Hello everyone. I am trying to run the nf-core/raredisease pipeline for the test_full dataset provided on GitHub. I am getting the following error:

nextflow run nf-core/raredisease -r 2.4.0  -profile test_full,amd --outdir results -bg -resume

It seems that haplogrep3 is having trouble recognizing vcf.

[adminrig@dlcfe-dnalink 785512ba02f6f3cd5247bfd78bf5f7]$ cat .command.sh
#!/usr/bin/env bash -C -e -u -o pipefail
haplogrep3 \
    classify \
    --tree phylotree-rsrs@17.1 \
    --in justhusky_mitochondria_hmtnote_vcfanno.vcf.gz \
    --out justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT":
    haplogrep3: $(echo $(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
END_VERSIONS
[adminrig@dlcfe-dnalink 785512ba02f6f3cd5247bfd78bf5f7]$ cat .command.log
Unable to find image '<http://quay.io/biocontainers/haplogrep3:3.2.2--hdfd78af_0|quay.io/biocontainers/haplogrep3:3.2.2--hdfd78af_0>' locally
3.2.2--hdfd78af_0: Pulling from biocontainers/haplogrep3
0cacab098358: Already exists
bd9ddc54bea9: Already exists
32d7d81c25e1: Pulling fs layer
32d7d81c25e1: Verifying Checksum
32d7d81c25e1: Download complete
32d7d81c25e1: Pull complete
Digest: sha256:ea4feff3e9dafc35d5952fcdd36cfe87b5ec89dd43f464470ad622a1fce59cf6
Status: Downloaded newer image for <http://quay.io/biocontainers/haplogrep3:3.2.2--hdfd78af_0|quay.io/biocontainers/haplogrep3:3.2.2--hdfd78af_0>

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

Hello! Yes, we noticed this error occurs occasionally when you are working with a merged vcf (in this case a trio). There is an open issue in the haplogrep3 repo about this, but don't think any fix has been implemented so far. https://github.com/genepi/haplogrep3/issues/35