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Hi, I am unable to process data from the with_config folder except the "issue_1205" subfolder:
![Screenshot from 2022-09-12 13-33-44](https://user-images.githubusercontent.com/44240739/189644228-7165…
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Hi,
I am a fresh user of nextNEOpi and exciting to explore this well-built pipeline! But I met some errors when run my test dataset.
The Error:
```
Error executing process > 'fastp (Patient353…
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I am running mutation calling and HLA with optitype (separatily), and I'm encountering the same error involving bgzf
Error: unhandled exception: invalid bgzf file [ValueError]
[hla.config.yaml.txt…
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See https://github.com/umccr-illumina/ica_v2/issues/116 for more information.
Will complete a full list of steps that exceed this length.
21 characters is the upper limit for steps that are s…
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### Description of bug
Currently, MultiQC does not seem to be able to pick up custom data when the file is specified in a custom configuration.
I used the test data provided in the repository to p…
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Hi,
Sorry for bothering again. I found that
```
nextflow run /scratch/u/kfang/Software/nextNEOpi/nextNEOpi.nf -bg --batchFile test2.csv -config conf/params.config -profile singularity -resume --…
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I ran
```
nextflow run -c params.config -profile nbis,conda ~/git/NBIS/pipelines-nextflow/TranscriptAssembly/TranscriptAssembly.nf
```
and got the following error :
```
Caused by:
Process …
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Getting this when using the bcbio_v1.2.4 branch on Gadi:
```
Looking for: ['python==3.7.3', 'pip', 'git', 'cython', 'bcftools==1.10.2', "openssl[version='>=1.1']", 'bedtools==2.29.2', 'samtools==1…
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Hello,
I am using conda to install AMR++ pipeline but the demo crashed while parsing nextflow.config with the following error:
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ nextflow run main_A…