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Error for Smart-seq protocol #398

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irenemaring opened this issue Dec 4, 2024 · 0 comments
Open

Error for Smart-seq protocol #398

irenemaring opened this issue Dec 4, 2024 · 0 comments
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bug Something isn't working

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@irenemaring
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irenemaring commented Dec 4, 2024

Description of the bug

I tried to run the pipeline for data generated with Smart-seq. If I set -protocol Smart-seq (as specified in Star Documentation) then in the .mextflow.log I get

WARN nextflow.Nextflow - Protocol 'SmartSeq' not recognized by the pipeline. Passing on the protocol to the aligner unmodified.

But the pipeline runs, it generates teh index and when it starts the alignment with STAR_ALIGN I get the error:

EXITING because of fatal PARAMETERS error: --soloUMIdedup = 1MM_All is not allowed for --soloType SmartSeq
SOLUTION: use allowed options: Exact and/or NoDedup

However there is no way to pass the argument --soloUMIdedup on the pipeline command (or I do not knwo how.
Thanks.

Command used and terminal output

nextflow run nf-core/scrnaseq -r 2.7.1 -name test4 -profile singularity -resume -params-file nf-params.json -c nextflow.config

Relevant files

{
"input": "./samplesheet_test.csv",
"outdir": "./out",
"multiqc_title": "Mytest",
"aligner": "star",
"protocol": "SmartSeq",
"gtf": "/gencode.v44.primary_assembly.annotation.gtf",
"fasta": "/Homo_sapiens.GRCh38.dna.primary_assembly.fasta",
"soloUMIdedup": "NoDedup"
}

System information

No response

@irenemaring irenemaring added the bug Something isn't working label Dec 4, 2024
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