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# sarek
  • a
    hi all. Are there any plans/developments to support Element Aviti data in sarek going forward. I'm working with this data. I believe GATk wont accept PL tag of `element`so I was thinking of adding this to the meta (in via samplesheet) to potentially use that in modules to switch between aviti and illumina command options . Or via params to switch between illumina and element workflow options as required. eg running lofreq viterbi (only for illumina data) & indelqual upstream of lofreq call or not. Any thoughts would be great.....
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  • g
    Hi. I am running tests with sarek 3.8.1 (w Sentieon inside) and I noticed that the pipeline is performing base quality recalibration with gatk. Is there a way to force it to switch to sentieon-bqsr? This is the command:
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  • g
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    nextflow run nf-core/sarek -r 3.8.1 \
    -profile singularity,hpcbio \
    --sentieon_extension \
    --aligner sentieon-bwamem \
    --tools sentieon_dedup \
    --outdir ./results_test_sentieon_run3 \
    --custom_config_base /some/path/hpcbio/apps/configs/ \
    --input samplesheet.csv \
    --save_reference true \
    --save_mapped true \
    --save_output_as_bam true \
    --download_cache true \
    --outdir_cache /some/path/hpcbio/data/sarek/3.8.1 \
    --no_intervals
  • g
    my version of nextflow is 25.10.2
  • g
    The reason is that we are migrating from an older version of sarek to the current one. The old version performed these analyses with Sentieon (alignment, dedup, recalibration, dnascope, dnaseq). We need the results of both version of the pipeline to be as close as possible.
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  • t
    Hey guys, when I have numeric patient IDs in the samplesheet, I get a validation error: 
    Error for field 'patient' (1234): Value is [integer] but should be [string] (Patient ID must be provided, cannot contain spaces and must be a string value)
    I remember that this issue had been discussed (maybe a couple years ago?), but I don't remember if this had been resolved (and I'm looking at a regression) or not (tried to search, but can't find it). Can someone please remind me? Thank you!
    🚫 1
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  • r
    Hello, I am using TNScope and was thinking of adding to the module so that it can handle tumor normal pairs as described here. Would that be ok?
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  • k
    Dear @Rike Hanssen @Maxime Garcia, I am the developer of VarNet somatic variant caller (https://github.com/skandlab/VarNet). I have made a pull request to add VarNet to nf-core/sarek here https://github.com/nf-core/modules/pull/11787 Kindly let me know if it looks ok! Thank you -Kiran
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  • p
    Picking up on a discussion I've had with @Maxime Garcia in the distant past: I've tried to implement some additional validation checks into my own pipeline to deal with gatk read groups. It's not only checking for lanes though, but also for flowcells and libraries (i.e. a biological sample is allowed to have multiple fastq (pair) entries in the samplesheet, as long as they differ in lane or flowcell, and those that differ in flowcell can share a lane). Samples labelled as coming from the same biological sample, but different libraries, are also treated correctly now by downstream GATK tools. Checks happen during samplesheet parsing, but also modify metamap to contain a 
    sample_LIB_LANE_FC
    id. There's also some functions that tries to extract this info from either the file name or the fastq headers (based on sarek's current implementation actually 😉 ). If sarek currently also has this functionality too, just ignore this, but if it sounds interesting, feel free to reach out. (WIP code: https://github.com/ITMmalaria/plasmovar/blob/dev/subworkflows/local/utils_nfcore_plasmovar_pipeline/main.nf)
    👀 1
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  • e
    If I use an externally-made BAM, how can I tell sarek not to look for sample names that are 
    PatientID_SampleID
    in the BAM header when using it in the variant calling step as normal? Otherwise MuTect2 puts 
    PatientID_SampleID
    as normal sample in the CLI, and it breaks (because the 
    SM
    tag in the BAM is different)
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  • e
    When was FilterVariantTranches added to sarek (GATK)? It's systematically killing my variants, so I want to see if I can turn it off
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  • m
    Release 3.9.0 is live: https://github.com/nf-core/sarek/releases/tag/3.9.0 Full changelog: https://github.com/nf-core/sarek/blob/master/CHANGELOG.md We have strict syntax, improvements with valorciraptor, better CI, update and fix on sentieon related modules, fix on the --save_output_as_bam flag, and some more parabricks magic, and the ANIMATED SUBWAY MAP, and many other bugfixes. Thanks to everyone involved, the usual suspects: @Famke Bäuerle and @Rike Hanssen who actually did most of the work, I was merely here to release, but they really deserve all the glory. Thanks to @Ben Sherman for his first direct #CGFUX04HZ contribution. Thanks to @Nico and @Anders Sune Pedersen for coming back, and help fix some issues we didn't notice. Thanks to @James Fellows Yates, @Jonathan Manning and @Simon Pearce for all the review comments. Thanks to all of you for your support.
    👌 1
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  • i
    I would like to bump 2 very old issues that remain relevant (e.g. for agrogenomics applications): github.com/nf-core/sarek/issues/1152 github.com/nf-core/sarek/issues/1276
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  • a
    Hi everyone, We are deploying nf-core/Sarek in a restricted enterprise environment and are currently working with our infrastructure team on outbound whitelisting requirements. Based on our investigation, we have identified the following domains/endpoints: github.com codeload.github.com raw.githubusercontent.com objects.githubusercontent.com registry.nextflow.io ngi-igenomes.s3.eu-west-1.amazonaws.com s3.eu-west-1.amazonaws.com community.wave.seqera.io community-cr-prod.seqera.io wave.seqera.io quay.io cdn.quay.io registry-1.docker.io auth.docker.io production.cloudflare.docker.com Could anyone confirm whether this list is sufficient for a standard nf-core/Sarek deployment, or if there are additional domains/endpoints that should also be considered? Thanks!
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  • i
    Hi, I have a question about paired sample mode. I will have some data where I have one FASTQ from a wild type sample and several FASTQs from different mutant lines (separate specimen, not timepoints). Will the pipeline behave correctly if I enter the WT as "normal" and each mutant as "tumour" with the same "patient" ID, or do I need a more elaborate approach?
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  • a
    Hi everyone! I'm setting up nf-core/sarek (v3.6.1) for tumor-only somatic variant calling (Mutect2) on Azure Batch, and I'd really appreciate any guidance from folks who have successfully run this setup. My setup: - nf-core/sarek 3.5.1 (stock remote, not a local clone) - Nextflow 24.10.5 - Azure Batch with a pre-existing pool (Standard_DS3_v2, Ubuntu HPC 24.04, dockerCompatible) - Authentication: Managed identity only (no account keys) - Storage: Azure Blob — separate containers for reference (GRCh37), input FASTQs, work dir, and results - All paths use az:// (e.g., az://nextflow-reference/reference.fa) - Reference: GRCh37 (Ensembl), af-only-gnomad, skipping BQSR for initial validation - Test data: 100 MB paired tumor FASTQ Where I'm stuck: Our pool had a start-task (blobfuse2 mount script) that fails with 
    CommandProgramNotFound
    — the node can't download the script from blob, so it goes to 
    startTaskFailed
    and no Nextflow tasks can execute. I now understand that Nextflow's azurebatch executor uses az:// paths + azcopy for data movement (not blobfuse2 mounts), so the start-task isn't needed for the pipeline itself. But I want to make sure I'm not missing something before removing it. My questions: 1. Has anyone successfully run nf-core/sarek on Azure Batch with managed identity auth (no account keys)? If so, could you share your nextflow.config structure? 2. Does your pool use a start-task, or does it boot clean with just dockerCompatible? What does your pool configuration look like? 3. Any gotchas with az:// paths for --fasta, --bwa, --germline_resource etc.? Do they resolve correctly on the compute nodes? 4. For those who ran sarek 3.5.1 specifically — did you need to pin NXF_VER to avoid the "Variable declarations cannot be mixed with config statements" error on newer Nextflow versions? If anyone has a working config or a step-by-step doc they followed, I'd be incredibly grateful. Happy to share what I've learned so far as well. Thanks in advance!
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  • a
    I’m trying to run the test_full-profile of Sarek v.3.9.0 and I get
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    touch: cannot touch 'dbsnp_146.hg38.vcf.gz.tbi': Permission denied
    from MUSE_SUMP, because of this touch-command. The file 
    dbsnp_146.hg38.vcf.gz.tbi
    is read-only on our system, and that is how we would like to keep it.
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  • a
    This might not be the right Slack channel for this rant, but I still get error messages like
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    The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ascat
    in stdout from Sarek, when the real problem something completely different. In this case, the 
    .nextflow.log
    reports the real error:
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    Jul-21 15:30:39.633 [main] ERROR nextflow.cli.Launcher - @unknown
nextflow.exception.WorkflowScriptErrorException: Path provided with SnpEff cache is invalid.
Make sure there is a directory named GRCh38.115 in <some_path>
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  • h
    Hi everyone, I’m running the 
    nf-core/sarek
    pipeline in germline mode on mouse data. It looks like the built-in mm10 reference from iGenomes only includes the 22 primary chromosomes (1–19, X, Y, MT). Could someone please confirm if this is expected? If I need unplaced/unlocalized contigs for my analysis, should I build and supply a custom reference genome instead? Thanks!
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  • r
    github.com/nf-core/sarek/…/3.10.0 new release is out 🌈. It looks huge, but mostly due to syntax updates. We just have two new features, and some bug fixes: 🆕 • Parabricks HaplotypeCaller with 
    --tools parabricks_haplotypecaller
    by @Gary Burnett • Varlociraptor FDR filtering for germline, somatic and tumor-only workflows by @Famke Bäuerle 🐛 • Fix 
    --normalize_vcfs
    dropping an allele from multiallelic sites by @apolotics. • Fix VEP LoFTEE plugin execution with Conda by @Maxime Garcia • Skip nf-schema path validation for 
    --annotation_cache
    and 
    --igenomes_base
    by @Jonathan Manning 🚧 • Topic channels everywhere • Lots and lots of version updates • Full strict syntax compliance 💔 some breaking changes: • Somatic FreeBayes no longer uses 
    --pooled-discrete
    , and its default minimum alternative allele fraction changes from 
    0.03
    to 
    0.01
    . • When starting from CRAM or BAM files with 
    --step variant_calling
    , CNVKit output names are now based on the input filename instead of the sample name • The output format of 
    GATK4_APPLYBQSR
    and 
    GATK4SPARK_APPLYBQSR
    can no longer be changed using 
    ext.suffix
    Thank you to everyone, that has contributed, and in particular @Daniel Lundin and @Jonathan Manning for reviewing this monster.
    🎉 6
    ❤️ 2
    sarek wine 1
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  • s
    Hello, I work on an offline server and used to run Sarek 3.4.4, and now trying to run version 3.9.0 and nextflow-25.10.6-dist. I have copied all the plugins, etc to the offline server after test running this version on the dev system. I am running with these params below and it keeps crashing at the validation step (on the offline server). Is there any other params that I can add to stop it from checking these online files?
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    igenomes_ignore : true
no_intervals : true
fasta : '/path/to/fasta'
    ERROR:
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    The following invalid input values have been detected:

* --igenomes_base (<s3://ngi-igenomes/igenomes/>): could not validate file format of '<s3://ngi-igenomes/igenomes/>': Unable to execute HTTP request: Connect to <http://ngi-igenomes.s3.us-east-1.amazonaws.com:443|ngi-igenomes.s3.us-east-1.amazonaws.com:443> [<http://ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.244.238|ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.244.238>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.236.217|ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.236.217>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.245.15|ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.245.15>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/52.217.121.226|ngi-igenomes.s3.us-east-1.amazonaws.com/52.217.121.226>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.199.32|ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.199.32>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.223.39|ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.223.39>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.245.84|ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.245.84>, <http://ngi-igenomes.s3.us-east-1.amazonaws.com/52.217.115.82]|ngi-igenomes.s3.us-east-1.amazonaws.com/52.217.115.82]> failed: Connect timed out (SDK Attempt Count: 6)
* --snpeff_cache (<s3://annotation-cache/snpeff_cache/>): could not validate file format of '<s3://annotation-cache/snpeff_cache/>': Unable to execute HTTP request: Connect to <http://annotation-cache.s3.us-east-1.amazonaws.com:443|annotation-cache.s3.us-east-1.amazonaws.com:443> [<http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.252.222|annotation-cache.s3.us-east-1.amazonaws.com/16.15.252.222>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.183.240|annotation-cache.s3.us-east-1.amazonaws.com/16.15.183.240>, <http://annotation-cache.s3.us-east-1.amazonaws.com/52.217.118.178|annotation-cache.s3.us-east-1.amazonaws.com/52.217.118.178>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.253.218|annotation-cache.s3.us-east-1.amazonaws.com/16.15.253.218>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.247.141|annotation-cache.s3.us-east-1.amazonaws.com/16.15.247.141>, <http://annotation-cache.s3.us-east-1.amazonaws.com/52.217.90.184|annotation-cache.s3.us-east-1.amazonaws.com/52.217.90.184>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.229.212|annotation-cache.s3.us-east-1.amazonaws.com/16.15.229.212>, <http://annotation-cache.s3.us-east-1.amazonaws.com/52.217.86.120]|annotation-cache.s3.us-east-1.amazonaws.com/52.217.86.120]> failed: Connect timed out (SDK Attempt Count: 6)
* --vep_cache (<s3://annotation-cache/vep_cache/>): could not validate file format of '<s3://annotation-cache/vep_cache/>': Unable to execute HTTP request: Connect to <http://annotation-cache.s3.us-east-1.amazonaws.com:443|annotation-cache.s3.us-east-1.amazonaws.com:443> [<http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.252.171|annotation-cache.s3.us-east-1.amazonaws.com/16.15.252.171>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.191.132|annotation-cache.s3.us-east-1.amazonaws.com/16.15.191.132>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.223.16|annotation-cache.s3.us-east-1.amazonaws.com/16.15.223.16>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.237.67|annotation-cache.s3.us-east-1.amazonaws.com/16.15.237.67>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.245.111|annotation-cache.s3.us-east-1.amazonaws.com/16.15.245.111>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.207.152|annotation-cache.s3.us-east-1.amazonaws.com/16.15.207.152>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.253.15|annotation-cache.s3.us-east-1.amazonaws.com/16.15.253.15>, <http://annotation-cache.s3.us-east-1.amazonaws.com/16.15.255.229]|annotation-cache.s3.us-east-1.amazonaws.com/16.15.255.229]> failed: Connect timed out (SDK Attempt Count: 6)

 -- Check script /shared/pipelines/sarek/nf-core-sarek_3.9.0/3_9_0/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 72 or see '.nextflow.log' file for more details
    Thanks!
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  • a
    Hi all. When using the umi workflow and fgbio consensus calling, is it expected that the downstream samtools etc tasks still run (eg 
    FASTQ_PREPROCESS_GATK:CONVERT_FASTQ_UMI:SAMTOOLS_VIEW_MAP_MAP
    ) before going to realignment ? For me at least, that means all reads will be unaligned reads (consequence of fgbio consensus calling) , which eventually get merged (cat) together with empty aligned reads before the downstream BWA realignment.
    s
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  • m
    Hi everyone. I just updated from Sarek 3.5.1 to 3.10.0 I'm noticing a lot of Java stack info in the logs that wasn't there before. It looks like exception stack calls, but nothing is failing, it just has tons of this sort of thing:
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    at org.pf4j.DefaultExtensionFinder.find(DefaultExtensionFinder.java:45)
	at org.pf4j.AbstractPluginManager.getExtensions(AbstractPluginManager.java:635)
	at nextflow.plugin.PluginsFacade.getExtensions(PluginsFacade.groovy:329)
	at nextflow.plugin.Plugins.getExtensions(Plugins.groovy:61)
	at nextflow.config.ConfigValidator.loadPluginScopes(ConfigValidator.groovy:75)
	at nextflow.config.ConfigValidator.<init>(ConfigValidator.groovy:70)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:405)
	at nextflow.cli.Launcher.run(Launcher.groovy:526)
	at nextflow.cli.Launcher.main(Launcher.groovy:686)
	at org.pf4j.PluginClassLoader.loadClass(PluginClassLoader.java:169)
	at org.pf4j.AbstractExtensionFinder.find(AbstractExtensionFinder.java:140)
	at org.pf4j.AbstractExtensionFinder.find(AbstractExtensionFinder.java:61)
	at org.pf4j.DefaultExtensionFinder.find(DefaultExtensionFinder.java:45)
	at org.pf4j.AbstractPluginManager.getExtensions(AbstractPluginManager.java:635)
	at nextflow.plugin.PluginsFacade.getExtensions(PluginsFacade.groovy:329)
	at nextflow.plugin.Plugins.getExtensions(Plugins.groovy:61)
	at nextflow.config.ConfigValidator.loadPluginScopes(ConfigValidator.groovy:75)
	at nextflow.config.ConfigValidator.<init>(ConfigValidator.groovy:70)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:405)
	at nextflow.cli.Launcher.run(Launcher.groovy:526)
	at nextflow.cli.Launcher.main(Launcher.groovy:686)
	at org.pf4j.PluginClassLoader.loadClass(PluginClassLoader.java:169)
    and by tons i mean hundreds of thousands of lines. Anyone seen this?
    🫠 1
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  • m
    Separate question regarding the same upgrade. I'm getting
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    ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE

Command executed:

  tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'

Command exit status:
  2

Command output:
  grep: invalid option -- 'P'
  BusyBox v1.36.1 (2024-06-02 11:42:27 UTC) multi-call binary.
    This is running on the ensembl-vep image from quay : 
    quay/biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0
    It used to work fine, but it looks like somewhere along the way the grep command was added / changed (used to be 
    sed
    ). Is there a version of the ensembl image that uses GNU grep and/or should I be running ANNOTATE_MERGE on a different image?
    👀 1
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  • a
    Hi channel - I run sarek and then run another workflow to execute verifyBAMId . It's wrapped in a shell script. My question is there a way to write a workflow that runs sarek and then ingests the relevant input from sarek output channel? Basically, I need the aligned sample id, bam, bam index from sarek.
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    # --- Stage 1: Sarek ----------------------------------------------------------
echo ">>> Stage 1: nf-core/sarek using samplesheet: ${input}"
nextflow run nf-core/sarek -r "3.5.1" \
  --input "${input}" \
  --save_output_as_bam \
  -c "sarek.config" \
  -with-tower \
  -resume &&

# --- Stage 2: VerifyBamID2 ---------------------------------------------------
{
  echo ">>> Stage 1 succeeded. Stage 2: VerifyBamID2"
  nextflow run <http://run-verifyBAMID.nf|run-verifyBAMID.nf> \
    --input "${input}" \
    -c "pipeline.config" \
    -with-tower \
    -resume
} &&

echo ">>> Both stages completed successfully."
  • j
    I know I've seen this information somewhere but for the life of me I can't find how to pass command line options to variant callers. I want to use --disableEVS for Strelka. I am using sarek 3.6.0 which I know is old at this point but that was the version originally used on these samples.
    📝 1
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  • p
    Hello everyone, I have been running nf-core/sarek 3.9.0 using the hg19 reference genome and the SnpEff GRCh37.87 database for variant annotation. I noticed that mitochondrial variants were not annotated correctly. In the hg19 reference genome, the mitochondrial chromosome is named 
    chrM
    , whereas in the SnpEff GRCh37.87 database it is named 
    MT
    . This chromosome-name mismatch appears to prevent SnpEff from annotating the mitochondrial variants. Using the SnpEff 
    hg19
    database resolves the chromosome-name mismatch, but the resulting annotations appear to be less comprehensive than those obtained with GRCh37.87 for the other chromosomes. Has anyone encountered this issue? What would be the recommended way to annotate mitochondrial variants while retaining the more comprehensive GRCh37.87 annotations?
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  • j
    Hello everyone! I’m exploring 
    --vep_loftee
    , but I’m unsure how to supply LOFTEE’s support files. In the Sarek revision we use, 
    --vep_loftee
    adds the LoF plugin argument. I can see staging for other VEP plugin files, but I haven’t found equivalent LOFTEE file parameters. Is there an existing supported way to place these files in the VEP cache and pass their paths to LOFTEE? If not, would an upstream PR adding LOFTEE file parameters, staging, and validation be welcome?
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  • t
    depictio Depictio dashboard for sarek: 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 sarek 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 sarek: coverage and sex check, variant yield per caller, call quality, concordance between callers, SnpEff consequences, the genes carrying the calls and a locus view, next to the MultiQC report. 👀 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: sarek dashboard (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to sarek. ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏 🎤 In you're interested in the project, I was speaking about Depictio at the Nextflow Summit (session page), and the recording will be available in the coming weeks.
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    sarek nf-core/sarek 3.11.0 – Guhkesvákkjåhkå is released! sarek cat jam https://github.com/nf-core/sarek/releases/tag/3.11.0 New: • 🚀 Parabricks DeepVariant (--tools parabricks_deepvariant) for GPU-accelerated germline calling •🚀 Parabricks ApplyBQSR, and Parabricks HaplotypeCaller in gVCF mode for joint calling • 🧬 DeepSomatic and Parabricks DeepSomatic for tumour-normal short-read calling (--tools deepsomatic, --tools parabricks_deepsomatic) • 🔨 New --ascat_penalty parameter (default 70) Changed: • 🪶 GATK 4.6.2.0 → 4.7.0.0 (Lite containers). Recalibrated CRAMs stay CRAM 3.0 so legacy tools can still read them, and CRAI indexes are now published with them. • ⚡ Recalibration now uses the nf-core bam_applybqsr subworkflow • ➕ ensembl-vep 116.3, varlociraptor 8.12.0 • 📖 ASCAT resource docs now point to Zenodo, with clearer WES and targeted-sequencing steps Fixed: • 🐛 Several Parabricks fixes: fq2bam no longer silently produces nothing with --no_intervals or without known sites, BQSR no longer stalls or runs out of memory from unindexed known-sites VCFs, and the germline callers now fail early on tumour-only samplesheets • 🦗 Varlociraptor custom scenario parsing • 🐞 the Spark MarkDuplicates pixel distance • 🐝 BCFtools mpileup prefix Huge thanks to everyone who contributed to this release 🙏 @Gary Burnett, @Rike Hanssen, @Famke Bäuerle, @jfischba, @Adam Talbot, @Edmund, @dlt481, @Phil Ewels, @p, @mashehu, @Peter Z, @Charles-Alexandre Roy, @Agrima Bhattand @Michael Heuer, plus everyone who reported issues and reviewed PRs.
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