A Python script (and accompanying Dockerfile) to generate spreadsheet rows for the UMCCR Samples spreadsheet.
Data is generated from the bcl2fastq output for a specific Illumina run ID.
The script is invoked with a runID. It will then scan for bcl2fasta output directories (name being or starting with the run ID) in the configurabnle bcl2fastq-outdir location.
For each found .fastq.gz file it create a row record for the spreadsheet trying to parse information our of the run ID and FASTQ file name.
The generated data rows can then be written to a CSV file or directly appended to a Google Spreadsheet. The first use-case (CSV) requires an output location, whereas the second case (GOOGLE) requires Google access credentials to the spreadsheet (Google sheets API).
Example use cases (where local/usdu is the Docker container build from the Dockerfile):
# assumes CSV as default use case
docker run --rm -v /tmp/foo/fastq_base/:/fastq -v /tmp/foo/output/:/output local/usdu:latest 180718_A00130_0067_AH5M5MDSXX# requires Google credentials
docker run --rm -v /tmp/google-credsdentials-dir/:/creds -v /tmp/fastq-base-dir/:/fastq local/usdu:latest 180718_A00130_0067_AH5M5MDSXX --use-case GOOGLE