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Commit 114faf26 authored by Pavel Jirásek's avatar Pavel Jirásek
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fix html in internal link

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......@@ -231,7 +231,7 @@ second one.
--project>. Project ID of your supercomputer allocation.
--queue. [Queue](../../introduction.html) to run the jobs in.
--queue. [Queue](../../resources-allocation-policy/) to run the jobs in.
```
Input, output and ped arguments are mandatory. If the output folder does not exist, the pipeline will create it.
......@@ -278,7 +278,7 @@ Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID):
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod
```
This command submits the processing [jobs to the queue](../../job-submission-and-execution.html).
This command submits the processing [jobs to the queue](../../job-submission-and-execution/).
If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:
......@@ -334,7 +334,7 @@ This listing show which tools are used in each step of the pipeline
## Interpretation
The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team.html) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team/) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
![TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts.]\((../../../img/fig7.png)
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