-
### Description of bug
I'm trying to change the name of the default file pattern for `dragen/wgs_contig_mean_cov` using a config file:
```yml
sp:
dragen/wgs_contig_mean_cov:
fn: 'contig…
-
### Description of bug
We've noticed a few problems with the `mosdepth` module of MultiQC.
- Some samples (very few) have partial dropouts. In the general stats table, they'll have a value for "Me…
-
See also: https://github.com/nf-core/test-datasets/pull/356 for details
TODO:
- [x] update modules config file by adding the cram files
Modules that need recalculated output md5sums possib…
-
After updating the input file for the `optitype` module, see [here](https://github.com/nf-core/modules/pull/782/files), the test fail with the following error message:
```
WARNING: Your kernel do…
-
OptiType was installed with `conda install optitype` , and it can print help message, but cannot deal with small data( HLA_1.fastq = 31k and HLA1_2.fastq = 31k).
The command is `python OptiTypePipeli…
-
Should / could be a nice little table or custom module - could also have a simple `samtools idxstats` output in the same to display mapping stats of the different libraries independent of the mapper b…
-
### Description of bug
Trying to run multiqc on fastp json/html output but it fails with the message "No analysis results found".
I tried running both the conda install v1.14 release and then the …
-
Consider migration from quay.io containers to public.ecr.containers. This may speed up download of containers and initialisation time for some of our tasks on ICAv1 and ICAv2 since both are hosted on…
-
The exit status of the task that caused the workflow execution to fail was: 1
Error executing process > 'pre_map_hla (1)'
Caused by:
Process `pre_map_hla (1)` terminated with an error exit st…
-
Currently for the optitype step we request 64GB of ram and say nothing about CPUs.
https://github.com/griffithlab/analysis-wdls/blob/main/definitions/tools/optitype_dna.wdl
But when Cromwell req…