This PR adds a new entry point for PHoeNIx, called PHOENIX_QC. What this does is allow users to run their samples through other pipelines, then determining if their samples pass PHoeNIx QC metrics.
PHOENIX_QC requires a different type of CSV file with the following columns:
sample A sample name for the input
fastq_1 R1 of reads run through Fastp
fastq_2 R2 of reads run through Fastp
fastp_pass_json JSON output from initial Fastp run
fastp_failed_json JSON output from rerun of Fastp on failed reads
spades Assembly created by SPAdes
mlst TSV output from mlst tool
quast TSV report generated from quast
amrfinderplus TSV report generated from amrfinderplus
The remained steps in PHOENIX_QC match the rest of the PHOENIX pipeline. I thought it best to let analyses (e.g. kraken, gamma) with PHoeNIx-specific databases still be handled by PHoeNIx.
This PR adds a new entry point for PHoeNIx, called
PHOENIX_QC. What this does is allow users to run their samples through other pipelines, then determining if their samples pass PHoeNIx QC metrics.PHOENIX_QCrequires a different type of CSV file with the following columns:The remained steps in
PHOENIX_QCmatch the rest of thePHOENIXpipeline. I thought it best to let analyses (e.g. kraken, gamma) with PHoeNIx-specific databases still be handled by PHoeNIx.Right now I've pointed this at the
v1.0.1branch.Happy to take any suggestions and feedback.