nf-core #genomeassembler

Ida Karlsson

01/28/2026, 2:36 PM

Hello, and thanks for this very useful pipeline! I have previously run the pipeline to do an assembly which I have manually edited. Now I want to run the pipeline with

--skip_assembly

, but it stops with an error before any jobs have been started:

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ERROR ~ Execution aborted due to an unexpected error
-- Check script '/home/user/.nextflow/assets/nf-core/genomeassembler/./workflows/../subworkflows/local/polishing/./medaka/polish_medaka/../../../liftoff/../../../modules/nf-core/liftoff/main.nf' at line: 6 or see '.nextflow.log' file for more details

Is there something wrong with my sample sheet or combination of parameters (see below)?

Rike Hanssen

02/16/2026, 10:15 AM

Hello! I am currently reviewing pipelines that are missing their AWS full size test results. Looks like genomeassembler has some parameter validation errors, if someone could look into it:

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ERROR ~ Cannot invoke method toBoolean() on null object
-- Check script '.nextflow/assets/nf-core/genomeassembler/subworkflows/local/prepare_shortreads/main.nf' at line: 37 or see 'nf-3Raqkm5qxoyOec.log' file for more details
ERROR ~ Argument of `file()` function cannot be null
-- Check script '.nextflow/assets/nf-core/genomeassembler/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf' at line: 76 or see 'nf-3Raqkm5qxoyOec.log' file for more details
ERROR ~ Argument of `file()` function cannot be null
-- Check script '.nextflow/assets/nf-core/genomeassembler/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf' at line: 81 or see 'nf-3Raqkm5qxoyOec.log' file for more details
-[nf-core/genomeassembler] Pipeline completed with errors-
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
-- Check 'nf-3Raqkm5qxoyOec.log' file for details

Platform link: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3Raqkm5qxoyOec/v2/logs let me know if you don't have the necessary access

Conner Johnson

03/23/2026, 5:43 PM

Hi @Niklas Schandry, it looks like you're refactoring on a personal fork on GitHub. Are you open to people submitting pull requests and/or issues there? I had some things I would like to suggest to include and fix from the current release version, but want to make sure they would fit with the updated version that's coming

oliviercoen

04/02/2026, 6:08 AM

Hi! I saw that a big PR is curretly reviewed and it really looks amazing! 🙂 However, I think that adding more E2E tests would make the pipeline much more stable and reproducible. I won't be able to work on it until next May / June, but if you want, I made Hi-C test files adapted to the genome you are using in the pipeline: https://github.com/OlivierCoen/nf-genome-assembler/tree/main/tests/test_data/hic_short_reads/a_thaliana Hope it helps!

Alexander Bontempo

07/08/2026, 2:06 AM

hi, who may help me to understand what model to use in the mendaka step of the pipeline?

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09/08/2026, 11:20 AM

❌ genomeassembler/test_full failed 😿 Run Name suspicious_sanger Duration 2m 19s Status ❌ Failed Error Message

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Unknown error

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name suspicious_sanger -params-file '<https://api.cloud.seqera.io/ephemeral/yl0oYlmy8QmG6R0o5vTTZw.json>' -with-tower -r dev -profile test_full

Sep 8, 2026 at 11:20 AM

👍 1

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09/09/2026, 9:11 AM

❌ genomeassembler/test_full failed 😿 Run Name gigantic_ramanujan Duration 19m 18s Status ❌ Failed Error Message

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SIGTERM

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name gigantic_ramanujan -params-file '<https://api.cloud.seqera.io/ephemeral/wo1RLW9g-nqhq9uFQG4IoQ.json>' -with-tower -r dev -profile test_full

Sep 9, 2026 at 9:11 AM

ohno2 1

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09/09/2026, 12:40 PM

❌ genomeassembler/test_full failed 😿 Run Name nostalgic_morse Duration 3h 24m 48s Status ❌ Failed Error Message

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12:39PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
12:39PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0ecd12dde78effde3 instance-type=r6id.16xlarge
12:39PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
WARNING: Python locale settings can't be changed
ERROR! File not found (reference_bam): /nf-core-awsmegatests/work/genomeassembler/work-dev/a5/500664fd475a61af4a2b4820cb564a/test_hifi_hifiasm_to_reference.bam
In case you have troubles running QUAST, you can write to <mailto:alexey.gurevich@helmholtz-hips.de|alexey.gurevich@helmholtz-hips.de>
or report an issue on our GitHub repository <https://github.com/ablab/quast/issues>
Please provide us with quast.log file from the output directory.
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:3.2TB, min:3.2TB, max:3.2TB, end:3.2TB
    clone_namespace: false
    download: 88.77MB, drops:0, skip:0, sync:0, req:3
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 0.00MB, drops:0, skip:0, sync:9, req:9

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name nostalgic_morse -params-file '<https://api.cloud.seqera.io/ephemeral/RkU0n-UYZFaMIWVmMHVztQ.json>' -with-tower -r dev -profile test_full

Sep 9, 2026 at 12:40 PM

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09/09/2026, 2:09 PM

❌ genomeassembler/test_full failed 😿 Run Name high_laplace Duration 1h 4m 5s Status ❌ Failed Error Message

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SIGTERM

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name high_laplace -params-file '<https://api.cloud.seqera.io/ephemeral/yNlu9biVc-cw0Am3LSd-pw.json>' -with-tower -r dev -profile test_full

Sep 9, 2026 at 2:09 PM

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09/09/2026, 2:09 PM

❌ genomeassembler/test_full failed 😿 Run Name nostalgic_morse_2 Duration 1h 10m 38s Status ❌ Failed Error Message

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SIGTERM

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name nostalgic_morse_2 -params-file '<https://api.cloud.seqera.io/ephemeral/HHyz_vyK6uwiN_AXgsf52A.json>' -with-tower -r 00d7a7f8c574cce3e34e40e677374caf340cd402 -profile test_full -resume 96e0d329-0f0c-4cb2-b472-1e653679b340

Sep 9, 2026 at 2:09 PM

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09/10/2026, 1:05 PM

❌ genomeassembler/test_full failed 😿 Run Name jovial_ptolemy Duration 6h 28m 38s Status ❌ Failed Error Message

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(more omitted..)
LINKS_CPP -f assembly.fa -s readfile.fof   -d 500,2000,5000 -k 15 -t 40,200 -j 4 -l 5 -o 0 -e 0.1 -z 500 -p 0.001 -b test_hifi_hifiasm_links -v 0 -x 0
LINKS running options:
  -f assembly.fa
  -s readfile.fof
  -d 500,2000,5000
  -k 15
  -j 4
  -t 40,200
  -o 0
  -e 0.1
  -l 5
  -a 0.3
  -z 500
  -b test_hifi_hifiasm_links
  -r 
  -p 0.001
  -x 0
  -v 0
STAGE: Bloom filter construction/read
- Number of BF Elements: 180203732
- Input file path: test_hifi_hifiasm_links
- Input file: assembly.fa
- kmersize: 15
- m: 2590894920
- fpr: 0.001
- hashFct: 9
- Filter output file : 15
Writing Bloom filter to disk (test_hifi_hifiasm_links.bloom)
Bloom filter generated or loaded in: 0h 1m 6s 252ms
STAGE: Reading sequence reads
Reading: singles_hifi.fastplong.fastq
Processed read count: 100000 - 200000 - 300000 - 40000012:58PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
 - 500000 - 600000 - 696921
Read fasta stage completed in: 0h 5m 58s 295ms
STAGE: Reading contigs
Reading: assembly.fa
Processed read count: 760
1:03PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
[2026-09-10 13:03:14.845] [WARN] Warn  (dumprestore.c:235): predump failed, starting new chain for future dumps
[2026-09-10 13:03:14.846] [ERROR] Error (exec.c:102): incremental dump failed with code: -52
make: *** [/usr/local/bin/LINKS-make-real:122: test_hifi_hifiasm_links.tigpair_checkpoint.tsv] Killed
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.5TB, min:2.4TB, max:3.5TB, end:3.5TB
    clone_namespace: false
    download: 47210.36MB, drops:0, skip:0, sync:0, req:370
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 169466.41MB, drops:0, skip:0, sync:79, req:1402

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name jovial_ptolemy -params-file '<https://api.cloud.seqera.io/ephemeral/_EAK6cYTaoH1sc7FRrbaOg.json>' -with-tower -r dev -profile test_full

Sep 10, 2026 at 1:05 PM

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09/10/2026, 8:35 PM

❌ genomeassembler/test_full failed 😿 Run Name jovial_ritchie Duration 6h 17m 13s Status ❌ Failed Error Message

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(more omitted..)
8:24PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
Running Command: LINKS-make LINKS draft=assembly.fa readsFof=readfile.fof d=500,2000,5000  t=40,200 j=4      b=test_hifiasm_hifiasm_links     
LINKS_CPP -f assembly.fa -s readfile.fof   -d 500,2000,5000 -k 15 -t 40,200 -j 4 -l 5 -o 0 -e 0.1 -z 500 -p 0.001 -b test_hifiasm_hifiasm_links -v 0 -x 0
LINKS running options:
  -f assembly.fa
  -s readfile.fof
  -d 500,2000,5000
  -k 15
  -j 4
  -t 40,200
  -o 0
  -e 0.1
  -l 5
  -a 0.3
  -z 500
  -b test_hifiasm_hifiasm_links
  -r 
  -p 0.001
  -x 0
  -v 0
STAGE: Bloom filter construction/read
- Number of BF Elements: 178404349
- Input file path: test_hifiasm_hifiasm_links
- Input file: assembly.fa
- kmersize: 15
- m: 2565024136
- fpr: 0.001
- hashFct: 9
- Filter output file : 15
Writing Bloom filter to disk (test_hifiasm_hifiasm_links.bloom)
Bloom filter generated or loaded in: 0h 1m 2s 573ms
STAGE: Reading sequence reads
Reading: test_hifiasm_hifiasm_ont.fastplong.fastq
Processed read count: 100000 - 200000 - 300000 - 400000 - 500000 - 600000 - 700000 - 800000 - 900000 - 1000000 - 1100000 - 1200000 - 1300000 - 1400000 - 1500000 - 1600000 - 1700000 - 1800000 - 1900000 - 2000000 - 2100000 - 2200000 - 2300000 - 2400000 - 2500000 - 26000008:29PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
 - 2700000 - 2800000 - 2900000 - 3000000 - 3100000 - 3200000 - 3300000 - 3400000 - 3500000 - 3600000 - 3700000 - 3800000 - 3900000 - 4000000 - 4089945
Read fasta stage completed in: 0h 5m 30s 204ms
STAGE: Reading contigs
Reading: assembly.fa
Processed read count: 759
8:34PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
make: *** [/usr/local/bin/LINKS-make-real:122: test_hifiasm_hifiasm_links.tigpair_checkpoint.tsv] Killed
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.8TB, min:2.7TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 13657.73MB, drops:0, skip:0, sync:0, req:108
    fu...

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name jovial_ritchie -params-file '<https://api.cloud.seqera.io/ephemeral/_lpQRt0837-icM-tOUcULA.json>' -with-tower -r dev -profile test_full

Sep 10, 2026 at 8:35 PM

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09/11/2026, 2:09 PM

❌ genomeassembler/test_full failed 😿 Run Name small_carlsson Duration 6h 20m 8s Status ❌ Failed Error Message

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Cannot get property 'strategy' on null object

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name small_carlsson -params-file '<https://api.cloud.seqera.io/ephemeral/08oNH5HFdWO4IuyD18U76w.json>' -with-tower -r dev -profile test_full

Sep 11, 2026 at 2:09 PM

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09/11/2026, 4:18 PM

❌ genomeassembler/test_full failed 😿 Run Name small_carlsson_2 Duration 2m 50s Status ❌ Failed Error Message

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SIGTERM

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name small_carlsson_2 -params-file '<https://api.cloud.seqera.io/ephemeral/5JISfqDjq-Ru6ndSvWGFHg.json>' -with-tower -r 7b52eac44b0312bd484b3f684f48f8d50f5becb0 -profile test_full -resume dfbd64fd-c6ce-45fe-899e-1a12382afbc0

Sep 11, 2026 at 4:18 PM

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09/11/2026, 11:20 PM

❌ genomeassembler/test_full failed 😿 Run Name gloomy_fermi Duration 7h 20s Status ❌ Failed Error Message

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Cannot get property 'strategy' on null object

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name gloomy_fermi -params-file '<https://api.cloud.seqera.io/ephemeral/tvppkqtxh509-rpElW2qiw.json>' -with-tower -r 7b52eac44b0312bd484b3f684f48f8d50f5becb0 -profile test_full

Sep 11, 2026 at 11:20 PM

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09/16/2026, 3:57 PM

❌ genomeassembler/test_full failed 😿 Run Name infallible_borg Duration 7h 23m 27s Status ❌ Failed Error Message

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(more omitted..)
[2026-09-16 14:55:46] INFO: Reads N50/N90: 5906 / 1777
[2026-09-16 14:55:46] INFO: Minimum overlap set to 2000
[2026-09-16 14:55:46] INFO: >>>STAGE: assembly
[2026-09-16 14:55:46] INFO: Assembling disjointigs
[2026-09-16 14:55:46] INFO: Reading sequences
2:57PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
[2026-09-16 14:59:02] INFO: Building minimizer index
[2026-09-16 14:59:02] INFO: Pre-calculating index storage
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2026-09-16 14:59:52] INFO: Filling index
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2026-09-16 15:00:37] INFO: Extending reads
[2026-09-16 15:01:23] INFO: Overlap-based coverage: 56
[2026-09-16 15:01:23] INFO: Median overlap divergence: 0.034713
3:02PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:07PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:12PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2026-09-16 15:16:39] INFO: Assembled 17697 disjointigs
[2026-09-16 15:16:47] INFO: Generating sequence
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2026-09-16 15:16:57] INFO: Filtering contained disjointigs
3:17PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:22PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2026-09-16 15:23:05] INFO: Contained seqs: 14134
[2026-09-16 15:23:14] INFO: >>>STAGE: consensus
[2026-09-16 15:23:14] INFO: Running Minimap2
3:27PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:32PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:37PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:42PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:47PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
3:52PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
[202...

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name infallible_borg -params-file '<https://api.cloud.seqera.io/ephemeral/_uWRB1tqbxwQZ65QbMHQag.json>' -with-tower -r 847c832ae9b9fc000e654d70d537bb7b28d73dcc -profile test_full

Sep 16, 2026 at 3:57 PM

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09/17/2026, 3:58 AM

❌ genomeassembler/test_full failed 😿 Run Name infallible_borg_2 Duration 11h 9m 44s Status ❌ Failed Error Message

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3:57AM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
3:57AM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-06cfdd6bf8338a71f instance-type=m6id.8xlarge
3:57AM INF [seqera-fusion] starting incremental snapshot timer interval=300000
Looking to launch executable "/opt/conda/bin/bwa-mem2.avx512bw", simd = .avx512bw
Launching executable "/opt/conda/bin/bwa-mem2.avx512bw"
[bwa_index] Pack FASTA... 1.07 sec
* Entering FMI_search
init ticks = 9614049980
ref seq len = 315317090
binary seq ticks = 6985007334
ref_seq_len = 315317090
build suffix-array ticks = 98823407524
count = 0, 98084247, 157658545, 217232843, 315317090
BWT[42216469] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
/fusion/s3/nf-core-awsmegatests/work/genomeassembler/work-847c832ae9b9fc000e654d70d537bb7b28d73dcc/61/652702e4f08d08bec213ddc3a5325a/.command.sh: line 7:    92 Killed                  bwa-mem2 index -p bwamem2/test_hifiasm_hic_bwamem_index test_hifiasm_hic.fa.gz
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:1.9TB, min:1.9TB, max:1.9TB, end:1.9TB
    clone_namespace: false
    download: 38.02MB, drops:0, skip:0, sync:0, req:1
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 338.31MB, drops:0, skip:0, sync:11, req:13

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name infallible_borg_2 -params-file '<https://api.cloud.seqera.io/ephemeral/YFW1q-UJwOjfLfm7UoQVzA.json>' -with-tower -r 847c832ae9b9fc000e654d70d537bb7b28d73dcc -profile test_full -resume 2b9fbf16-05be-400a-8d6c-74c4185566b5

Sep 17, 2026 at 3:58 AM

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09/17/2026, 6:21 AM

❌ genomeassembler/test_full failed 😿 Run Name infallible_borg_3 Duration 37m 27s Status ❌ Failed Error Message

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6:20AM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
6:20AM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-05bcfbf2ecec05fac instance-type=c6id.8xlarge
6:20AM INF [seqera-fusion] starting incremental snapshot timer interval=300000
Looking to launch executable "/opt/conda/bin/bwa-mem2.avx512bw", simd = .avx512bw
Launching executable "/opt/conda/bin/bwa-mem2.avx512bw"
[bwa_index] Pack FASTA... 1.06 sec
* Entering FMI_search
init ticks = 9651068428
ref seq len = 315317090
binary seq ticks = 6576708296
build suffix-array ticks = 99557304730
ref_seq_len = 315317090
count = 0, 98084247, 157658545, 217232843, 315317090
BWT[42216469] = 4
CP_SHIFT = 6, CP_MASK = 63
sizeof CP_OCC = 64
/fusion/s3/nf-core-awsmegatests/work/genomeassembler/work-847c832ae9b9fc000e654d70d537bb7b28d73dcc/82/af7cfb82430e3359ea4d2bac78cae1/.command.sh: line 7:    92 Killed                  bwa-mem2 index -p bwamem2/test_hifiasm_hic_bwamem_index test_hifiasm_hic.fa.gz
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:1.9TB, min:1.9TB, max:1.9TB, end:1.9TB
    clone_namespace: false
    download: 38.02MB, drops:0, skip:0, sync:0, req:1
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 338.31MB, drops:0, skip:0, sync:11, req:13

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name infallible_borg_3 -params-file '<https://api.cloud.seqera.io/ephemeral/kHTqMes5CYnJhAsmwgYziQ.json>' -with-tower -r 847c832ae9b9fc000e654d70d537bb7b28d73dcc -profile test_full -resume 2b9fbf16-05be-400a-8d6c-74c4185566b5

Sep 17, 2026 at 6:21 AM

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09/18/2026, 3:48 AM

✅ genomeassembler/test_full completed successfully! 🎉 Run Name distracted_bernard Duration 17h 48m 28s Status ✅ Success Tasks Completed: 464, Failed: 5 Sep 18, 2026 at 3:48 AM

beer parrot 3

Niklas Schandry

09/18/2026, 9:02 AM

alert v2.0.0 is out zenodo.org/records/22827182

🎉 2

Jim Downie

09/18/2026, 9:04 AM

Congratulations @Niklas Schandry!!!

Niklas Schandry

09/18/2026, 9:08 AM

Thanks! Also thanks back to your for your constructive reviews @Jim Downie!!

❤️ 1

Niklas Schandry

09/18/2026, 9:11 AM

And also thanks to @Daniel Lundin whos reviews helped a lot for this release

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09/18/2026, 2:58 PM

❌ genomeassembler/test_full failed 😿 Run Name ridiculous_fermat Duration 0ms Status ❌ Failed Failed Process

NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:SCAFFOLD:RUN_LINKS:LINKS

Error Message

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Unknown error

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name ridiculous_fermat -params-file '<https://api.cloud.seqera.io/ephemeral/iA-NOm4x1bI8X8_pgOBdPA.json>' -with-tower -r a72d47d9cdb50f21b97882dfb2abf4af8f4c74ad -profile test_full

Sep 18, 2026 at 2:58 PM

Niklas Schandry

09/19/2026, 1:14 PM

Maybe i just deprecate links

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10/08/2026, 9:13 AM

❌ genomeassembler/test_full failed 😿 Run Name admiring_jones Duration 44.8s Status ❌ Failed Error Message

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Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/genomeassembler>, projectDir: /.nextflow/assets/.repos/nf-core/genomeassembler/clones/ba8f911a17246bd2299bd49f0cf33ade11406c4a, commitId: ba8f911a17246bd2299bd49f0cf33ade11406c4a, revision: dev, startTime: 2026-10-08T09:13:07.535989510Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/genomeassembler>' -name admiring_jones -params-file '<https://api.cloud.seqera.io/ephemeral/MqnlRLQUtts-0lJfsvTemA.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$Preview@3503e68e, enable:nextflow.NextflowMeta$Features@7c2d4398, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/genomeassembler/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name admiring_jones -params-file '<https://api.cloud.seqera.io/ephemeral/MqnlRLQUtts-0lJfsvTemA.json>' -with-tower -r dev -profile test_full

Oct 8, 2026 at 9:13 AM

Thomas Weber

10/15/2026, 7:38 PM

depictio Depictio dashboard for genomeassembler: feedback wanted Depictio (open source, from EMBL) turns the output of a workflow run into an interactive dashboard you can share, so nobody has to write a Shiny or Streamlit app for each project. Point a template at any run of a pipeline and you get the same dashboard, which you can edit (UI & YAML), version and comment. 🧩 The genomeassembler dashboard template (no account needed) shows the best assembly, what each polishing and scaffolding stage adds, and contiguity (N50), k-mer accuracy and gene completeness (BUSCO). 🙌 We need your help! Feedback and ideas welcome in #C0AFS06G9HR (all templates and details there) or in the genomeassembler GitHub discussion.

magic 1

🎉 1

Full test notifications

10/23/2026, 3:51 PM

❌ genomeassembler/test_full failed 😿 Run Name lonely_goodall Duration 46.5s Status ❌ Failed Error Message

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Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/genomeassembler>, projectDir: /.nextflow/assets/.repos/nf-core/genomeassembler/clones/6811ea18853d8d051c361ebb491b5d837d80281a, commitId: 6811ea18853d8d051c361ebb491b5d837d80281a, revision: dev, startTime: 2026-10-23T15:50:44.840499611Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/genomeassembler>' -name lonely_goodall -params-file '<https://api.cloud.seqera.io/ephemeral/R5s21SLT3Y_UgB_JGAQ7_A.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.7, build:13988, timestamp:08-10-2026 16:23 UTC, preview:nextflow.NextflowMeta$Preview@551fefe8, enable:nextflow.NextflowMeta$Features@6affa355, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/genomeassembler/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name lonely_goodall -params-file '<https://api.cloud.seqera.io/ephemeral/R5s21SLT3Y_UgB_JGAQ7_A.json>' -with-tower -r dev -profile test_full

Oct 23, 2026 at 3:51 PM

confused dog 1

Full test notifications

10/23/2026, 5:06 PM

❌ genomeassembler/test_full failed 😿 Run Name ecstatic_wozniak Duration 49s Status ❌ Failed Error Message

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Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/genomeassembler>, projectDir: /.nextflow/assets/.repos/nf-core/genomeassembler/clones/c608622876dc627020e6627a5ea8cffd0d2e3f3d, commitId: c608622876dc627020e6627a5ea8cffd0d2e3f3d, revision: 2.0.1, startTime: 2026-10-23T17:05:13.997038013Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/genomeassembler>' -name ecstatic_wozniak -params-file '<https://api.cloud.seqera.io/ephemeral/SpWxbRDfgoQmXZzki4GCyQ.json>' -with-tower -r c608622876dc627020e6627a5ea8cffd0d2e3f3d -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.7, build:13988, timestamp:08-10-2026 16:23 UTC, preview:nextflow.NextflowMeta$Preview@7a3c541e, enable:nextflow.NextflowMeta$Features@2be89ba5, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/genomeassembler/work-c608622876dc627020e6627a5ea8cffd0d2e3f3d, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

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nextflow run '<https://github.com/nf-core/genomeassembler>' -name ecstatic_wozniak -params-file '<https://api.cloud.seqera.io/ephemeral/SpWxbRDfgoQmXZzki4GCyQ.json>' -with-tower -r c608622876dc627020e6627a5ea8cffd0d2e3f3d -profile test_full

Oct 23, 2026 at 5:06 PM

Rike Hanssen

10/23/2026, 7:40 PM

@Niklas Schandry if you update the full size yml with this: github.com/nf-core/tools/pull/4501/changes it should get passed the error or merge in the template update

👍 1