diff --git a/README.md b/README.md index 4504491c086419180237142fc38de151513a7892..9fd71c2dbf490bcd0c4e1b4fd56b87fc0645161c 100644 --- a/README.md +++ b/README.md @@ -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/>