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git clone https://github.com/eresearchqut/VirReport.git |
All the required modules are included in the environment.yml file in the pipeline base directory and shows all the tools used in the pipeline.
4. Running the pipeline
You can either invoke the pipeline by pointing to the location of main.nf in the version of VirReport you cloned, for example:
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The PBS script example below (VirReport_nextflow.sh) will run on raw fastq files that will need to be merged and then quality filtered.
We are also asking to run a process that will derive an RNA source profile for the each samples during the quality filtering step.
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qsub VirReport_nextflow.sh |
You can monitor your jobs using the command:
qstat -u $USER
Alternatively use the following command to check on the jobs you are running.:
qjobs
You can also check the .nextflow.log file for details on progress.
Finally, if you have configured the connection to the NFTower you can logon and check your run.
5. Outputs
5A. Nextflow folder structure:
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-Results folder where all the generated data files to be kept are saved. The pipeline will populate outputs under separate folders for each step. These will be stored in subfolders for each sample.
5B. VirReport results folder structure
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◦ under the QC_report folder, read size distribution pdf file and read RNA source pdf file are created. The folder also includes a run_qc_report text file
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01_VirReport folder content:
For each sample:
assembly: results associated with de novo assembly
blastn: megablast results (NCBI NT or viral database PVirDB)
blastx: blastx results against NR
tblastn: tblastn results against viral database PVirDB
alignments: alignment against top reference hit and associated statistic derivation
Summary
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