sampleARC_nfcore
Description
This ARC has been build as an example on how to store a nf-core pipeline run (more precisely: nf-core/funcscan) on a publicly available dataset in an ARC-conform way. The dataset consists of assembled contigs from metagenomic sequences of yam leaf nodule samples from Madagascar (de Meyer et al., 2019).
The sampleARC_nfcore consists of two studies YamDataset and YamFuncscan, describing the study that produced the dataset and the nf-core/funcscan pipeline run performed on these data, respectively.
The YamDataset study is linked to the assay YamMetagenome, which contains details about the sequencing, as described in the publication.
The workflows folder contains the description of the nf-core/funcscan pipeline in CWL. This CWL wrapper was generated with DataPlant's nf-core-pipeline-to-arc tool.
Details of the parameter settings used for this sample-run are stored in runs/nfcore_funcscan_yam.yml.
Instalation
DataPlant
In order to use the DataHUB and other DataPLANT infrastructure and services, please sign up with DataPLANT.
CWL tool
See here how to install cwltool on your operating system or in a conda environment.
Nextflow
See here how to install nextflow on your operating system or in a conda environment.
Usage
Re-run this ARCs analysis
If you would like to re-run the workflow inside this ARC, you can do this via the cwltool as follows:
cwltool ./workflows/nfcore_funcscan.cwl ./runs/nfcore_funcscan_yam.ymlIf you prefer to use nextflow directly, navigate into the runs-folder and call
sh funcscan.shApply the workflow to your own data
If you would like to run nf-core/funcscan on your own data, generate a samplesheet specifying the paths to your data-files. Then, create your own .yml file setting the input:-parameter to your samplesheet.csv. Specify any parameter changes in your .yml file.
Alternatively, you can modify the .sh file by setting the --input parameter to your samplesheet.csv.
Support
Please contact DataPlant's Helpdesk for questions and support.
Contributing
This project is open and contributions to improve it are welcome. See here how to contribute to DataPlant projects.
Authors and acknowledgment
SAMPLEARC_NFCORE was originally written by Louisa Perelo (Quantitative Biology Centre QBiC, University of Tübingen) for DataPlant.
License
MIT License
Copyright (c) Louisa Perelo
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Project status
Closed