I would also be ok with 1. 👍

@Jonas S @James Fellows Yates thanks again for your patience in reviewing this. We have checks passing on github.com/nf-core/funcprofiler/pull/52. Hopefully now all comments have been addressed, apologies for missing them last time. Let us know if there's anything we can do to help with the review!

I have a working computer again, but trying to catch up on a bunch of stuff. Will try to get to it ASAP

Note I've opened a 'pseudo PR' to make reviewing easier: https://github.com/nf-core/funcprofiler/pull/79 (I started on the release PR but noticed additional stuff that I didn't need to look at)

Review completed: https://github.com/nf-core/funcprofiler/pull/79

Looking good, might seem a lot of comments but I don't see any huge things other than pushing some of your validation to the pipeline initialisation

Thank you @James Fellows Yates know it has been a busy time for you recently, we are really grateful that you could take the time for a review! 🙂

Thanks @James Fellows Yates!

@James Fellows Yates just echoing the gratitude for your review efforts - thanks, we really appreciate it. Just finished working on the comments, addressed in the #79 PR

OK thank you! I will try to get to it ASAP (once again, sorry). I'm on kid duty still this week...

OK my Son skipped his midday nap so fell asleep quickly this evening before I crumbled myself (as what happens normally). Looked through all the changes - thank you for addressing everything and more(!) @Vini Salazar (and I guess @Nick Waters and @Mirae Baichoo)! I'm basically ready to give a ✅ on the main dev branch. Here are the last remaining queries (rather than change requests), which we can discuss here and if all good I can give the approval 🙂 • Metromap: much better weird multiple tiny stations behind the merge point after databases and before profiling • AWS megatest: I fair enough about DIAMOND/eggNot, but mi-faser why is it a problem if the database comes within the container? Or is this a 'bug' not yet solved? If it's not solved then i personally would not offer it as an option. • docs/usage.md, if you want to keep them available on first release, whenever you refer to DIAMOND/eggnog as work in progress (e.g. the flag table), maybe add - e.g. 'interpret results with caution', just make it clearer what WIP/Beta means in this context. • Humann4: ugh that's shitty about bioconda/containers... but OK I guess... I'll let it slide in this case ;); for the attributions in the HUMANn4 metas - did Daniel Straub help you with writing the modules for the pipeline then (jut to confirm 🙂 )? - I didn't see him in the GitHbu commit list of the pipeline so I had assumed you had taken them from other source... (I also only now see the difference between humann3 / humann4 facepalm my bad) • Moved validation: thjis error doesn't appear to have been transferred: https://github.com/nf-core/funcprofiler/blob/07bed543a3fdb7bd031d2040780f58e843eff08f/subworkflows/local/dataprep/main.nf#L27-L33

(oh and probs best to include the template merge that just went out before release 😉 )

Thanks @James Fellows Yates! • let me look into the mifaser megatest situation -- I don't remember this being related to containers. • Humann4. Yeah, its a problem that should be handled by the authors of the tool IMO. I'm curious about v4 so we went through the bother of containerizing and implementing it, but I don't necessarily want to be on the hook for managing the conda recipe long term. • @Daniel Straub isn't in the git commit history but I pulled in his code from an unmerged PR from a few years ago. We wen't the first ones to try to add this tool to nf-core/modules. Happy to make any changes to make the attribution more clear! I'll do the template merge and look into the mifaser test

Looking back at my notes, I didn't enble AWS running of mifaser because normal tests execute with the full-sized database already; its not that big. I can enable it but was just trying to keep the megatests for mega things. @Vini Salazar was there an issue with containers I was not aware of?

Sorry I'm only referring to Aws Megatest, this corresponds to

test_full

or was I looking at the wrong test again 😅?

❌ funcprofiler/test_full failed 😿 Run Name elated_lorenz Duration 37.1s Status ❌ Failed Error Message

Please check input samplesheet: multiple runs of a sample must all be single-end or all paired-end (sample: 2612).

Command Line

nextflow run '<https://github.com/nf-core/funcprofiler>' -name elated_lorenz -params-file '<https://api.cloud.seqera.io/ephemeral/9U6T7C66ZjlqPmWPRMUFdA.json>' -with-tower -r dev -profile test_full

Sep 3, 2026 at 5:35 PM

@Nick Waters @James Fellows Yates there wasn't, apologies, I misunderstood and thought the db came packaged in the container (instead of being in

database.csv

file), and that is why it was off. Since the tests are fairly small, I think we could just have mifaser on for the megatests anyway, some redundancy won't hurt (unless there is a policy to keep it strictly to larger tests)

❌ funcprofiler/test_full failed 😿 Run Name nice_gates Duration 37.5s Status ❌ Failed Error Message

Please check input samplesheet: multiple runs of a sample must all be single-end or all paired-end (sample: 2612).

Command Line

nextflow run '<https://github.com/nf-core/funcprofiler>' -name nice_gates -params-file '<https://api.cloud.seqera.io/ephemeral/Gb38fOnfz4CDFKIRo2eVnw.json>' -with-tower -r dev -profile test_full

Sep 4, 2026 at 4:49 AM

@Vini Salazar @Nick Waters the failure is because you're still using the taxprofiler short-read only input sheet in

test_full.conf

, which indeed mixes single-end and paired-end data. At this point you should probably split form taxprofiler and upload to your own funcprofiler test-dataset branch copies of the files and your own input FASTQ samplesheet

❌ funcprofiler/test_full failed 😿 Run Name cheeky_perlman Duration 18.2s Status ❌ Failed Error Message

--run_mifaser is set but the database sheet '<https://raw.githubusercontent.com/nf-core/test-datasets/funcprofiler/database_full.csv>' has no row with tool 'mifaser'.

Command Line

nextflow run '<https://github.com/nf-core/funcprofiler>' -name cheeky_perlman -params-file '<https://api.cloud.seqera.io/ephemeral/5F81cGOHImt2lkYkHGYDkg.json>' -with-tower -r b1e2b0d86f50cd61b71a4716d35f8478af9f481f -profile test_full

Sep 14, 2026 at 1:53 PM

❌ funcprofiler/test_full failed 😿 Run Name condescending_edison Duration 6m 7s Status ❌ Failed Error Message

2:46PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
2:46PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-076858c00fbd5bb62 instance-type=m6id.4xlarge
2:46PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
usage: metaphlan --input_type {fastq,fasta,bowtie2out,sam} [--force]
                 [--bowtie2db METAPHLAN_BOWTIE2_DB] [-x INDEX]
                 [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE]
                 [--bowtie2_build BOWTIE2_BUILD] [--bowtie2out FILE_NAME]
                 [--min_mapq_val MIN_MAPQ_VAL] [--no_map] [--tmp_dir]
                 [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len]
                 [--min_alignment_len] [--add_viruses] [--ignore_eukaryotes]
                 [--ignore_bacteria] [--ignore_archaea] [--ignore_ksgbs]
                 [--ignore_usgbs] [--stat_q] [--perc_nonzero]
                 [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat]
                 [-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS]
                 [--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab]
                 [--profile_vsc] [--vsc_out VSC_OUT]
                 [--vsc_breadth VSC_BREADTH] [-o output file]
                 [--sample_id_key name] [--use_group_representative]
                 [--sample_id value] [-s sam_output_file] [--legacy-output]
                 [--CAMI_format_output] [--unclassified_estimation] [--mpa3]
                 [--biom biom_output] [--mdelim mdelim] [--nproc N]
                 [--subsampling SUBSAMPLING]
                 [--subsampling_output SUBSAMPLING_OUTPUT]
                 [--subsampling_paired SUBSAMPLING_PAIRED] [-1 FORWARD_READS]
                 [-2 REVERSE_READS] [--mapping_subsampling]
                 [--subsampling_seed SUBSAMPLING_SEED] [--install] [--offline]
                 [--force_download] [--read_min_len READ_MIN_LEN] [-v] [-h]
                 [INPUT_FILE] [OUTPUT_FILE]
metaphlan: error: argu...

Command Line

nextflow run '<https://github.com/nf-core/funcprofiler>' -name condescending_edison -params-file '<https://api.cloud.seqera.io/ephemeral/xBwUc8yyAQGhr_-dKqplHg.json>' -with-tower -r 58d8d59a096bb0238e1d1c4773909c4ca7000827 -profile test_full

Sep 14, 2026 at 2:46 PM

✅ funcprofiler/test_full completed successfully! 🎉 Run Name golden_jepsen Duration 1h 3m 55s Status ✅ Success Tasks Completed: 14 Sep 15, 2026 at 6:19 PM

✅ funcprofiler/test_full completed successfully! 🎉 Run Name cheeky_albattani Duration 1h 6m 17s Status ✅ Success Tasks Completed: 14 Sep 18, 2026 at 2:41 PM

@Nick Waters I assume these green checks come from the work you've been doing lately! Thanks a lot for that

✅ funcprofiler/test_full completed successfully! 🎉 Run Name jovial_mandelbrot Duration 1h 3m 4s Status ✅ Success Tasks Completed: 14 Sep 21, 2026 at 4:31 PM

Congrats #C09A1GY7J4B team! We've got 1.0.0 and ready for analysis. I'm going to be spending some time the next few week processing our collection of a few thousand samples; hopefully that will help shake out any bugs. As a reminder, we have a catch-all issue here for recommendations for sensible defaults that we can configure for a 1.1.0 release. Thank you all for your effort to get this over the line!

Hi people! Congrats for the 1.0 release! I noticed in the funcprofiler pipeline's README a mention about eggNOG-mapper not being completely stable at the moment. Perhaps you can check what I did in this pipeline: github.com/OlivierCoen/nf-genome-annotator which is most probably going to become the next nf-core/genomeannotation pipeline. You can have a look specifically here for the implementation of eggnog-mapper: github.com/OlivierCoen/nf-genome-annotator/blob/…/main.nf I made a custom script to accelerate drastically the download of the eggNOG db, but you can stick to the script provided in the eggnog-mapper package. I don't have time to make PRs on funcprofiler for the moment, but feel free to copy any code you want 😉 Cheers

Hi @oliviercoen, thank you for the tip! We will definitely look into it 👍

@Nick Waters @Mirae Baichoo and team, I'll be able to make some time for development around mid / second half of October, would be good to have a quick discussion on some goals for the next release, as well if we want to have any sort of process around the release cycle (every six months? every quarter?). Also Nick keen to hear your experience in processing lots of data with the pipeline.

Hi @Vini Salazar! So sorry for the later reply. Thats great that you have some bandwidth for dev work! I'd say the next target would be refining the eggnog-mapper and diamond approaches that are currently in beta status. I don't have any set plans for a release cycle, I imagine aiming for a minor release at least one a year would make sense, but we can judge that based on how everything is performing and on how often the tools are releasing new versions.