We need it for

☝️

roger

And same will apply for pretty much to all AMR tools, if you come across them

Big big thanks to @Haidong Yi and @Xinpeng Zhang a CAZyme screening subworkflow has been integrated into

dev

of funcscan! I will start preparing for a release - so for those who have asked for this it's coming very soon!

Hi everyone, awesome how you got the cazyme screening PR running nf core party and huuuuge thanks from my side as pipeline dev for taking care of it while I was away. I am slowly coming back now 🙂 And yes, please go ahead with the release, awesome! I'm trying to wrap my head around what I missed in the next days. I have especially time tomorrow and Wednesday if anyone wants to meet up! Let me know if there is anything to help out right now.

Update on the release: @Jasmin Frangenberg is going to see if she can speedrun a lingering fix for AMPcombi, if it's as simple as we hope it is we will throw that into the release. If not we will release tentatively named '3.1.0 Chinese Baozi' !

Hi everyone! Would you consider including the following tools in the pipeline: Traitar, MacSyFinder, ISEScan, geNomad, dbCAN, and CarveMe? I’ve already developed modules for Traitar and MacSyFinder; dbCAN and geNomad are already available as nf-core modules. CarveMe and ISEScan are on my to-do list for development.

Hi @Jasmin Frangenberg! Given that you're already dealing with some AmpCombi2 problems these days, could you also have a look at the following issue report on GitHub? https://github.com/nf-core/funcscan/issues/524

If I annotate a Eukaryote and I get a

proteins.faa

file, is this pipeline appropriate or is it more for screening prokaryotes?

Hey All! Just found an interesting tool called METABOLIC and I wanted to ask if it could be a good fit for funcscan (I'm specifically interested in the METABOLIC-C module). https://github.com/AnantharamanLab/METABOLIC There's an Anaconda package (sadly, not Bioconda) available for the latest published version of the tool (which is from 2021): https://anaconda.org/channels/hcc/packages/metabolic/overview There's also a Docker image available in Docker Hub: https://hub.docker.com/r/tin6150/metabolic/tags

❌ funcscan/test_full failed 😿 Run Name agitated_lalande Duration 21m 46s Status ❌ Failed Error Message

12:54PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
12:54PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-054b8b19157a650c7 instance-type=r6id.4xlarge
12:54PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
[2026-05-21 12:54:07.392] [ERROR] Error (helpers.c:1002): dump #1: file missing: pre_20260521_124739.log
[2026-05-21 12:54:07.709] [ERROR] Error (helpers.c:1002): dump #1: file missing: pagemap-360.img
[2026-05-21 12:54:07.710] [ERROR] Error (helpers.c:1002): dump #1: file missing: pages-7.img
[2026-05-21 12:54:07.710] [ERROR] Error (helpers.c:1002): dump #1: file missing: pagemap-34075.img
[2026-05-21 12:54:07.710] [ERROR] Error (helpers.c:1002): dump #1: file missing: pages-8.img
[2026-05-21 12:54:07.941] [ERROR] Error (helpers.c:1002): dump #1: file missing: stats-dump
[2026-05-21 12:54:07.941] [ERROR] Error (helpers.c:1024): dump #1: 6 of 26 files failed verification
[2026-05-21 12:54:09.779] [ERROR] Error (helpers.c:1062): chain #0: 1 dumps failed verification
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:930GB, min:930GB, max:930GB, end:930GB
    clone_namespace: false
    download: 0.00MB, drops:0, skip:0, sync:1, req:1
    fusion_version: 2.5.12-8ea351d
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 0.00MB, drops:0, skip:0, sync:2, req:2

Command Line

nextflow run '<https://github.com/nf-core/funcscan>' -name agitated_lalande -params-file '<https://api.cloud.seqera.io/ephemeral/cq9BwvEijtonsecp1SuiuA.json>' -with-tower -r 6b27bd874cf25fc63b2b350ee057c96d777e6567 -profile test_full

May 21, 2026 at 12:54 PM

❌ funcscan/test_full failed 😿 Run Name small_plateau Duration 25m 52s Status ❌ Failed Error Message

1:30PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
1:30PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0da83e3fa0df13e14 instance-type=c6id.12xlarge
1:30PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
[2026-05-21 13:30:00.766] [ERROR] Error (helpers.c:1002): dump #1: file missing: pre_20260521_131946.log
[2026-05-21 13:30:01.022] [ERROR] Error (helpers.c:1002): dump #1: file missing: pagemap-360.img
[2026-05-21 13:30:01.022] [ERROR] Error (helpers.c:1002): dump #1: file missing: pages-7.img
[2026-05-21 13:30:01.022] [ERROR] Error (helpers.c:1002): dump #1: file missing: pagemap-38973.img
[2026-05-21 13:30:01.022] [ERROR] Error (helpers.c:1002): dump #1: file missing: pages-8.img
[2026-05-21 13:30:01.132] [ERROR] Error (helpers.c:1002): dump #1: file missing: stats-dump
[2026-05-21 13:30:01.132] [ERROR] Error (helpers.c:1024): dump #1: 6 of 26 files failed verification
[2026-05-21 13:30:04.691] [ERROR] Error (helpers.c:1062): chain #0: 1 dumps failed verification
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.8TB, min:2.8TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 0.00MB, drops:0, skip:0, sync:1, req:1
    fusion_version: 2.5.12-8ea351d
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 0.00MB, drops:0, skip:0, sync:2, req:2

Command Line

nextflow run '<https://github.com/nf-core/funcscan>' -name small_plateau -params-file '<https://api.cloud.seqera.io/ephemeral/x_wO0BzLNCydO45Sc07zhQ.json>' -with-tower -r 6b27bd874cf25fc63b2b350ee057c96d777e6567 -profile test_full

May 21, 2026 at 1:30 PM

✅ funcscan/test_full completed successfully! 🎉 Run Name small_plateau_2 Duration 1h 9m 43s Status ✅ Success Tasks Cached: 910, Completed: 271 May 21, 2026 at 2:44 PM

Hello! I am running this: NXF_VER=24.10.5 nextflow run nf-core/funcscan -r 3.0.0 \ -profile apptainer \ --input input.csv --amp_skip_ampcombi_clustering \ --run_amp_screening \ --outdir output \ -resume and I am getting a strange error -[nf-core/funcscan] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_FUNCSCANFUNCSCANAMP:AMPCOMBI2_CLUSTER (ampcombi2)' Caused by: Process

NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER (ampcombi2)

terminated with an error exit status (1) Command executed: ampcombi cluster \ --ampcombi_summary Ampcombi_summary.tsv \ --cluster_cov_mode 0 --cluster_mode 1 --cluster_coverage 0.8 --cluster_seq_id 0.4 --cluster_sensitivity 4.0 --cluster_min_member 0 --log TRUE \ --threads 6 cat <<-END_VERSIONS > versions.yml "NFCORE_FUNCSCANFUNCSCANAMP:AMPCOMBI2_CLUSTER": ampcombi: $(ampcombi --version | sed 's/ampcombi //') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: ^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/computation/expressions.py", line 241, in evaluate return _evaluate(op, op_str, a, b) # type: ignore[misc] ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/computation/expressions.py", line 70, in _evaluate_standard return op(a, b) File "/usr/local/bin/clustering_hits.py", line 19, in parsing_input_for_cluster merged_df['seq_headers'] = merged_df['sample_id'] + '!' + merged_df['contig_id'] + '!' + merged_df['CDS_id'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/common.py", line 72, in new_method return method(self, other) ^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/arraylike.py", line 102, in add return self._arith_method(other, operator.add) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/series.py", line 6259, in _arith_method return base.IndexOpsMixin._arith_method(self, other, op) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/base.py", line 1325, in _arith_method result = ops.arithmetic_op(lvalues, rvalues, op) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/array_ops.py", line 226, in arithmetic_op res_values = _na_arithmetic_op(left, right, op) # type: ignore[arg-type] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/array_ops.py", line 172, in _na_arithmetic_op result = _masked_arith_op(left, right, op) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/array_ops.py", line 110, in _masked_arith_op result[mask] = op(xrav[mask], yrav[mask]) ^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: can only concatenate str (not "int") to str Work dir: /gpfs1/home/r/b/rbarrant/projects/simran/work/a7/e59a4f0e145b81eb2c706d01c94295 Container: /gpfs2/scratch/pi/jdragon/NXF_APPTAINER_CACHEDIR/quay.io-biocontainers-ampcombi-2.0.1--pyhdfd78af_0.img I have tried other versions of ampcombi and have had the same issue, unless the version is much older so I get other type of error. Any ideas?

Hi all, have you considered arg_ranker for your pipeline https://github.com/caozhichongchong/arg_ranker ?This is a tool that estimates clinical significance of the detected ARGs

Hi all, I want to reopen this discussion https://nfcore.slack.com/archives/C02K5GX2W93/p1776940829275139 After working deeper on the pipeline bacmodel, I'm not entirely convinced that it is the best home for METABOLIC tool. Bacmodel metabolic profiling is centered around GEMs, while METABOLIC focuses more on trait profiling than on reconstructing simulation-ready models.

Guess who is opening the release PR for next version of #C02K5GX2W93 tomorrow? 👀

Hi all! Conceptual question. I know this pipeline is meant for longer reads / contigs, but I'm curious if the following application might work: Is it possible to use funcscan on a whole genome fasta file to identify virulence factors / ARGs that are present in a given genome?

❌ funcscan/test_full failed 😿 Run Name pedantic_laplace Duration 2m 44s Status ❌ Failed Error Message

9:54AM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
9:54AM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0c4bbb7294476677d instance-type=r6id.12xlarge
9:54AM INF [seqera-fusion] starting incremental snapshot timer interval=300000
File downloaded successfully and saved to amp_DRAMP_database/general_amps_2026_06_26.txt
Traceback (most recent call last):
  File "/usr/local/bin/ampcombi_download.py", line 144, in <module>
    download_ref_db(args.database, args.threads)
  File "/usr/local/bin/ampcombi_download.py", line 61, in download_ref_db
    if valid_sequence_pattern.match(sequence):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: expected string or bytes-like object, got 'float'
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.7TB, min:2.7TB, max:2.7TB, end:2.7TB
    clone_namespace: false
    download: 0.00MB, drops:0, skip:0, sync:0, req:0
    fusion_version: 2.5.12-8ea351d
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 11.84MB, drops:0, skip:0, sync:7, req:7

Command Line

nextflow run '<https://github.com/nf-core/funcscan>' -name pedantic_laplace -params-file '<https://api.cloud.seqera.io/ephemeral/xtBkzM0Rvlk2kOPEyxzDzQ.json>' -with-tower -r dev -profile test_full

Jun 26, 2026 at 9:55 AM

❌ funcscan/test_full failed 😿 Run Name sleepy_kalman Duration 37m 35s Status ❌ Failed Error Message

1:19PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
1:19PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-064d15f63902ff579 instance-type=c6id.8xlarge
1:19PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
[2026-06-26 13:19:59.678] [ERROR] Error (helpers.c:1002): dump #1: file missing: pre_20260626_125542.log
[2026-06-26 13:19:59.837] [ERROR] Error (helpers.c:1002): dump #1: file missing: pagemap-344.img
[2026-06-26 13:19:59.837] [ERROR] Error (helpers.c:1002): dump #1: file missing: pages-7.img
[2026-06-26 13:19:59.837] [ERROR] Error (helpers.c:1002): dump #1: file missing: pagemap-51379.img
[2026-06-26 13:19:59.837] [ERROR] Error (helpers.c:1002): dump #1: file missing: pages-8.img
[2026-06-26 13:19:59.920] [ERROR] Error (helpers.c:1002): dump #1: file missing: irmap-cache
[2026-06-26 13:19:59.920] [ERROR] Error (helpers.c:1002): dump #1: file missing: inventory.img
[2026-06-26 13:19:59.920] [ERROR] Error (helpers.c:1002): dump #1: file missing: stats-dump
[2026-06-26 13:19:59.920] [ERROR] Error (helpers.c:1024): dump #1: 8 of 26 files failed verification
[2026-06-26 13:20:00.036] [ERROR] Error (helpers.c:1002): dump #2: file missing: pre_20260626_130042.log
[2026-06-26 13:20:00.183] [ERROR] Error (helpers.c:1002): dump #2: file missing: pagemap-60913.img
[2026-06-26 13:20:00.183] [ERROR] Error (helpers.c:1002): dump #2: file missing: pages-7.img
[2026-06-26 13:20:00.294] [ERROR] Error (helpers.c:1002): dump #2: file missing: stats-dump
[2026-06-26 13:20:00.294] [ERROR] Error (helpers.c:1024): dump #2: 4 of 24 files failed verification
[2026-06-26 13:20:02.675] [ERROR] Error (helpers.c:1062): chain #0: 2 dumps failed verification
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:1.9TB, min:1.9TB, max:1.9TB, end:1.9TB
    clone_namespace: false
    download: 0.00MB, drops:0, skip:0, sync:1, req:1
    fusion_version: 2.5.12-8ea351d
    kernel_version: 6.1
   ...

Command Line

nextflow run '<https://github.com/nf-core/funcscan>' -name sleepy_kalman -params-file '<https://api.cloud.seqera.io/ephemeral/hTWDhAdWzMEzcnJM-zV5tA.json>' -with-tower -r dev -profile test_full

Jun 26, 2026 at 1:20 PM

✅ funcscan/test_full completed successfully! 🎉 Run Name sleepy_kalam Duration 1h 29m 58s Status ✅ Success Tasks Completed: 1181 Jun 26, 2026 at 2:52 PM

✅ funcscan/test_full completed successfully! 🎉 Run Name lonely_mcclintock Duration 1h 7m 52s Status ✅ Success Tasks Completed: 1181 Jun 27, 2026 at 8:30 AM

<!channel> As you can see from the passing tests above, I'm happy to announce the final release of the long awaited nf-core/funcscan release 4.0.0 - Chinese Baozi! This is a particularly spectacular release due to the addition of a whole brand new subworkflow for screening the of Carbohydrates and Carbohydrate-Active enzymes a.k.a CAZymes, by @Haidong Yi with the support of @Xinpeng Zhang - so huge thanks to them! The other bits of nice shiny new bigs includes some more BGC functionality with support for GECCO Convert and BiG-SLiCE for BGC clustering thanks to @Codrin Dediu (with the support of (@Alexandru Mizeranschi) Otherwise we have the typical version updates (including to Bakta 1.12 and AMPcombi to 3.0.0) from myself and @Jasmin Frangenberg The full changelog is here: https://github.com/nf-core/funcscan/releases/tag/4.0.0 Thanks to all the contributors again!

Hi all, I ran into a pretty serious bug with the

merge_taxonomy.py

script that I saw was posted to the issue tracker in 2025 (this was using the latest 4.0.0 release). The issue is marked as ‘requires-upstream-fix’ but seems to be dormant with no response. I could post a possible fix for this (at the moment it’s centered on AMR), but I wanted to know if there was any reason this was marked as upstream. Thanks!

📣 PSA re: nf-core/funcscan development 📣 Hello <!channel> We are looking for new developers for funcscan! Unfortunately both @Jasmin Frangenberg and I have undergone job transitions and are no longer working in the microbial/genomics space. Therefore we are unable to develop the pipeline further ourselves. In our small bits of free time, we will endeavour to keep the pipeline up-to-date and aligned with the nf-core template as far as possible - but we will not be able to extend pipeline features or perform major bug fixes ourselves. That said, one of the great things about nf-core is that it is community owned! We are looking for potential new curators to take over the development of the pipeline to make it even better, more relevant, and make it their own. If you would be interested in taking over and applying your own vision, feel free to contact either of us to discuss 'handing over of the (proverbial) keys'! We will of course help advise during the transition and be open for questions/chats (almost 🕔) anytime.

❌ funcscan/test_full failed 😿 Run Name fabulous_celsius Duration 26.7s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/funcscan>, projectDir: /.nextflow/assets/.repos/nf-core/funcscan/clones/9ad01cf31814e403b127567948a0af388f331653, commitId: 9ad01cf31814e403b127567948a0af388f331653, revision: dev, startTime: 2026-10-08T08:09:38.197368771Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/funcscan>' -name fabulous_celsius -params-file '<https://api.cloud.seqera.io/ephemeral/2N2Fxwdfc-pyourcmHCmAg.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$Preview@598f065f, enable:nextflow.NextflowMeta$Features@21f48f6c, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/funcscan/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/funcscan>' -name fabulous_celsius -params-file '<https://api.cloud.seqera.io/ephemeral/2N2Fxwdfc-pyourcmHCmAg.json>' -with-tower -r dev -profile test_full

Oct 8, 2026 at 8:10 AM

depictio Depictio dashboard for funcscan: your feedback wanted Hi all! 👋 I am building Depictio, an open-source platform from EMBL to explore pipeline results without writing a Shiny or Streamlit app each time. A pipeline gets a dashboard template: a short definition that turns the outputs of any run into an interactive dashboard. I am now sharing it more widely, so I would like the view of funcscan users and developers. ✨ What it does • MultiQC reports (aggregated across runs) next to result tables, images, phylogenetic trees, maps... with linked filters • Reusable: point the template at any new run of the same pipeline and you get the same dashboard • Fully editable: modify any dashboard from the GUI or in YAML, so the template is a starting point, not a constraint • Versioned, with comments and annotations on any component • Runs as a Python package, with Docker Compose or on Kubernetes, and can serve as a companion web app for a publication 🔍 For funcscan: which screens and tools ran, findings per assembly and per contig, resistance genes, antimicrobial peptides, biosynthetic gene clusters and CAZymes. 👀 What I need: I have built 25 templates and want people who really use these pipelines to review and criticise them. What is useful? What is misleading? 👉 Dashboard: funcscan dashboard (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to funcscan. ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏 🎤 I was speaking about Depictio at the Nextflow Summit (session page), and the recording will be available in the coming weeks.

Any thoughts on replacing antiSMASH with metaSMASH? biorxiv.org/content/10.64898/… github.com/canerbagci/metasmash

Hi! I'm working on updating the modules to use Seqera containers. I got a problem with the amrfinderplus_run module. I raised an issue in funcscan as that is where it used. I thought I'd let you know: github.com/nf-core/funcscan/issues/558