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