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zavolan_group
pipelines
ZARP
Commits
1782ea86
Commit
1782ea86
authored
5 years ago
by
Alex Kanitz
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fix broken links in docs
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885c5692
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!29
Add pipeline updates into MultiQC dev branch
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1782ea86
...
...
@@ -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
>
[
L
ab
K
ey
]:
<
https://www.labkey.com/
>
[
l
ab
k
ey
]:
<
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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