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**the exact command you tried to run**
Feel free to leave any original paths, we don't have access to your system
srun -N 1 -n 1 bash -c "flair collapse -g /home/mbauer/genome/gencode.43.GRCh38.prim…
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I had recently did a Nanopore sequencing run for SARS-CoV-2 in MinION with midnight primers 1200 bp amplicons (Nikki Freed protocol) and native barcoding kit (EXP-NBD96). I have earlier used EPI2ME pi…
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## Is your feature request related to a problem? Please describe
At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only).
…
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### Operating System
Other Linux (please specify below)
### Other Linux
Red Hat Enterprise Linux 9.4
### Workflow Version
2.2.3
### Workflow Execution
Command line (Local)
### Other workflow e…
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### Operating System
Other Linux (please specify below)
### Other Linux
Ubuntu 20.04.6 LTS
### Workflow Version
v1.0.0
### Workflow Execution
Command line
### EPI2ME Version
_No response_
##…
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I am installing this pipeline on Stallo; a rocks distro cluster in Norway. I am struggling to understand how the number of parallel processes are defined. If I set the number of cores to 20 and the nu…
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### Ask away!
I'm using this workflow on our HPC via Singularity. The input bam is a Promethion run mini bams merged via samtools merge into a single bam (140GB). Is this a missing header issue or a …
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### Operating System
Windows 10
### Other Linux
_No response_
### Workflow Version
v2.10.1
### Workflow Execution
EPI2ME Desktop (Local)
### Other workflow execution
_No response_
### EPI2ME…
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Hi,
When I run 10 samples separately, the percentage of novel isoforms with CAGE support are like 50% in each samples.
But, I want to generate one GTF file. So, I run 10 samples together. The resul…
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The following lines in step 5 of the makefile:
```
# index the draft assembly for bwa
draft_genome.fasta.bwt: raw.reads.np.fasta
bwa index $<
# index the draft assembly for faidx
draft_genom…