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NextSeqPostRunDataProcessor

This bash script automates NextSeq Illumina raw data processing by generating ready to upload FASTQ files. The FASTQ files are basecalled using bcl2fastq Illumina software. The final raw sequences can be uploaded to NML IRIDA server via the IRIDA Uploader.

For more information please consult the documentation website

Local Config

Local configuration file to try out for the command line upload. It works if config file is structured correctly. See example config file here.

Example run on waffles server and irida command line uploader

/Drives/P/conda_envs/irida-uploader-0.2.1) [kbessono@waffles Data]$ irida-uploader --config config-v2.conf -f 190329_NB551633_0004_AHGCNCAFXY/
2019-07-03 21:43:42 INFO     looking for run in 190329_NB551633_0004_AHGCNCAFXY/
2019-07-03 21:43:42 INFO     Adding log file to 190329_NB551633_0004_AHGCNCAFXY/
2019-07-03 21:43:42 INFO     ==================================================
2019-07-03 21:43:42 INFO     ---------------STARTING UPLOAD RUN----------------
2019-07-03 21:43:42 INFO     Uploader Version 0.2.1
2019-07-03 21:43:42 INFO     Logging to file in: /home/CSCScience.ca/kbessono/.cache/irida_uploader/log
2019-07-03 21:43:42 INFO     ==================================================
2019-07-03 21:43:42 INFO     Reading data from sample sheet 190329_NB551633_0004_AHGCNCAFXY/SampleSheet.csv
2019-07-03 21:43:43 INFO     Looking for files with pattern SA20190644n_S1_L\d{3}_R(\d+)_\S+\.fastq.*$
2019-07-03 21:43:43 INFO     Looking for files with pattern SA20191119n_S2_L\d{3}_R(\d+)_\S+\.fastq.*$
2019-07-03 21:43:43 INFO     Looking for files with pattern SA20191120n_S3_L\d{3}_R(\d+)_\S+\.fastq.*$
2019-07-03 21:43:49 INFO     Getting samples from project '938'
2019-07-03 21:44:00 INFO     Creating sample 'SA20190644n' for project '938' on IRIDA.
2019-07-03 21:44:11 INFO     Getting samples from project '938'
2019-07-03 21:44:24 INFO     Getting samples from project '938'
2019-07-03 21:44:24 INFO     Creating sample 'SA20191119n' for project '938' on IRIDA.
2019-07-03 21:44:36 INFO     Getting samples from project '938'
2019-07-03 21:44:49 INFO     Getting samples from project '938'
2019-07-03 21:44:49 INFO     Creating sample 'SA20191120n' for project '938' on IRIDA.

2019-07-03 21:45:13 INFO     *** Starting Upload ***
2019-07-03 21:45:18 INFO     Sequencing run id '2943' has been created for upload
2019-07-03 21:45:23 INFO     Uploading to Sample SA20190644n on Project 938
2019-07-03 21:45:34 INFO     Starting to send file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20190644n_S1_L001_R2_001.fastq.gz
Progress:  100.0 % Uploaded
2019-07-03 21:45:36 INFO     Finished sending file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20190644n_S1_L001_R2_001.fastq.gz
2019-07-03 21:45:36 INFO     Starting to send file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20190644n_S1_L001_R1_001.fastq.gz
Progress:  100.0 % Uploaded
2019-07-03 21:45:38 INFO     Finished sending file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20190644n_S1_L001_R1_001.fastq.gz
2019-07-03 21:45:40 INFO     Uploading to Sample SA20191119n on Project 938
2019-07-03 21:45:53 INFO     Starting to send file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20191119n_S2_L001_R2_001.fastq.gz
Progress:  100.0 % Uploaded
2019-07-03 21:45:56 INFO     Finished sending file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20191119n_S2_L001_R2_001.fastq.gz
2019-07-03 21:45:56 INFO     Starting to send file 190329_NB551633_0004_AHGCNCAFXY/Data/Intensities/BaseCalls/SA20191119n_S2_L001_R1_001.fastq.gz
Progress:  100.0 % Uploaded
2019-07-03 21:46:23 INFO     Samples in directory '190329_NB551633_0004_AHGCNCAFXY/' have finished uploading!
2019-07-03 21:46:23 INFO     ==================================================
2019-07-03 21:46:23 INFO     ----------------ENDING UPLOAD RUN-----------------
2019-07-03 21:46:23 INFO     ==================================================
2019-07-03 21:46:23 INFO     Stopped active logging to run directory

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NextSeq raw data processor for IRIDA Uploader

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