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I have 2 following steps in CWL workflow that are executed conditionally (using when statement) and output from one of them is input for the second one, and second one contains scatter. There is a fra…
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Hi There,
I got following issues when I was trying to run the program:
```
fasta=/data1/workspace/DCI/Kirsch/Jianguo.Huang/circRNA/bwaindex/genome.fa
gtf=/data1/Annotation/iGenome/Mus_musculus/U…
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Hello,
I was able to install megSAP on our server and after a successful test run with provided panel data I am trying to run analysis of WES data. Everything runs smoothly until the VCFAnnotatefromV…
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I think we need to revisit our trimming parameters for ThruPlex NGS16S libraries (more an issue for the clampi pipeline than this one). If it's straightforward to do, it might be helpful to preserve t…
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Hallo again,
This something new:
```bash
DNA-mapping -i /mnt/Z/Shared\ folder/Shared\ data/DNA/NGS_AP06_apouikli_A006200409/ -o /mnt/Z/Shared\ folder/Shared\ data/DNA/NGS_AP06_apouikli_A006200409/b…
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Unit testing each process is great for making sure we get expected outputs during development. However, all of these unit tests really end up hampering development time when a new pipeline is forked o…
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**I used following commands to prepare the reference genome**
```
rsem-prepare-reference --gtf ref/Homo_sapiens.GRCh37.69.gtf \
--bowtie2 --bowtie2-path /home/ngs/bin/bowtie2 \
ref/Homo_…
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It would be nice to have a workflow option to 'delete intermediate files' after they have been used as input. There is currently a workflow option to 'Delete intermediate jobs if they are not used as …
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Hi,
I'm having issues trying to run SigProfiler for CNV data using custom CNV calls. We have an in-house pipeline for CNV calls that is similar to the ASCAT approach, tailored to our WGS data. I t…
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GPU pipeline raises `Bad argument value: Number of GPUs requested (6) is more than number of GPUs`
* Java version used for NextFlow run:
```
$ java --version
openjdk 17.0.6 2023-01-17
OpenJDK R…