I am running the pipeline in a Slurm cluster and I have skipped this germlinecnvcaller, but I am still asked for the parameters.

code
nextflow run nf-core/raredisease --skip_tools gens,germlinecnvcaller  -revision  2.5.0 -params-file params.yaml

 N E X T F L O W   ~  version 24.10.6

Launching `<https://github.com/nf-core/raredisease>` [serene_heyrovsky] DSL2 - revision: 46afe31a36 [2.5.0]

params.ploidy_model not set.
params.gcnvcaller_model not set.
params.readcount_intervals not set.

Hello, I am running the 2.4 version of the pipeline and I was wondering if someone could help me with a parameter. I want to do ME calling and annotation but I am using grch38 and I am not sure where to get the appropriate files. The TSV listed in the example has 4 separate bed files for grch37 but it doesn't really give details on what I need for grch38 or where I could find those files.

I’ve tried to run nf-core/raredisease pipeline.. I got error : “vcfanno.go116 found 7 sources from 3 files vcfanno.go157 falling back to non-bgzip” And after that pipeline didn’t make index file Has anyone experienced a similar error?

Hello everyone! Im trying to run the pipeline with

nextflow run nf-core/raredisease \
    -profile docker \
    --input ../extra/PRJNA1077459_sheet.csv \
    --outdir ../nfcore_raredisease_results \
    --genome GRCh38 \
    --save_reference \
    --analysis_type wes \
    -resume \
&& echo -e "pipeline executed successfully"

but i got the error

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter(s): intervals_wgs, intervals_y, fasta

what im missing? Its supposed that the parameter --genome GRCh38 downloads all the required files but it is not doing it

Can someone help me understand the vep_plugin_files parameter? I am confused on exactly what I am suppose to provide. I have the plugins installed in the same directory as the vep_cache. I am not sure what databases or tools to use for the recommended plugins: LofTool, pLI,SpliceAI, and MaxentScan

Hey, just discovered this reddit thread that could use some assistance from the #C025UH66DA8 maintainer side

I was running the pipeline with multiple samples and recently got this error for this specific sample other samples run fine. Is it possible to skip haplogrep3 for a specific sample. Moreover would there be a patch for this specific error for some samples where the coverage is apparently very low?

Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (case_KiGS23)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (case_KiGS23)` terminated with an error exit status (1)


Command executed:

  haplogrep3 \
      classify \
      --tree phylotree-rsrs@17.1 \
      --in case_KiGS23_mitochondria_hmtnote_vcfanno.vcf.gz \
      --out case_KiGS23_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT":
      haplogrep3: $(echo $(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
  END_VERSIONS

Command exit status:
  1

Command output:
  
  Haplogrep 3 3.2.2
  (c) 2022-2024 Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer
  Error: For input string: "."

Command error:
  java.lang.NumberFormatException: For input string: "."
      at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
      at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
      at java.base/java.lang.Double.parseDouble(Double.java:944)
      at java.base/java.lang.Double.valueOf(Double.java:906)
      at importer.VcfImporter.load(VcfImporter.java:209)
      at genepi.haplogrep3.haplogrep.io.readers.impl.VcfInputFileReader.read(VcfInputFileReader.java:39)
      at genepi.haplogrep3.haplogrep.io.readers.InputFileReaderFactory.read(InputFileReaderFactory.java:33)
      at genepi.haplogrep3.tasks.ClassificationTask.run(ClassificationTask.java:90)
      at genepi.haplogrep3.commands.ClassifyCommand.call(ClassifyCommand.java:96)
      at genepi.haplogrep3.commands.ClassifyCommand.call(ClassifyCommand.java:22)
      at picocli.CommandLine.executeUserObject(CommandLine.java:1783)
      at picocli.CommandLine.access$900(CommandLine.java:145)
      at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2150)
      at picocli.CommandLine$RunLast.handle(CommandLine.java:2144)
      at picocli.CommandLine$RunLast.handle(CommandLine.java:2108)
      at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:1975)
      at picocli.CommandLine.execute(CommandLine.java:1904)
      at genepi.haplogrep3.App.main(App.java:131)
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Greetings, I was trying to run multiple unrelated singleton samples in one CSV file. The pipeline works fine initially, it does the alignment for each sample separately and also generates the multiqc report but the SNV_calls as well as the SV calls are only done for the first sample (S001). I just wanted to confirm if it is possible to run multiple samples using one csv or we need seprate csv files for each sample.

sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id
S001,1,/data/S001.R1.fq.gz,/data/S001.R2.fq.gz,0,2,0,0,case_S001
S002,1,/data/S002.R1.fq.gz,/data/S002.R2.fq.gz,0,2,0,0,case_S002
S003,1,/data/S003.R1.fq.gz,/data/S003.R2.fq.gz,0,2,0,0,case_S003

Secondly I wanted to ask that is it possible to do cohort analysis to run all unrelated samples together? Thanks in advance. Best, Ali

Hi, I am running the pipeline and I get this error:

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (SRR1598405)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (SRR1598405)` terminated with an error exit status (1)


Command executed:

  picard \
      RenameSampleInVcf \
      -Xmx4915M \
      --INPUT SRR1598405_repeat_expansion.vcf \
      --OUTPUT SRR1598405_renam.vcf.gz \
       --NEW_SAMPLE_NAME SRR1598405
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP":
      picard: $(picard RenameSampleInVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
  14:14:45.850 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.3.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
  [Tue Oct 14 14:14:45 GMT 2025] RenameSampleInVcf --INPUT SRR1598405_repeat_expansion.vcf --OUTPUT SRR1598405_renam.vcf.gz --NEW_SAMPLE_NAME SRR1598405 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
  [Tue Oct 14 14:14:46 GMT 2025] Executing as karla.ruiz@cnode33 on Linux 4.18.0-477.13.1.el8_8.x86_64 amd64; OpenJDK 64-Bit Server VM 22.0.1-internal-adhoc.conda.src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
  [Tue Oct 14 14:14:46 GMT 2025] picard.vcf.RenameSampleInVcf done. Elapsed time: 0.01 minutes.
  Runtime.totalMemory()=2075918336
  To get help, see <http://broadinstitute.github.io/picard/index.html#GettingHelp>
  Exception in thread "main" java.lang.IllegalStateException: Key REF found in VariantContext field INFO at chr1:57367043 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
  	at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:215)
  	at htsjdk.variant.vcf.VCFEncoder.write(VCFEncoder.java:148)
  	at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:250)
  	at picard.vcf.RenameSampleInVcf.doWork(RenameSampleInVcf.java:134)
  	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
  	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
  	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:115)

I use the variant catalog provided here: https://github.com/Clinical-Genomics/reference-files/blob/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/variant_catalog_grch38.json At this point I'm skipping this step but it would be nice to have some feedback about this.

Hi team, I have a quick question regarding the

phenotype

column in the

samplesheet.csv

for nf-core/raredisease v2.6.0. For example, if the proband (ID = A001) is affected (

phenotype = 2

), and his father (ID = B001) is also affected, should I also set the father’s

phenotype

to 2? I’d like to confirm whether the pipeline assumes that there is only one affected individual per family/trio (i.e., only the proband should have

phenotype = 2

), or if multiple affected individuals within the same family are supported. Many thanks in advance!

Hi, I have been struggling to get the annotation steps to work (v 2.6.0). The issue is that my annotated VCF files are all empty. I think the issue starts at the step

ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB

because the output file returns no variants, although the input file has plenty of variants that should be annotated. It doesn't throw any errors at this point, but it subsequently causes the pipeline to crash at the genmod rank variants step (guessing because there are no variants to rank?) Below is a table summarising a few variants that are both in the query and reference, and thus should be present in the final file right? Or am I missing something here? Is the issue that the annotation differs between the query/ref? Anyone else seen this problem? This is a test sample

I think a good feature to add would be inlcuding a strand-bias value for a given var - even though it doesn't come out directly for DeepVariant. Not sure how to implement it post-variant-calling yet but I will make an attempt at it later.

Hello, I have an issue regarding the step: ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME. This step failed on many cases:

[93/255ffe] NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (SRR8082060_LNUMBER95) [  0%] 0 of 179, retries: 73

I go to the

work/

directory to check some of the error message. So far as I see the error message is always:

samtools sort: truncated file. Aborting

I checked raw fastq files and they are not broken. I also tried to run bwa + samtool in two steps outside of the pipeline using some of the failed samples. I don't see the error and the sorted bam files can be generated successfully. I'm wondering if any of you happen to know how to solve this issue? Many thanks in advance.

Hey 🙂 I noticed that you compiled a subset of the VEP cache for testing at some point but its based on the GRCh37 genome. Do you have any notes on how you downsampled the VEP cache? I want / need to do that for CI testing of #C05URH17X5Z and would love something similar to your setup

Hello everyone! We have been starting to use the nfcore/rare disease pipeline and I have a question regarding logging of run commands. I know you can see the commands that have been run in a given work folder and in the file .command.sh. Is there a complete log of all commands at the end of a completed pipeline? Is there a way to generate this? Perhaps this is a basic nextflow configuration that I have overlooked. The purpose is to be able too easily see what the commands were for different steps in the pipeline. For example, what was the actual command and arguments given when running Deep variant? Now I try to backtrack through config files and subworkflow/module files to understand the commands that have been used. Thankful for insights and suggestions!

hi I'm trying to test sentieon just for the variant calling part with the raredisease pipeline (so using my own bams)? this was already in the config

ml_model             	    = "<https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model>"

so is adding this

variant_caller		    = "sentieon"

to params and then

env {
    SENTIEON_LICENSE_BASE64 = secrets.SENTIEON_LICENSE_BASE64
}

to my config sufficient? or is it more complicated. I set my secrets using

nextflow secrets set SENTIEON_LICENSE_BASE64 $(cat /path/to/your/license.lic | base64 -w 0)

ok so that wasn't sufficient I had to add

--network=host

to the docker env and run the license server outside of the pipeline.... with license key set as the server:port and I needed to bump the container image version (mentioned in #C03AWT0PVRD). I'm a little confused on how this pipeline is currently being used (or is nobody using sentieon?)? the last release was in June 2025 v2.6.0 - Cacofonix but in May 2025 the nf-core changed all the senteion module images to new images due to changes in the license software. it seems to me that it is NOT possible to run the senteion tools in the existing raredisease release but I do see on the dev branch that these containers will finally be updated for the next release. am I missing something here?

Hey! I am cleaning up the AWS Megatests: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/45IvPgXOfxKY1R/v2/logs When running

test_full

the pipeline errors with :

Set missing parameters and restart the run. For more information please check usage documentation on github.

How can I make the full_test profile work?

hey so urgent bug I found... I don't really understand why nobody noticed this. essentially manta runs on all samples in the sample sheet but with a randomness due to the channel input. all the other tools seems to run one-by-one on each sample. so a second bug in svdbmerge where it doesn't check the sample names in the vcf essentially replaces all the merged vcf samples with the sample names of the first priority vcf. if you were running WGS manta doesn't take precedence so you would just get FP from manta. for me with WES, manta takes precedence so I'm getting potential FN from ALL other tools (include my main cnv powerhouse gatk germlinecnv caller). which given the way we are supposed to be analysing sample in accordance with Swiss regulations would result in critical cnvs being missed !!!! hopefully everyone is running this pipeline on 1 patient at a time per sample sheet or on trios as this would mostly avoid problems... but scary nonetheless https://github.com/nf-core/raredisease/issues/814

to be clear potentially not a bug in svdb merge but maybe related to a param choice in the svdb merge config

Hi. I'm trying to run raredisease (2.6.0) for just the germline CNV analysis for a targeted panel. I've set type to wes, and set skip for everything else:

Analysis options
  analysis_type             : wes
  skip_subworkflows         : mt_annotation,mt_subsample,me_calling,me_annotation,repeat_annotation,repeat_calling,snv_annotation,snv_calling,sv_annotation,generate_clinical_set
  skip_tools                : fastp,gens,haplogrep3,peddy,smncopynumbercaller,vcf2cytosure,fastqc,qualimap,eklipse,ngsbits

I'm getting a parameter validation error:

* Missing required parameter(s): intervals_wgs, intervals_y

Previous discussion on these params indicate they're for WGS coverage stats and not appropriate for WES, and it seems like this was addressed - https://github.com/nf-core/raredisease/pull/396#event-10006745584 Any way to skip this or get this validation to be quiet, or just pull/generate the files in order to provide them?

(I did grab interval files to be able to move forward) Bug report: If skip_tools includes 'fastqc', workflow fails with error:

ERROR ~ No such variable: fastqc_report

 -- Check script '/Users/dkolbe/.nextflow/assets/nf-core/raredisease/workflows/raredisease.nf' at line: 914 or see [...]

This code section is collating results for MultiQC. The variable fastqc_report is defined earlier only inside the block protected by the skip_tools check.

hi guys im running the new v3.0.0 version with wes and it looks like my snvs are not having their multi-allelic vars split whereas previously they were being split... I can't really find the param. there is a new

params.skip_split_multiallelics

but im confused as to where this is being set to false by default? (if that is even the case...)

in the nextflow.config its set

skip_split_multiallelics    = false

and I wrong in assume that that is the default?

ok another potential threat to patient safety occurs when you run the WES version of the pipeline due the use of fewer CNV calling methods (so just gatk cnv+ manta) this likely also affects WGS but if CNVnator catches them (they should be easy to find) they should at least come out... so maybe not a huge priority for everyone. this time I don't have an easy fix because it depends on your reference genome... if you don't specify the allosomes : chrX/chrY duplications will be missed in male patients due to the default methods of https://gatk.broadinstitute.org/hc/en-us/articles/30332057809179-PostprocessGermlineCNVCalls which treats all chrs as autosomes (aka diploid) unless otherwise specified [i.e. it drops CN = 2 on chrX even in males]. so my fix internally is to add this to my config withName: '.*CALL_SV_GERMLINECNVCALLER:GATK4_POSTPROCESSGERMLINECNVCALLS' { ext.args = '--allosomal-contig chrX --allosomal-contig chrY' } I tried to do a blanket --allosomal-contig X --allosomal-contig Y --allosomal-contig chrX --allosomal-contig chrY for all use-cases as a fix but it will error out when it matches back to the FASTA configs so it has to be custom set based on the reference genome

I’m experiencing some problems with using the iGenomes-functionality in raredisease v3.0.0. It seems that the some parameter validation is executed before the parameters are set through the iGenomes-functionality. Is that a known-issue?

@Ram we noticed some tiny issues with this pipeline using a bit too much GHA credits, rather than the runs-on runners: https://github.com/nf-core/raredisease/pull/1036

❌ raredisease/test_full failed 😿 Run Name boring_babbage Duration 1m 16s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/raredisease>, projectDir: /.nextflow/assets/.repos/nf-core/raredisease/clones/9769147989527e2267886af0641516a43d4cff63, commitId: 9769147989527e2267886af0641516a43d4cff63, revision: dev, startTime: 2026-10-16T12:17:41.334669462Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/raredisease>' -name boring_babbage -params-file '<https://api.cloud.seqera.io/ephemeral/LCHSDyW8muEyD-TT08ynig.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$Preview@2394fad2, enable:nextflow.NextflowMeta$Features@53785d1a, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/raredisease/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/raredisease>' -name boring_babbage -params-file '<https://api.cloud.seqera.io/ephemeral/LCHSDyW8muEyD-TT08ynig.json>' -with-tower -r dev -profile test_full

Oct 16, 2026 at 12:19 PM

❌ raredisease/test_full failed 😿 Run Name elated_lamarck Duration 1m 21s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/raredisease>, projectDir: /.nextflow/assets/.repos/nf-core/raredisease/clones/e972dbde1aba738c1b15281b26ad12c01072d2b1, commitId: e972dbde1aba738c1b15281b26ad12c01072d2b1, revision: dev, startTime: 2026-10-22T08:52:37.317378515Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/raredisease>' -name elated_lamarck -params-file '<https://api.cloud.seqera.io/ephemeral/WPkjDSB77wQH7xzVmqrXvw.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$Preview@233b5c71, enable:nextflow.NextflowMeta$Features@1e7edfb2, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/raredisease/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/raredisease>' -name elated_lamarck -params-file '<https://api.cloud.seqera.io/ephemeral/WPkjDSB77wQH7xzVmqrXvw.json>' -with-tower -r dev -profile test_full

Oct 22, 2026 at 8:54 AM

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