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zavolan_group
pipelines
ZARP
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e331f10e
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4 years ago
by
MihaelaZavolan
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# ZARP
pipeline
# ZARP
[
Snakemake
][
snakemake
]
workflow
for general purpose RNA-Seq library annotation
developed by the
[
Zavolan lab
][
zavolan-lab
]
.
[
Snakemake
][
snakemake
]
workflow
that covers common steps of short read RNA-Seq
library analysis
developed by the
[
Zavolan lab
][
zavolan-lab
]
.
Reads are processed, aligned, quantified and analyzed with state-of-the-art
tools to give meaningful initial insights into various aspects of an RNA-Seq
library while cutting down on hands-on time for bioinformaticians.
Reads are analyzed (pre-processed, aligned, quantified) with state-of-the-art
tools to give meaningful initial insights into the quality and composition
of an RNA-Seq library, reducing hands-on time for bioinformaticians and giving
experimentalists the possibility to rapidly assess their data.
Below is a schematic representation of the individual
workflow steps ("pe"
refers to "paired-end"):
Below is a schematic representation of the individual
steps of the workflow
("pe"
refers to "paired-end"):
> ![rule_graph][rule-graph]
For a more detailed description of each step, please refer to the
[
pipeline
documentation
][
pipeline
-documentation
]
.
For a more detailed description of each step, please refer to the
[
workflow
documentation
][
workflow
-documentation
]
.
## Requirements
...
...
@@ -28,8 +29,8 @@ on the following distributions:
### Cloning the repository
Traverse to the desired
path
on your file system, then clone the
repository and
move into it
with:
Traverse to the desired
directory/folder
on your file system, then clone
/get
the
repository and move into the respective directory
with:
```
bash
git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/zarp.git
...
...
@@ -49,8 +50,8 @@ Other versions are not guaranteed to work as expected.
For improved reproducibility and reusability of the workflow,
each individual step of the workflow runs in its own
[
Singularity
][
singularity
]
container. As a consequence, running this workflow has very few
individual dependencies.
It does, h
owever, require Singularity to be installed
on the system
running
the workflow. As the functional installation of
individual dependencies.
H
owever,
it
require
s
Singularity to be installed
on the system
where
the workflow
is executed
. As the functional installation of
Singularity requires root privileges, and Conda currently only provides
Singularity for Linux architectures, the installation instructions are
slightly different depending on your system/setup:
...
...
@@ -105,15 +106,14 @@ conda env update -f install/environment.dev.yml
## Testing the installation
We have prepared several tests to check the integrity of the workflow, its
components and non-essential processing scripts. These can be found in
subdirectories of the
`tests/`
directory. The most critical of these tests
lets you execute the entire workflow on a small set of example input files.
Note that for this and other tests to complete without issues,
[
additional dependencies
](
#installing-non-essential-dependencies
)
need to be
installed.
We have prepared several tests to check the integrity of the workflow and its
components. These can be found in subdirectories of the
`tests/`
directory.
The most critical of these tests enable you execute the entire workflow on a
set of small example input files. Note that for this and other tests to complete
successfully,
[
additional dependencies
](
#installing-non-essential-dependencies
)
need to be installed.
###
Run
workflow on local machine
###
Test
workflow on local machine
Execute the following command to run the test workflow on your local machine:
...
...
@@ -121,7 +121,7 @@ Execute the following command to run the test workflow on your local machine:
bash tests/test_integration_workflow/test.local.sh
```
###
Run
workflow via Slurm
###
Test
workflow via Slurm
Execute the following command to run the test workflow on a
[
Slurm
][
slurm
]
-managed high-performance computing (HPC) cluster:
...
...
@@ -131,15 +131,15 @@ bash tests/test_integration_workflow/test.slurm.sh
```
> **NOTE:** Depending on the configuration of your Slurm installation or if
> using a different work
f
lo
w
manager, you may need to adapt file `cluster.json`
> and the arguments to options `--config` and `--cores` in file
> using a different worklo
ad
manager, you may need to adapt file `cluster.json`
> and the arguments to options `--config` and `--cores` in
the
file
> `test.slurm.sh`, both located in directory `tests/test_integration_workflow`.
> Consult the manual of your workload manager as well as the section of the
> Snakemake manual dealing with [cluster execution].
## Running the workflow on your own samples
1.
Assuming that you
are
current
ly inside
the repository's root directory,
1.
Assuming that you
r
current
directory is
the repository's root directory,
create a directory for your workflow run and traverse inside it with:
```bash
...
...
@@ -156,7 +156,7 @@ configuration files:
touch cluster.json
```
3.
Use your editor of choice to
manually
populate these files with appropriate
3.
Use your editor of choice to populate these files with appropriate
values. Have a look at the examples in the
`tests/`
directory to see what the
files should look like, specifically:
...
...
@@ -166,7 +166,7 @@ files should look like, specifically:
4.
Create a runner script. Pick one of the following choices for either local
or cluster execution. Before execution of the respective command, you must
replace the data directory placeholders in the argument
t
o the
replace the data directory placeholders in the argument o
f
the
`--singularity-args`
option with a comma-separated list of _all_ directories
containing input data files (samples and any annoation files etc) required for
your run.
...
...
@@ -223,9 +223,11 @@ Our lab stores metadata for sequencing samples in a locally deployed
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).
However, as these scripts were written specifically for the needs of our lab,
they are likely not directly usable or, at least, will require considerable
modification for other setups (e.g., different LabKey table structure).
Nevertheless, they can serve as an example for interfacing between LabKey and
your workflow.
> **NOTE:** All of the below steps assume that your current working directory
> is the repository's root directory.
...
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