EACON-ONCOSCAN (✓ PRODUCTION)¶
Version: 1.0.0 Tags: CNV / EaCoN / Oncoscan / OncoScanCNV / Flamingo / Automated
This is the fully automated pipeline for Ampliseq on Flamingo. No config, no design, no time wasted.
« A good pipeline has no documentation » Someone on BiGR
Pipeline dependencies¶
This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.
Conda:
conda-forge::python ==3.9.2
conda-forge::git ==2.30.2
conda-forge::jinja2 ==2.11.3
conda-forge::pygraphviz ==1.7
conda-forge::flask ==1.1.2
conda-forge::pandas ==1.2.3
conda-forge::zlib ==1.2.11
conda-forge::openssl ==1.1.1k
conda-forge::networkx ==2.5.1
bioconda::snakemake ==6.1.1
conda-forge::black ==20.8b1
conda-forge::singularity ==3.7.1
conda-forge::mamba ==0.9.2
Additionally, the following prerequisites are non-optional:
None. Everything is on Flamingo already.
Output files¶
Please find below the list of expected output files:
Report on ASCAT segmentation
Genomic instability score
Notes¶
This pipeline runs EaCoN with ASCAT and default values highlighted for OncoScanCNV.
Installation¶
While installing the workflow, you may run the following commands (order matters):
Case |
Command line |
|---|---|
none |
# No installation needed.
|
Testing¶
In order to test the pipeline, you may try the following commands:
Case |
Command line |
|---|---|
quick-test |
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/eacon_oncoscan/test.sh
|
verbose-test |
bash -x /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/eacon_oncoscan/test.sh
|
Preparation¶
In order to prepare a run, you may try the following commands:
Case |
Command line |
|---|---|
none |
# No preparation, everything is available.
|
Execution¶
In order to execute the pipeline, you may run the following commands:
Case |
Command line(s) |
|---|---|
hg19 |
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/eacon_oncoscan/run.sh
|