diff --git a/docs.it4i/anselm/software/omics-master/overview.md b/docs.it4i/anselm/software/omics-master/overview.md index 072994e9e862069afd8df7e42f2a661c1078a50b..7a827c97b6cd5212bc932779b870e4ac8f8464cf 100644 --- a/docs.it4i/anselm/software/omics-master/overview.md +++ b/docs.it4i/anselm/software/omics-master/overview.md @@ -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)