nf-core #rnavar

Eric Samorodnitsky

08/14/2025, 3:50 PM

Hi, small issue I found. On the https://nf-co.re/pipelines/, the link to rnavar is for 1.1.0, but the latest stable release is 1.1.1. Can you guys fix the link?

Rike Hanssen

08/22/2025, 1:10 PM

This one is ready for review: https://github.com/nf-core/rnavar/pull/225

✅ 1

Giovanni Asole

08/25/2025, 5:19 PM

Hi all. Thanks a lot for developing and maintaining the pipeline! I would like to perform the alignment using the GATK.GRCh38 reference genome to maintain consistency with the subsequent variant calling step and improving alignment accuracy for variant calling (as it include extra decoy and ALT contigs). Does it make sense to use this specific genome for RNA-seq alignment? If so, where can I find a suitable GTF compatible with the GATK.GRCh38 reference, considering the added contigs? I've checked the GATK resource bundle, but it doesn't seem to include any annotation file. I'm concerned that a standard GTF from sources like GENCODE might not fully account for the extra contigs, potentially causing issues. Thanks in advance!

🎉 1

Maxime Garcia

08/27/2025, 8:19 AM

https://github.com/nf-core/rnavar/releases/tag/1.2.0 has been released: • it contains a couple of fixes in the schema thanks to @Rike Hanssen • the proper inclusion of bcftools_annotate (stolen from #CGFUX04HZ) - (thanks to @Kübra Narcı for noticing an issue in the previous release that pushed me to fix this upstream in both #CGFUX04HZ and #C01NHS4CC91 and include it properly here in #C01NHS4CC91 finally) • some #CFVDZCA23 possibilities thanks to @Rike Hanssen • minor refactoring from me and trying to make the code compliant with the coming

nextflow lint

keanu thanks 1

🎉 3

❤️ 1

Aqib Hasnain

09/01/2025, 8:21 PM

I'm using the example samplesheet from the docs and getting this issue if anyone can help resolve this:

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╰─ nextflow run nf-core/rnavar --input samplesheet.csv --genome GRCh38 -profile docker

Nextflow 25.04.6 is available - Please consider updating your version to it

 N E X T F L O W  ~ version 24.10.5

Pulling nf-core/rnavar ...
 downloaded from <https://github.com/nf-core/rnavar.git>
Launching `<https://github.com/nf-core/rnavar>` [zen_edison] DSL2 - revision: 0a9036c82b [master]

Downloading plugin nf-schema@2.4.2
ERROR ~ Module compilation error
- file : /Users/aqib/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf
- cause: Variable `Channel` already defined in the process scope @ line 129, column 31.
    def umi_extracted_reads = Channel.empty()
                 ^

Module compilation error
- file : /Users/aqib/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf
- cause: Variable `Channel` already defined in the process scope @ line 148, column 31.
    def interval_list_split = Channel.empty()
                 ^

Module compilation error
- file : /Users/aqib/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf
- cause: Variable `Channel` already defined in the process scope @ line 224, column 35.
      def bam_variant_calling = Channel.empty()
                   ^

Module compilation error
- file : /Users/aqib/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf
- cause: Variable `Channel` already defined in the process scope @ line 321, column 35.
      def haplotypecaller_vcf = Channel.empty()
                   ^

Module compilation error
- file : /Users/aqib/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf
- cause: Variable `Channel` already defined in the process scope @ line 343, column 29.
        def final_vcf = Channel.empty()
                ^

5 errors

👀 1

Giovanni Asole

09/09/2025, 1:06 PM

Hello all! I have a technical question related to RNA-seq variant calling using STAR and mutect2 or Haplotypecaller. Considering that mutect2 filter by default reads with a MAPQ < 20, and STAR multimapped reads have always a MAPQ < 20 (due to the used formula

int(-10 * log10(1 - 1/NH))

). Should not be better to set the

--outFilterMultimapNmax 1

to avoid saving multimapped reads that will never be used by mutect2? It will be useful to save memory and reducing storage cost. Is there any contraindication that I am not considering?

Yeahji

09/10/2025, 11:40 AM

Hi I have been running rnavar on 480 samples and it doesn't work after couple of sample ran bc all the files saved in work folder use more quota than I have so my job get halted Has anyone had same issues ? Do you remove everything in work in between the batches of samples ?

Marcel Costa-Garcia

09/17/2025, 2:37 PM

Hi! Thanks for your work 😃. I am using rnavar pipeline and, although it runs without error it doesn't really complete, skipping from variant calling steps. This is the final output:

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executor >  slurm (49)
[-        ] NFC…REPARE_GENOME:GUNZIP_FASTA -
[a9/003b82] NFC…ENCEDICTIONARY (genome.fa) | 1 of 1 ✔
[-        ] NFC…:PREPARE_GENOME:GUNZIP_GTF -
[-        ] NFC…VAR:PREPARE_GENOME:GFFREAD -
[23/5160aa] NFC…GENOME:GTF2BED (genes.gtf) | 1 of 1 ✔
[57/87e840] NFC…VE_UNKNOWN_REGIONS (genes) | 1 of 1 ✔
[-        ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[-        ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[-        ] NFC…RE_GENOME:BGZIPTABIX_DBSNP -
[-        ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[-        ] NFC…ME:BGZIPTABIX_KNOWN_INDELS -
[-        ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[0c/054db4] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔
[-        ] NFC…NAVAR:PREPARE_GENOME:UNTAR -
[29/20321c] NFC…E_GENOME:STAR_INDEXVERSION | 1 of 1 ✔
[a9/fcd636] NFC…GENOMEGENERATE (genome.fa) | 1 of 1 ✔
[-        ] NFC…E_ALIGNMENT:SAMTOOLS_INDEX -
[7c/161c80] NFC…R:RNAVAR:CAT_FASTQ (CMT64) | 1 of 1 ✔
[b3/c79108] NFC…AVAR:RNAVAR:FASTQC (CMT64) | 1 of 1 ✔
[ac/a595ca] NFC…_BEDTOINTERVALLIST (genes) | 1 of 1 ✔
[78/46550e] NFC…_INTERVALLISTTOOLS (genes) | 1 of 1 ✔
[06/1a2bae] NFC…GN_STAR:STAR_ALIGN (CMT64) | 1 of 1 ✔
[63/9df02c] NFC…NOME:SAMTOOLS_SORT (CMT64) | 1 of 1 ✔
[ca/480c41] NFC…OME:SAMTOOLS_INDEX (CMT64) | 1 of 1 ✔
[10/18bf53] NFC…OLS:SAMTOOLS_STATS (CMT64) | 1 of 1 ✔
[a1/54ba4a] NFC…:SAMTOOLS_FLAGSTAT (CMT64) | 1 of 1 ✔
[05/2368ce] NFC…:SAMTOOLS_IDXSTATS (CMT64) | 1 of 1 ✔
[69/031cf5] NFC…ARD_MARKDUPLICATES (CMT64) | 1 of 1 ✔
[27/b87ea8] NFC…ARD:SAMTOOLS_INDEX (CMT64) | 1 of 1 ✔
[60/d4cae1] NFC…OLS:SAMTOOLS_STATS (CMT64) | 1 of 1 ✔
[75/d3e06e] NFC…:SAMTOOLS_FLAGSTAT (CMT64) | 1 of 1 ✔
[19/1e4100] NFC…:SAMTOOLS_IDXSTATS (CMT64) | 1 of 1 ✔
[40/be5ce7] NFC…RREADS (CMT64_19scattered) | 25 of 25 ✔
[95/f2cacb] NFC…GAR:SAMTOOLS_MERGE (CMT64) | 1 of 1 ✔
[01/f32579] NFC…GAR:SAMTOOLS_INDEX (CMT64) | 1 of 1 ✔
[2c/19f9d3] MULTIQC                        | 1 of 1 ✔
Plus 9 more processes waiting for tasks…
-[nf-core/rnavar] Pipeline completed successfully-
Completed at: 10-Sep-2025 18:54:20
Duration    : 2h 13m 29s
CPU hours   : 18.9
Succeeded   : 49

Cris Tuñí

09/25/2025, 2:10 PM

Hi all! We recently ran a small experiment comparing variant calls across different nf-core pipelines and mappers using the same sample. Specifically: • nf-core/sarek (germline workflow, BWAMEM2 mapper) • nf-core/rnavar (STAR mapper) Both were run with HaplotypeCaller followed by SnpEff annotation. Surprisingly, we observed substantial differences in the number of variants identified between the two approaches. nf-sarek identified 871553 variants, whereas nf-rnavar identified 22407 variants. Has anyone seen similar behavior before, or do you have ideas on why such discrepancies might arise? We’d really appreciate insights on potential sources of divergence. Thanks a lot in advance!

Charlotte Stubbe

09/30/2025, 12:13 PM

Hi! Thanks for the pipeline! I was wondering if there would be a possibility to adapt this pipeline or add extra steps for somatic variant calling in tumour only rna data? Thank you! Kind regards Charlotte

👀 1

Alice Massacci

10/20/2025, 7:39 AM

Hi everyone, thanks for the great work on this pipeline. I’d like to perform somatic variant calling with GATK Mutect2 using the BAM files after Base Quality Score Recalibration. However, it seems that these recalibrated BAM files are not saved among the final outputs of the pipeline. Is there currently a way to either: Save the recalibrated BAMs produced after ApplyBQSR, or Access them from within the workflow (e.g., via a specific channel or parameter), so they can be reused for downstream analyses such as Mutect2? Thanks a lot for your help!

Rike Hanssen

10/20/2025, 8:56 AM

I think there is still a bug about dbsnp and known_indels. I specified

dbsnp

, but not

known_indels

and I am getting:

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A USER ERROR has occurred: Argument known-sites was missing: Argument 'known-sites' is required


Command executed:

  gatk --java-options "-Xmx9830M -XX:-UsePerfData" \
      BaseRecalibrator  \
      --input in.bam \
      --output out.table \
      --reference Homo_sapiens.fa \
      --intervals Homo_sapiens.interval_list \
       \
      --tmp-dir . \
      --use-original-qualities

I am using 1.2.1

👀 1

Aqib Hasnain

11/05/2025, 2:35 AM

Hi! I ran this pipeline for the first time today and the outputs don't have any variant info in it. Attaching two images 1) showing the set of tasks that were run successfully and 2) showing the output directories. What should I change to get variant info out? I called the pipeline with very minimal parameters set so mainly defaults are being used

Júlia Mir

11/19/2025, 4:05 PM

Hello, I have triggered a template sync PR to this pipeline, if someone is available could you try to resolve possible conflicts and do the template update to report any possible difficulty you may find?

✅ 1

Luca

12/01/2025, 10:05 AM

Dear all, the pipeline results as complete but I cannot find the snpeff output, is this problem common ? Basically the last output produced is the variant_calling original and filtered. I post the last 7 lines of the log

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-[nf-core/rnavar] Pipeline completed successfully-
Completed at: 29-Nov-2025 05:47:16
Duration    : 10h 38m 48s
CPU hours   : 73.3 (0.4% failed)
Succeeded   : 77
Failed      : 1

Maxime Garcia

12/05/2025, 10:22 AM

New release is out 🎄: https://github.com/nf-core/rnavar/releases/tag/1.2.2 Important: • Fixing an issue with known_indels and dbsnp params that were badly passed to GATK BaseRecalibrator 🧰 Lots of tools were updated • bcftools from

1.21

1.22

• ensembl-vep from

115.1

115.2

• gatk4 from

4.6.1.0

4.6.2.0

• htslib from

1.21

1.22.1

• multiqc from

1.30

1.31

• picard from

3.3.0

3.4.0

• samtools from

1.21

1.22.1

• snpeff from

5.1d

5.3.0a

• umi_tools from

1.1.5

1.1.6

alert SNPEFF alert snpeff default cache version is now 99 since the change of storage this summer. Please check the documentation for more info on how to set it up 📚 https://nf-co.re/rnavar/dev/docs/usage/#what-happened-with-snpeff-db-105 cattyping From the developers front: Pipeline now use TEMPLATE from the nf-core/tools v3.5.1 Nextflow plugins have been updated: • nf-core-schema from

2.4.2

2.6.1

• nf-core-utils was added with

0.4.0

Minimal Nextflow version is now

25.10.2

, and we're working on converting the pipeline to the coming strict syntax and all the Nextflow new features 🚀

woohoo 5

Luca

12/09/2025, 11:17 AM

Dear all, one question: how is it possible to integrate the argument

-fastaProt z.prot.fa

when running snpeff within the command? Thanks! here my command:

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LOGFILE="/data/myname/projects/rnavar_test/logs/rnavar_run_$(date +%Y%m%d_%H%M%S).log"

nextflow run nf-core/rnavar \
  -profile singularity \
  -resume \
  -c /data/myname/bins/custom.config3 \
  --input /data/myname/projects/rnavar_test/samplesheet_test.csv \
  --outdir /data/myname/projects/rnavar_test/results_test \
  --genome Olea_europaea \
  --skip_baserecalibration \
  --tools snpeff \
  &> "$LOGFILE"

here my config:

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process {
  // Shell robusta
  shell = 'bash -euo pipefail'

  // Risorse di default
  cpus = 8
  memory = '28 GB'
  beforeScript = 'chmod +x .command.run || true'

  // Profili per label
  withLabel: process_low {
    cpus = 4
    memory = '8 GB'
  }

  withLabel: process_medium {
    cpus = 6
    memory = '16 GB'
  }

  withLabel: process_high {
    cpus = 8
    memory = '28 GB'
  }

  withLabel: process_long {
    cpus = 8
    memory = '28 GB'
  }

  // ⚙️ Processo STAR genomeGenerate → alto uso di RAM
  withName: 'NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE' {
    cpus = 8
    memory = '28 GB'
  }

  // ⚙️ Processo fastp + umi-tools → medio uso di RAM
  withName: 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
    cpus = 6
    memory = '16 GB'
  }

  // 🧪 PATCH: usa container aggiornato per snpEff
  withName: SNPEFF_SNPEFF {
    container = '<https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/37/37a5be8afdc2e112fd1bb4aa226e009a437e6537f50a51ed909fe2018fd62e99/data>'
  }
}

executor {
  queueSize = 2
  maxForks = 2
}

params {
  genome = 'Olea_europaea'
  params.snpeff_db         = 'Olea_europaea'
  params.snpeff_cache      = '/data/myname/bins/snpEff/data'  

  genomes {
    'Olea_europaea' {
      fasta      = '/data/myname/refs/genomes/Olea_europaea/Olea_europaea.OLEA9.dna.toplevel.fa'
      gtf        = '/data/myname/refs/genomes/Olea_europaea/Olea_europaea.OLEA9.62.gtf'
      star_index = '/data/myname/refs/STAR/Olea_europaea'
    }
  }
}

👀 1

Mylena Santander

12/17/2025, 2:35 PM

Hi all! thank you for developing this pipeline, it has been very useful. I was wondering if there is a way to get a a mergerd vcf of all samples. I know it is a very simple action to perform with bcftools, but as filtered outputs are vcf and not gvcf, then reference calls will appear as "./.". Maybe there is a way to merge gvcf before and then to apply the filters. Have you thought about that?

Maxime Garcia

02/10/2026, 1:24 PM

<!here> new release is out: https://github.com/nf-core/rnavar/releases/tag/1.2.3 • Minor code refactoring • Topic versions everywhere • Nextflow strict syntax everywhere • workflow output conversion started • minor bugfixes Please shout out if you encounter any issues

🎉 3

Ben Fixman

03/29/2026, 7:43 PM

Hi, I've been running a few other nf-core pipelines using Nextflow version 25.04.8, but I am having some trouble running even the test profile of rnavar. Does it require a newer version of Nextflow? Thanks. Here is the error I am running into: N E X T F L O W ~ version 25.04.8 Launching

<https://github.com/nf-core/rnavar>

[scruffy_goldberg] DSL2 - revision: 9db0282668 [master] Downloading plugin nf-core-utils@0.4.0 ERROR ~ Plugin nf-core-utils with version @0.4.0 does not exist in the repository

Full test notifications

05/27/2026, 2:24 PM

❌ rnavar/test_full failed 😿 Run Name agitated_fermat Duration 19.8s Status ❌ Failed Error Message

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Known sites are required for performing base recalibration. Supply them with either --dbsnp and/or --known_indels or disable base recalibration with --skip_baserecalibration

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name agitated_fermat -params-file '<https://api.cloud.seqera.io/ephemeral/jUcKDiBW79yQyc7oKTfF2A.json>' -with-tower -r 3cc083d337d2c72fe803018c63aa41b807854122 -profile test_full

May 27, 2026 at 2:24 PM

screams 1

shakefist 1

🚫 2

Full test notifications

06/01/2026, 7:50 PM

✅ rnavar/test_full completed successfully! 🎉 Run Name sad_ampere Duration 3h 52m 44s Status ✅ Success Tasks Completed: 553 Jun 1, 2026 at 7:50 PM

extreme teamwork 1

Full test notifications

06/02/2026, 1:25 PM

❌ rnavar/test_full failed 😿 Run Name evil_hamilton Duration 13m 3s Status ❌ Failed Error Message

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1:24PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
1:24PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-03df7359adc64e2ba instance-type=c6id.32xlarge
1:24PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
FUSION_GPU_USED=false
1:25PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: 81GB79G2P05KF9VH, HostID: lkH62NxACJkrAujwHwvyu8AEVD56IQqd9WZEKySc8VfFfEtTL7dVkcepgK98TfYJFHnKkiSSJf6NN/GYIBdQ14KM+uTONx3u, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=37212 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/1d/e720d272d02d093ee5196444262ba8/K562_REP1_1.merged.fastq.gz length=6710886400 offset=0
1:25PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=37213 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/1d/e720d272d02d093ee5196444262ba8/K562_REP1_1.merged.fastq.gz.d8fdj14sf1os761fige0.6710886400.d8fdiu4sf1os761fieog.chk length=134217728 offset=0
1:25PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=37216 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/1d/e720d272d02d093ee5196444262ba8/K562_REP1_1.merged.fastq.gz.d8fdj1ssf1os761figh0.7113539584.d8fdiu4sf1os761fieog.chk length=134217728 offset=0
1:25PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=37215 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/1d/e720d272d02d093ee5196444262ba8/K562_REP1_1.merged.fastq.gz.d8fdj1ksf1os761figg0.6979321856.d8fdiu4sf1os761fieog.chk ...

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name evil_hamilton -params-file '<https://api.cloud.seqera.io/ephemeral/O4KrNwT8MYzCOtK1cKzQMg.json>' -with-tower -r dev -profile test_full

Jun 2, 2026 at 1:25 PM

🫠 1

Full test notifications

06/02/2026, 1:55 PM

❌ rnavar/test_full failed 😿 Run Name stoic_dubinsky Duration 8m 36s Status ❌ Failed Error Message

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1:53PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
1:53PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0a6be31d7fe8eea4c instance-type=c6id.2xlarge
1:53PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
FUSION_GPU_USED=false
1:54PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: H2M58YMR98N0V0X3, HostID: qGx/2jv9fzRDdu65JgvKn3Jk0wJs6ymBKWscIlImKmCWjkP/INi5ivcLMmumMn6xmgwWfqzXXHwXfcv55QOIoq3B4aaQmzim, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=34467 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/5b/4d86622d4e1c63d44ca00e8163338c/GM12878_REP2_1.merged.fastq.gz length=7247757312 offset=0
1:54PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=34471 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/5b/4d86622d4e1c63d44ca00e8163338c/GM12878_REP2_1.merged.fastq.gz.d8fe0u64pm9s7691m290.7650410496.d8fe0rm4pm9s7691m0s0.chk length=57636110 offset=0
1:54PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=34468 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/5b/4d86622d4e1c63d44ca00e8163338c/GM12878_REP2_1.merged.fastq.gz.d8fe0tu4pm9s7691m27g.7247757312.d8fe0rm4pm9s7691m0s0.chk length=134217728 offset=0
1:54PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=34469 id=/s3/nf-core-awsmegatests/work/rnavar/work-dev/5b/4d86622d4e1c63d44ca00e8163338c/GM12878_REP2_1.merged.fastq.gz.d8fe0u64pm9s7691m280.7381975040.d8fe0rm4pm9s769...

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name stoic_dubinsky -params-file '<https://api.cloud.seqera.io/ephemeral/i8QGA1fBXd_gMikLONykvA.json>' -with-tower -r dev -profile test_full

Jun 2, 2026 at 1:55 PM

Maxime Garcia

06/03/2026, 11:16 AM

We have a new release: https://github.com/nf-core/rnavar/releases/tag/1.3.0 Hopefully that should solve the lastest issues. Please let me know if you encounter any bugs, I will continue working on it as I make my way into more improvements in the other pipelines I work on

Full test notifications

06/03/2026, 11:51 AM

❌ rnavar/test_full failed 😿 Run Name gigantic_plateau Duration 2h 13m 23s Status ❌ Failed Error Message

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11:34AM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
11:34AM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-09baed2ec8e22125d instance-type=c6id.32xlarge
11:34AM INF [seqera-fusion] starting incremental snapshot timer interval=300000
11:39AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
11:44AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
11:49AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
11:50AM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: 7HAFESYY4SB7NVEM, HostID: obYBEUuwCKeeKiuLEdSuBSt+0cM1OuRC8yUrA4TlCK5/w7L6y8lGjJ1ERLZq/ES9Qgh9k/ZQOEf5CnKDsMAK7aBpRTWachLs, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=240374 id=/s3/nf-core-awsmegatests/work/rnavar/work-59e2f912b1f6aeca44450a8f8f030e7fedc84028/9c/81c00c26e56a85211e971cc2a003a8/GM12878_REP1.md.bam length=9663676416 offset=0
11:50AM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=240385 id=/s3/nf-core-awsmegatests/work/rnavar/work-59e2f912b1f6aeca44450a8f8f030e7fedc84028/9c/81c00c26e56a85211e971cc2a003a8/GM12878_REP1.md.bam.d8g15ap1u1ds7667rmug.11005853696.d8g12f91u1ds7667rbt0.chk length=134217728 offset=0
11:50AM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=240377 id=/s3/nf-core-awsmegatests/work/rnavar/work-59e2f912b1f6aeca44450a8f8f030e7fedc84028/9c/81c00c26e56a85211e971cc2a003a8/GM12878_REP1.md.bam.d8g13r91u1ds7667rl90.9932111872.d8g12f91u1ds7667rbt0.chk length=134217728 offset=0
11:50AM ERR [seqera-fusion] cannot upload...

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name gigantic_plateau -params-file '<https://api.cloud.seqera.io/ephemeral/MtyXqIfr635sjzaEa3S1FA.json>' -with-tower -r 59e2f912b1f6aeca44450a8f8f030e7fedc84028 -profile test_full

Jun 3, 2026 at 11:51 AM

🚫 1

Full test notifications

06/03/2026, 1:11 PM

❌ rnavar/test_full failed 😿 Run Name cranky_banach Duration 1h 54m 39s Status ❌ Failed Error Message

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12:52PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
12:52PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0cee36be726bf1de3 instance-type=c6id.24xlarge
12:52PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
12:57PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
1:02PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
1:07PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
1:11PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: BBCGSPKTWK1WJY35, HostID: 3Dp5b8rBy5DZ9896XIlx655nfJFx5/2ZAu5BLVIpjzk3Sy1El7vCQyirx+H2tQlj0mj9szO44D4=, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=264744 id=/s3/nf-core-awsmegatests/work/rnavar/work-a0e4641409eb7aed4b325e543d20577f9c08e437/85/61f4c70d70ee37e5459383dcbe0814/H1_REP2.md.bam length=6845104128 offset=0
1:11PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=264749 id=/s3/nf-core-awsmegatests/work/rnavar/work-a0e4641409eb7aed4b325e543d20577f9c08e437/85/61f4c70d70ee37e5459383dcbe0814/H1_REP2.md.bam.d8g293hrlhnc75pk5bhg.7381975040.d8g2771rlhnc75pk52rg.chk length=134217728 offset=0
1:11PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=264757 id=/s3/nf-core-awsmegatests/work/rnavar/work-a0e4641409eb7aed4b325e543d20577f9c08e437/85/61f4c70d70ee37e5459383dcbe0814/H1_REP2.md.bam.d8g2aahrlhnc75pk5fbg.8455716864.d8g2771rlhnc75pk52rg.chk length=134217728 offset=0
1:11PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: Uplo...

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name cranky_banach -params-file '<https://api.cloud.seqera.io/ephemeral/wtYRYkmZUFdjvum-Ze1Ccg.json>' -with-tower -r a0e4641409eb7aed4b325e543d20577f9c08e437 -profile test_full

Jun 3, 2026 at 1:11 PM

🚫 1

Full test notifications

06/08/2026, 12:40 PM

❌ rnavar/test_full failed 😿 Run Name cranky_banach_2 Duration 1h 3m 9s Status ❌ Failed Error Message

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12:32PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
12:32PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0fc0777c66c2e4720 instance-type=c6id.8xlarge
12:32PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
12:37PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
12:39PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: CBC53A3J432Y5TDM, HostID: AHjISuX5cbr1wH/C40V+wX8/J+whLZoTceYAD/znPtoVxCn7hI5v8xTDQw0b7oWUv3NACyqo9Zw=, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=129836 id=/s3/nf-core-awsmegatests/work/rnavar/work-a0e4641409eb7aed4b325e543d20577f9c08e437/90/d9a2b93b53f08f3f86ae25692df9c9/H1_REP1.md.bam length=13421772800 offset=0
12:39PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=129868 id=/s3/nf-core-awsmegatests/work/rnavar/work-a0e4641409eb7aed4b325e543d20577f9c08e437/90/d9a2b93b53f08f3f86ae25692df9c9/H1_REP1.md.bam.d8jbfv007fsc75c5so9g.15435038720.d8jbcso07fsc75c5sfbg.chk length=28295377 offset=0
12:39PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=129837 id=/s3/nf-core-awsmegatests/work/rnavar/work-a0e4641409eb7aed4b325e543d20577f9c08e437/90/d9a2b93b53f08f3f86ae25692df9c9/H1_REP1.md.bam.d8jbdqo07fsc75c5sll0.13421772800.d8jbcso07fsc75c5sfbg.chk length=134217728 offset=0
12:39PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=129867 id=/s3/nf-core-awsmegatests/wo...

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name cranky_banach_2 -params-file '<https://api.cloud.seqera.io/ephemeral/bdw0NyTpSxGzeqtreVgP_A.json>' -with-tower -r a0e4641409eb7aed4b325e543d20577f9c08e437 -profile test_full -resume 3aabc7d0-6bcf-4401-926f-b0c965a5289d

Jun 8, 2026 at 12:40 PM

Mariachiara Grieco

06/08/2026, 3:32 PM

Hi all, I'm interesting in performing variant calling using only RNA-seq data (without matched normal neither matched WES/WGS). With this pipeline, germline mutations are identified. Has anyone ever tried to extend the workflow to also include somatic mutations? Thanks in advance

Full test notifications

06/15/2026, 1:12 PM

❌ rnavar/test_full failed 😿 Run Name cranky_banach_3 Duration 26m 5s Status ❌ Failed Error Message

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download failed: <s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370491_T1_2.fastq.gz> to input2/SRX2370491_T1_2.fastq.gz [Errno 28] No space left on device
download failed: <s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370491_T1_1.fastq.gz> to input1/SRX2370491_T1_1.fastq.gz [Errno 28] No space left on device

Command Line

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nextflow run '<https://github.com/nf-core/rnavar>' -name cranky_banach_3 -params-file '<https://api.cloud.seqera.io/ephemeral/FjiZQVaUcW72qwFbfaCb-g.json>' -with-tower -r a0e4641409eb7aed4b325e543d20577f9c08e437 -profile test_full -resume 3aabc7d0-6bcf-4401-926f-b0c965a5289d

Jun 15, 2026 at 1:12 PM

🫠 1