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Hi! Thanks for your work :smiley:. I am using rna...
# rnavar
m
Hi! Thanks for your work 😃. I am using rnavar pipeline and, although it runs without error it doesn't really complete, skipping from variant calling steps. This is the final output:
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executor >  slurm (49)
[-        ] NFC…REPARE_GENOME:GUNZIP_FASTA -
[a9/003b82] NFC…ENCEDICTIONARY (genome.fa) | 1 of 1 ✔
[-        ] NFC…:PREPARE_GENOME:GUNZIP_GTF -
[-        ] NFC…VAR:PREPARE_GENOME:GFFREAD -
[23/5160aa] NFC…GENOME:GTF2BED (genes.gtf) | 1 of 1 ✔
[57/87e840] NFC…VE_UNKNOWN_REGIONS (genes) | 1 of 1 ✔
[-        ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[-        ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[-        ] NFC…RE_GENOME:BGZIPTABIX_DBSNP -
[-        ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[-        ] NFC…ME:BGZIPTABIX_KNOWN_INDELS -
[-        ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[0c/054db4] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔
[-        ] NFC…NAVAR:PREPARE_GENOME:UNTAR -
[29/20321c] NFC…E_GENOME:STAR_INDEXVERSION | 1 of 1 ✔
[a9/fcd636] NFC…GENOMEGENERATE (genome.fa) | 1 of 1 ✔
[-        ] NFC…E_ALIGNMENT:SAMTOOLS_INDEX -
[7c/161c80] NFC…R:RNAVAR:CAT_FASTQ (CMT64) | 1 of 1 ✔
[b3/c79108] NFC…AVAR:RNAVAR:FASTQC (CMT64) | 1 of 1 ✔
[ac/a595ca] NFC…_BEDTOINTERVALLIST (genes) | 1 of 1 ✔
[78/46550e] NFC…_INTERVALLISTTOOLS (genes) | 1 of 1 ✔
[06/1a2bae] NFC…GN_STAR:STAR_ALIGN (CMT64) | 1 of 1 ✔
[63/9df02c] NFC…NOME:SAMTOOLS_SORT (CMT64) | 1 of 1 ✔
[ca/480c41] NFC…OME:SAMTOOLS_INDEX (CMT64) | 1 of 1 ✔
[10/18bf53] NFC…OLS:SAMTOOLS_STATS (CMT64) | 1 of 1 ✔
[a1/54ba4a] NFC…:SAMTOOLS_FLAGSTAT (CMT64) | 1 of 1 ✔
[05/2368ce] NFC…:SAMTOOLS_IDXSTATS (CMT64) | 1 of 1 ✔
[69/031cf5] NFC…ARD_MARKDUPLICATES (CMT64) | 1 of 1 ✔
[27/b87ea8] NFC…ARD:SAMTOOLS_INDEX (CMT64) | 1 of 1 ✔
[60/d4cae1] NFC…OLS:SAMTOOLS_STATS (CMT64) | 1 of 1 ✔
[75/d3e06e] NFC…:SAMTOOLS_FLAGSTAT (CMT64) | 1 of 1 ✔
[19/1e4100] NFC…:SAMTOOLS_IDXSTATS (CMT64) | 1 of 1 ✔
[40/be5ce7] NFC…RREADS (CMT64_19scattered) | 25 of 25 ✔
[95/f2cacb] NFC…GAR:SAMTOOLS_MERGE (CMT64) | 1 of 1 ✔
[01/f32579] NFC…GAR:SAMTOOLS_INDEX (CMT64) | 1 of 1 ✔
[2c/19f9d3] MULTIQC                        | 1 of 1 ✔
Plus 9 more processes waiting for tasks…
-[nf-core/rnavar] Pipeline completed successfully-
Completed at: 10-Sep-2025 18:54:20
Duration    : 2h 13m 29s
CPU hours   : 18.9
Succeeded   : 49
n
Hi what command did you use to start the pipeline?
m
Hi!
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NXF_VER=25.04.6 nextflow run nf-core/rnavar \
        --input samplesheet_rnavar.csv \
        --outdir PROCESSING_rnavar \
        --genome GRCm38 \
        --skip_baserecalibration \
        -r dev \
        -profile apptainer
I have to say that even if it is a cached genome (from mouse), I had to activate the 
skip_basecalibration
option.
n
Is there a reason you are running the 
dev
version?
m
n
Ah okay so it did work before 🤔
curious! can you also show your configuration and your full log file?
m
No! I thought it did because ended without errors. But after checking carefully the results I missed the variant calling part.
Sure. nexflow.config:
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process.executor = 'slurm'
executor.queueSize = 5
process.memory = '64 GB'
process.cpus = 16
apptainer.enabled = true
I attach the log.
n
what was the reason you activated the `skiprecalibration`option?
could you also provide the 
.nextflow.log
?
m
Because if not it gives me this error: 
Known sites are required for performing base recalibration. Supply them with either --dbsnp and/or --known_indels or disable base recalibration with --skip_baserecalibration
n
@Maxime Garcia do you know why this was changed?
r
ah yes I had this too. A workaround for this was adding my dbsnp file to both params 
known_indels
and 
dbsnp
m
Attaching .nextflow.log.
m
I think I might have merged the logic for the known_indels and dbsnp a bit too quick
that should be a quick fix
m
But I should be able to run the pipeline even if there aren't any known indels and dbsnp, isn't it?
m
you should indeed
That might be a mess that I introduce
I'm on it, I'll finish the fix tomorrow
🎉 1
that should do the trick
it has been merged in 
dev
Could you test and let us know if it solves this for you the way you expect
and if we're good I could work a release
m
Hey! (Yesterday I wasn't in the lab). I will try to run the pipeline and I tell you the result. Thanks!
🙏 1
Withouth the --skip_baserecalibration it gives the error requiring dbsnp or known_indels. Using skip_baserecalibration, it still ends without error but without doing the variant calling. The command:
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NXF_VER=25.04.6 nextflow run nf-core/rnavar \
        --input samplesheet_rnavar.csv \
        --outdir PROCESSING_rnavar \
        --genome GRCm38 \
        --skip_baserecalibration \
        -r dev \
        -profile apptainer
I don't know if I should do something different...
n
You need to add 
-latest
to make sure Nextflow pulls the latest version of the branch
m
You mean in addition to "-r dev"? I'll try!
meow yes 1
n
yes indeed 😛
Nextflow basically does a git clone of the pipeline repository and will only use the branches available in the cloned version instead of always pulling in new changes. Using this flag enables that feature 😛
m
Ok! 😄. One more thing I have learned.
🎉 1
It worked, now it outputs the vcf files. Thanks!
🎉 1
Good weekend.
m
Perfect
👌 1
I'll try to draft a release next week then
m
Thanks for your help!
m
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