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Hi!
I am trying to use isoquant within the polyTailor tool.
I am looking at viral sequences...
Isoquant does not like the viral gff files and throws the below error.
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2024-12-02 19…
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Hello,
I am using Isoquant to quantify my bam files, 6 samples (3 treatment Vs 3 control). the process seems to be frozen after some time. in the aux folder, I got OUT.save_chr (_bamstat, _collecte…
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Hey!
This is a great pipeline. I have been using sc_long_pipeline function and the gene quantification step fails. However, when I run this function with do_gene_quantification = FALSE in my configur…
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### Description of the bug
Hi,
I encountered an issue while running the pipeline with data generated using the nf-core/RNAseq pipeline. Specifically, when attempting to run the gprofiler analysis wi…
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### Description of the bug
Running the pipeline on "real" data returns an error, with the log showing the cause as a missing file (`test.fa`). Creating this file in the current/working directory (e.g…
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I’m facing an issue with the report below.
we have a total of six samples divided into two groups: treated and control. Each sample has been processed independently up to the DE Analysis step, w…
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Hi! I am not sure if this is a question for nextclade or augur.
I am using `augur ancestral` as part of a pipeline to create a tree for use in a nextclade dataset: https://github.com/anna-parker/ma…
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We want to be able to include some standard basic statistics on the gene/protein annotation set for an assembly in a genome note. This sub workflow should accept an annotation set and calculate some s…
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Running BRAKER 3.0.8 on Ubuntu-20.04 (WSL2) in Singularity-CE-4.2.1
On some genomes the pipeline crashes:
braker.log:
`/opt/conda/bin/python3 /opt/Augustus/scripts/fix_in_frame_stop_codon_genes…
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### Description of the bug
I am trying to run the scrnaseq nextflow workflow with the following error message:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER ([])'
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