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Commit 1f933bcc authored by Alex Kanitz's avatar Alex Kanitz
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Merge branch 'hotfix_docs_missing_link' into 'master'

fix broken links in docs

See merge request zavolan_group/pipelines/rnaseqpipeline!27
parents 885c5692 1782ea86
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2 merge requests!29Add pipeline updates into MultiQC dev branch,!27fix broken links in docs
Pipeline #10295 passed
......@@ -120,8 +120,8 @@ bash tests/test_integration_workflow/test.local.sh
### Run workflow via Slurm
Execute the following command to run the test workflow on a Slurm-managed
high-performance computing (HPC) cluster:
Execute the following command to run the test workflow on a
[Slurm][slurm]-managed high-performance computing (HPC) cluster:
```bash
bash tests/test_integration_workflow/test.slurm.sh
......@@ -216,14 +216,14 @@ your run.
### Configuring workflow runs via LabKey tables
Our lab stores metadata for sequencing samples in a locally deployed [LabKey]
instance. This repository provides two scripts that give programmatic access to
the LabKey data table and convert it to the corresponding workflow inputs
(`samples.tsv` and `config.yaml`), respectively. As such, these scripts largely
automate step 3. of the above instructions. However, as these scripts were
specifically for the needs of our lab, they are likely not portable or, at
least, will require considerable modification for other setups (e.g., different
LabKey table structure).
Our lab stores metadata for sequencing samples in a locally deployed
[LabKey][labkey] instance. This repository provides two scripts that give
programmatic access to the LabKey data table and convert it to the
corresponding workflow inputs (`samples.tsv` and `config.yaml`), respectively.
As such, these scripts largely automate step 3. of the above instructions.
However, as these scripts were specifically for the needs of our lab, they are
likely not portable or, at least, will require considerable modification for
other setups (e.g., different LabKey table structure).
> **NOTE:** All of the below steps assume that your current working directory
> is the repository's root directory.
......@@ -322,10 +322,11 @@ Contaminant sequences | contaminant_seqs
[conda]: <https://docs.conda.io/projects/conda/en/latest/index.html>
[cluster execution]: <https://snakemake.readthedocs.io/en/stable/executing/cluster-cloud.html#cluster-execution>
[LabKey]: <https://www.labkey.com/>
[labkey]: <https://www.labkey.com/>
[miniconda-installation]: <https://docs.conda.io/en/latest/miniconda.html>
[rule-graph]: images/rule_graph.svg
[snakemake]: <https://snakemake.readthedocs.io/en/stable/>
[Singularity]: <https://sylabs.io/singularity/>
[Slurm]: <https://slurm.schedmd.com/documentation.html>
[singularity]: <https://sylabs.io/singularity/>
[singularity-install]: <https://sylabs.io/guides/3.5/admin-guide/installation.html>
[slurm]: <https://slurm.schedmd.com/documentation.html>
[zavolan-lab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>
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