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Hi and thank you for all your work with this pipeline!
I am having a bit of trouble analyzing my PacBio Kinnex full length 16s rRNA data. The data I received from the sequencing center were alre…
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### Description of the bug
I encountered an error while running the nf-core/smrnaseq pipeline. The process NFCORE_SMRNASEQ:MIRTRACE:MIRTRACE_RUN (1) failed with the error message indicating an invali…
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### Description of the bug
I am trying to programmatically get the list of all containers in the pipeline. However the standard command `nextflow inspect` does not seem to work, even if you tell it t…
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Hi,
Whenever I run the pipeline, an error always occurs with Shovill.
When I check the .nextflow.log file, I see the following message:
10:40:30.287 [Task monitor] DEBUG nextflow.processor.Task…
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Hi!
I was trying to run the pipeline using a SMB-mounted directory in a network cluster, but I got an error at the beginning regarding symbolic links:
"Command error:
ln: failed to create sym…
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While running
process > RENAME (1)
an error comes up regarding the python env:
Command error:
/usr/bin/env: ‘python’: No such file or directory
Most presumably the pipeline is dependent on…
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### Description of the bug
Hello,
Following the instructions: https://pipelines.tol.sanger.ac.uk/curationpretext/1.0.0/usage , I am getting a FileNotFound error in the most recent version of th…
SamCT updated
3 weeks ago
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We recently set the default for `aws.batch.maxSpotAttempts` to `0` in https://github.com/nextflow-io/nextflow/pull/5215 to avoid unexpected costs in cloud.
This is good, but it means we go back to …
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1. Create one container with all dependencies
Pipeline:
1. cmalign query sequences to 16s profile
2. esl-alimerge query and reference alignments
3. pplacer
4. guppy classifications classificati…
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### Description of the bug
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (
earlycasualcaiman)' …