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### Description of the bug
ERROR ~ while scanning a simple key
in 'reader', line 3, column 1:
0.4.8
^ …
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### User story:
As a customer, I would like to be able to analyse dna samples with raredisease,
so that I don't have to analyse my own FASTQ files.
### Acceptance criteria:
- A customer should b…
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### Description of the bug
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (
earlycasualcaiman)' …
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Current samplesheets for raredisease look like below. As you can see, the lane field indicates the lane number where the sample was run in the flowcell.
```
sample,lane,fastq_1,fastq_2,sex,phenot…
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**Describe the bug**
This file is currently being uploaded to Scout for MIP. However, it doesn't seem to be stored for the Raredisease pipeline.
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### Description of the bug
Aug-12 14:30:26.359 [TaskFinalizer-10] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEP…
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## Bug report
### Expected behavior and actual behavior
Running an nf-core pipeline would download the charliecloud images on-demand.
When multiple different processes are scheduled at the s…
fa2k updated
10 months ago
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### Description of the bug
The ped file cannot be created when outdir is an s3 path, leading to an error.
For example, defining `--outdir s3:/rarediseases-workspace/results/` with the test data gi…
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### Description of the bug
Hi,
I am trying to install this pipeline using conda. The command used is mentioned below. Conda is expecting an environment.yml file to be present inside "raredisease/…
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### Description of the bug
Manta fails with a path error:
```
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-16 03:00:07.184 [Actor Thread 16] ERROR nextflow.processo…