questions about the hackathon project board, `-resume` with cloud infra and running pipeline nf-tests locally
- One person with questions about using design matrices as an input
- going through Funcscan release review with Jasmin

## 2025-02-18 (2PM ET)

Hosts: Florian, Edmund

- One of the developers of sammyseq had an issue with file staging for adding blacklists to some modules. They were passing the string of the filename path, rather than staging the file properly using channels. We were able to show how they can fix this problem and resolve their issue.

## 2025-02-13(10AM CET)

Hosts: Maxime, James

- Maxime disucssed world domination plans
- Question about adding bowtie to the sammyseq pipeline
- issue due to invalid tuple input format was fixed
- missing meta for fasta
- issue with missing prefix from samtools sort
- Maxime begins to believe in Simon's Point
- typo fixed
- User mentionned that he and his coworker agree with Maxime's philophy
- "Let's make it work first and then we make it pretty"
- Returning User Quote 'I find this helpdesk very helpful!'
- Question (slack) about MEGAHIT and generating bandage plots

## 2025-02-11 (2PM ET)

Hosts: Edmund, Florian

- One person visited and discussed some questions about differences they were observing for calculating FRIP scores for Atacseq. They were running coverageBed and nf-core/atacseq uses intersectBed and they were basically getting different results. Edmund pointed them towards opening an issue on nf-core/atacaseq to discuss.

## 2025-02-06 (10AM CET)

Hosts: Jose, Júlia

- No one showed up... :cry:

## 2025-02-04 (2PM ET)

Hosts: Lorena

- No one showed up...

## 2025-01-30 (10AM CET)

Hosts: Jon, Maxime

Notes:

- Questions about usage of blacklists in sammyseq
- Questions about how to deal with a custom config file on a fork of rnaseq and keeping up to date with the release
- Questions about diffab
- Maxime derailed the meeting to talk with Jon about references while there was no-one else

## 2025-01-28 (2PM ET)

Hosts: Florian, Lorena

Notes:

- No one showed up...

## 2025-01-23 (10AM ET)

Hosts: Julia, Maxime

Notes:

- Questions about passing over meta data from samplesheet into a downstream modules in oncoanalyzer

## 2025-01-21 (2PM ET)

Hosts: Florian, Lorena

Notes:

- No one visited the help desk unfortunately
- Lorena and Florian had a chat about general things nf-core, how newcomers are overwhelmed with the complexity and size of nf-core and some ideas on helping them get started

## 2025-01-16 (10AM ET)

Hosts: Rike, James

Notes:

- Question: about adding additional options to a module (sammyseq)
- Discussed using nf-core tooling and git instead of local copies and copying nf-core components
- Question: a tool is missing an R package dependecy that is not on CRAN/bioconductor, can I just copy the function (GPL)?
- Answer: we prefer to upstream to add to bioconda, pointed to bioconda docs for R packages, if doesn't work we come back and make a different solution
- Question: my module isn't not publishing a file even though it is produced and exported in the output channel. Not sure if it's process or publish dir yet - will investigate before next time

## 2025-01-14 (2PM ET)

Hosts: Florian

Notes

- One person visited the helpdesk and discussed creation of a subworkflow from multiple nf-core modules (COPTR suite) and how to run a mapping module to different databases dynamically based on parameter input

## 2024-12-19 (10AM CET)

Hosts: Nico, James, Simon

Notes

- Wave: A wave container does not seem to have installed tools correctly (STARfusion) -> More likely a bioconda issue, try running pipeline in conda first, if bioconda issue fix recipe, if not shout at seqera
- Tower: denovo/transcript full-test keeps breaking because of fusion breaks, causing constant retries to 1.3TB and dies again -> relaunched but with non-fusion CE, if works yay! if not shout at sequera
- Testdata: How to specify a URL pointing to a custom test-data repository that also points at a specific commit (for non-nf-core pipeline)s
- Testdata: Test data for oncoanalyzer is stored on cloudflare and too large for GitHub actions -> decreasing coverage and subsetting to a single chromosome can help

## 2024-12-12 (10AM CET)

Host: Jon, Mahesh, Maxime

Notes:

- Someone came asking about pipeline nf-tests and how best to write them
- Discussion about subworkflows and documentation, and splitting workflows
- Discussion about learning Nextflow

## 2024-12-05 (10AM CET)

Host: Maxime, Mahesh, Sateesh

Notes:

Sateesh, Mahesh and Maxime discussed about references, setup-nextflow java related issues, methylseq release and #request-review

- 1 dev joined wondering about issues with the setup-nextflow@v2 in the modules
- 1 dev joined wanting some details about metro maps and the graphical assets, and we talked about hackathon, communities and being a Nextflow ambassador

Mahesh and Maxime concluded by looking at https://blueskyroast.com/

## 2024-12-03 (2PM ET)

Host : Florian, Edmund

Rob Syme stopped by Gather for a friendly chat about small Nextflow and Cursor / LLM based programming.

- Someone joined in huddle: A developer of PacVar joined to ask about how to upload the test_full dataset for the pipeline. Edmund agreed to upload her data to S3 once the tests are passings.

## 2024-11-28 (10AM CET)

Host: Maxime, Jose

- 2 person joined:
- sammyseq dev: TEMPLATE sync broke igenomes + question about version (possible issue in tools with bump-version)
- phaseimpute dev: Finishing touches before first release (PRs in modules + test_datasets) + hackathon (Maxime thinks he just came to discuss)

Jose and Maxime discussing references, nf-pegAse/animal genomics, dev meetings and periodicity of the core retreat ([x] Jose will add a point to the agenda of the next core meeting on the 13th of December).

## 2024-11-26 (2PM ET)

Host: Nicolas, Lorena

No one joined

## 2024-11-21 (10AM CET)

Host: Jose, Rike, James (with bad internet)

- 1 person joined
- nf-cascade question: had set up genomeqc to go into a non nf-core pipeline, but only one sample was being executed in the next one... -> partial solution by changing one channel from queue to val channel, but didn't fully work -> Ask Mahesh for details
- Additional question from Jose:
- Collaborators have built singularity containers rather than docker - can we host them separately, or should they make a docker container -> James thinks yes should go docker container route for uploading to quay.io (as nextflow can auto-convert docker to singularity, not v.v.), confirmed by Rike

## 2024-11-19 (2PM ET)
Host: Rike

- 2 people joined
- denovotranscript debugging of full size tests
- Seqera Platform Dataset usage

## 2024-11-12 (2PM ET)
Host: Nicolas
Support:

- 1 person joined
- Asked me on how to start working with/contributing to nf-core, she was also interested into working with sarek so I pointed her to the right docs and managed to let her run the test profile.

## 2024-11-07 (10AM CET)

Host: Mahesh
Support: Sateesh

- 0 guests joined
- Discussion over using `if` vs `branch` only in workflows
- Are there any downsides to removing `if` and replacing only with `branch`/`filter`
- Can we ask Ben to separate logging from DAG resolution?
- Solve issue with nf-test ( stub had wrong output, but didn't solve out of memory error )
- Memory issues solved a little bit later in #nf-test channel.

## 2024-11-05 (2PM ET)

Host: Rike
Support: Florian

- 2 people joined
- 1 person had issues with nf-validation / schema and discussed template update
- The developer of nf-core/denovotranscripts wanted to discuss their [PR for release 1.1.0](https://github.com/nf-core/denovotranscript/pull/18). We reviewed it on the spot and Rike [re-triggered AWS full tests on Platform](https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/R7O419Qb7fSPh)