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CiiM-Bioinformatics-group / CellDemux

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VCF file reported to be missing although it is provided #1

Open m571c opened 6 months ago

m571c commented 6 months ago

Thank you for creating this pipeline. I've installed all the necessary components and I'm currently attempting a test run to demultiplex a single pool of 10X multiome data, which includes four multiplexed patients. Despite providing the VCF file with imputed SNPs, I encountered the following error message:

Dry run Using profile config/ for setting default command line arguments. Building DAG of jobs... MissingInputException in rule vireo in file /omics/groups/OE0130/internal/Mislav/AML_multiome_Freiburg/CellDemux/CellDemux/dmx.smk, line 637: Missing input files for rule vireo: output: /omics/groups/OE0130/internal/Mislav/AML_multiome_Freiburg/CellDemux/resultsPool2/rna/vireo/donor_ids.tsv wildcards: sample=Pool2 affected files: /omics/groups/OE0130/internal/Mislav/AML_multiome_Freiburg/CellDemux/resultsPool2/inputfiles/refvcf.vcf

MZoodsma commented 5 months ago

Hi @m571c ,

Sorry for this (very) late answer. Wondering whether you managed to solve this?

Any other rules are running / completed already? Files are softlinked correctly to an input directory?

Best, Martijn