Main tool: fastq-scan
In addition to fastq-scan, this docker image contains the CLI json parser jq.
Example stats for a uncompressed FASTQ: $ docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/fastq-scan:1.0.0 /bin/bash -c "cat /fastq-scan/example.fq | fastq-scan"
Example stats for a compressed (gzip) FASTQ: $ docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/fastq-scan:1.0.0 /bin/bash -c "zcat /data/SRX0000000_R1.fastq.gz | fastq-scan"
Eaxmple using jq to extract the total number of reads in the FASTQ: $ docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data fastq-scan:1.0.0 /bin/bash -c "cat /fastq-scan/example.fq | fastq-scan | jq .qc_stats.read_total"
View full fastq-scan help options: $ docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/fastq-scan:1.0.0 fastq-scan -h