oops sorry, did that by accident. @IGIRANEZA CLEMENT please ask @Sonalika Ray to join the nf-core Slack (https://nf-co.re/join) and then join this channel rather than sharing it across workspaces. We try to avoid doing that for pipeline channels too much as it causes problems at scale.

Thanks, Phil! No worries at all. I will ask her

Hello

I'm here

Hello folks, thanks for the invite. Could you please add my github account

wjlim

as a collaborator so I can access the repository?

<!here> We are organizing an onboarding meeting to talk more about where the pipeline currently stands, which modules or areas need the most support, and how we envision contributors getting involved. Once everyone has a clear understanding of the project, we will also use some interactive polls during the meeting to discuss your preferred areas of contribution and expected time commitment. Please select the time slot(s) that work best for you in the poll below (We’ve tried to find the best time slot that works across the four corners of the globe 🌍). We will choose the option that works for most people. Meeting time-slot poll: pollendar.com/?…

👋

Dear <!here>, most of us have selected 4 September at 12-2:00 PM CAT, so we will go ahead with this time slot for our onboarding meeting. During the meeting, we’ll talk more about where the pipeline (nf-co.re/pathogenepidemiology/latest) currently stands, which modules or areas need the most support, and how we envision contributors getting involved. We’ll also discuss your preferred areas of contribution and expected time commitment. If anyone has any inconvenience with this time slot, please let us know as soon as possible so we can consider solutions. Looking forward to meeting everyone and getting started!

Hello <!here>! 👋🏾 Could you please share your gmail address inbox (not here on the channel) so I can send you the invitation for our onboarding meeting on 04/09, from 1200–200 PM CAT via Google Meet? Thank you, and looking forward to seeing everyone there! 🙏🏾

Hello <!here>! 👋🏻 Just a quick reminder that our onboarding meeting is coming up today, 04/09, from 1200–200 PM CAT. Only a few hours to go! Looking forward to seeing everyone and starting the meeting together. The meeting is open to everyone, even if you are not registered or did not receive the calendar invitation. You can join directly using the Google Meet link below: onboarding meeting_nf/pathogenepedemiology Friday, September 4 · 12:00 – 2:00pm Time zone: Africa/Maputo Google Meet joining info Video call link: meet.google.com/zvb-kmng-rvd Feel free to join, and see you all soon!

Pathogen_Genomic_Surveillance_Scientific_Context_&_Requirements-1.pdf

github.com/nf-core/pathogenepidemiology/blob/…/original_local.nf ^ where the current "main" executable script lives before it is migrated to

workflows/pathogenepidemiology.nf

^

Also, since it was a condition of our proposal being approved, I just want to mention that in theory the pipeline can be applied to analysing any pathogen whose epidemiological analysis should consider mixed infections and resistance marker panels. An example disease is Tuberculosis.

Great to connect with you all. Thank you for coming. We hope it was interesting for you! Have a good weekend later

hey everyone, I’ve was looking into the issues and i think i'll start by #12 one “Get alignment stats to work” Is anyone currently working on it? and is there a known failing command or dataset I should use to reproduce the problem? @Bilal Asser I can first document the cause and then propose a focused fix

How to run

workflows/original_local.nf

, the temporary home of the code that wraps the rest of

nf-core/pathogenepidemiology

ncbi.nlm.nih.gov/Traces/study?acc=ERP158273&f=instrument_s%3An%3Bl…&… source attached: • SRA accession list/metadata for dataset I have been using (127 samples: 73 ONT, 54 ILL. See metadata because there are a couple of nuances we want to use later for testing) • shell script

get_dataset

to download subset of this dataset (just sets parameters for

nf-core/fetchngs

and makes use of the directory

testing

existing in

.gitignore

but you could use whatever ignored paths you like) Call I have been using to test the

<http://original_local.nf|original_local.nf>

executable:

nextflow run workflows/original_local.nf --threads 7 --clair3model r941_prom_hac_g360+g422    -profile docker,gpu --validation_monochromeLogs false

but you can surely just run:

nextflow run workflows/original_local.nf --threads 7 -profile docker

you'll get some harmless warnings, I expect

The article provides an overview of workflow management systems and bioinformatics tools used in P. falciparum genomic surveillance, with a particular focus on reproducibility, standardization, scalability, and implementation in diverse infrastructure settings. 🔗 link.springer.com/article/10.1186/s12936-026-06123-4

Hello @Phil Ewels please can you add me to the repository, my GitHub account is Nkiruka-Cynthia

@Manirabona Patience @Pedro Jiménez @Tabish Ali Ansari - the three of you are added to the repo manually for access. Instead, please could you post on #CEB982K2T to ask to join the nf-core organisation? Then you'll get access automatically and I can remove your individual permission sets. Thank you!

hey everyone, is anyone working on issue #8 (GATK step for Niaré et al.)? I'd like to pick it up if not. I have worked with GATK4 before but need to brush up. I had a look at the code, seems like some gatk4 modules are already installed but nothing's wired in yet past the BWA-MEM3 step, correct me if I am wrong, just checking before I start. Also, I'm new to nf-core specifically so will have questions as I go 😅, will post here. @Bilal Asser is it ok to take this on?

Hi @Bilal Asser, just left a comment on issue #13, want to try adding

storeDir

to the BBDUK step. Would appreciate a pointer to where the test profile config lives when you get a chance.

Hi @Bilal Asser , I’ve opened PR #22 for the remaining BWA-MEM3 stats issue #12. The fix creates the missing BAM index, and I verified that statistics from both BWA-MEM3 and Minimap2 now appear in MultiQC. Whenever you have time, could you please review it? Thanks!

@Bilal Asser the issue #12 is now merged and closed I'm interested in helping with #5 next if anyone is not doing it, since I’m already familiar with

<http://original_local.nf|original_local.nf>

and its channel structure. The integration looks fairly broad, so would you prefer that I start with a specific section or split it into smaller sub issues before making changes?

I have a wisdom tooth operation on Wed 7th, morning my time. My engagement with pipeline development this week will be relatively low, if any. Same goes for responsiveness to messages. Thanks for your understanding. Best, Bilal

Hi <!channel>, I’d appreciate your advice on a CI issue with my PR connecting GATK → BCFtools consensus → MAFFT → IQ-TREE. The PHYLOGENY test passes locally with Nextflow 25.10.4 and Docker, but the GitHub Actions test fails before execution because of a syntax issue in the existing

conf/modules.config

. I haven't modified that configuration because it is outside the scope of my PR. Would you recommend addressing this separately or taking another approach? Thanks for your guidance!

Hi @Bilal Asser Hi <!here>, I’ve been investigating a possible issue in the phylogeny workflow on

dev

. The workflow passes the joint cohort VCF from

GATK_MOI

into

PHYLOGENY

, pairing it with each WGS sample’s metadata. However,

BCFTOOLS_CONSENSUS

does not explicitly select the corresponding sample. In a controlled test with BCFtools 1.23.1, omitting sample selection produced an ambiguity-coded consensus when samples had different genotypes. This suggests that the workflow may not be generating truly sample-specific consensus sequences. I haven’t changed anything yet. Does this match the intended design? If so, I’d be happy to investigate a fix and add a regression test.

Thanks, @Debjit Pramanik. I independently tested the sample-selection fix using real Pf8 P. falciparum data from four Kilifi samples. The new regression test and existing phylogeny subworkflow test both passed, and all 72 genotype-to-consensus comparisons matched. I also noticed your note about duplicate FASTA headers. I'd be happy to investigate this as a separate follow-up, particularly for the multi-contig Plasmodium use case.

<!here>, While independently investigating the duplicate FASTA headers mentioned in relation to PR #68, I noticed a broader issue in the phylogeny subworkflow. Currently, all sample consensus FASTAs are combined and passed directly to MAFFT. This raises a concern for multi-contig reference genomes such as _P. falciparum_: simply adding sample IDs to the FASTA headers would prevent duplicate identifiers, but would not ensure that homologous contigs are aligned correctly. Could we clarify the intended scope of the phylogeny subworkflow? Is it intended to support whole-genome phylogenies for multi-contig references, or is the current implementation primarily designed for single-contig references? I'd like to understand the intended approach before suggesting any changes.

@Debjit Pramanik, I’ve completed my review and approved the PR #68. I’ll look separately into the duplicate FASTA header issue you mentioned, particularly in the context of multi-contig Plasmodium data.