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### Description of the bug
Dear All, I am testing the pipeline and I am facing the following error,
Not all conditions are included in the contrast file.
Thanks for your support
```
Error exec…
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Dear,
We are using your tool on spiked samples and come across some discrepancies between what we expect and what we get. For example we used a bought RNA virus at 100% that should be B.1.1.7 (this…
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### Description of the bug
I am running the rnaseq pipeline on a human data set. The process terminates with an exceeded time limit error for the HISAT2_ALIGN task. I have already increased the tim…
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Hi guys,
I am curious about the output from BRAKER3. I am running using the latest singularity container, with the following command (taken from the top of braker.log):
`/opt/BRAKER/scripts/brak…
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Hello,
I have been testing Arioc for a few days and I can see some clear speed advantages compared to Bowtie2. Also, by tweaking the parameters, I can get a higher percentage of mapped reads with A…
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## Bug report
Using nextflow with charliecloud.enabled=true with a shared `cacheDir` on a HPC
### Expected behavior and actual behavior
By default the `ch-run` command uses the result of `ma…
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## Bug report
### Expected behavior and actual behavior
Hello, I'm running the `nf-core/rnaseq` pipeline with AWS Batch backend. Everything is working fine except for one small issue, that …
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i met an STAR error since i have only 8 CPUs.
```console
[cailiangliang@localhost P20190401]$ nextflow run nf-core/rnaseq --reads '*_R{1,2}.fq.gz' --genome GRCh37 -profile docker
N E X T F L O W …
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Hi, I installed nanosim using `conda install -c bioconda nanosim` and then tried to run the read characterization using
`read_analysis.py transcriptome -i training_reads.fastq -rg reference_genome.f…
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### Description of the bug
I have tried running the pipeline with both bwa and bwamem, either way everything seems to run fine up until the samtools sort step, which does appear to complete on the …