Managing viralrecon execution

[Shettland]

Preparing the data to launch viralrecon and to extract the necessary data for read-bioinfo-metadata is a time-consuming process that has to be done manually right now. It could be rather easily automated with one or two modules.

[saramonzon]

duplicated #245?

[Shettland]

Not the same, this one aims to extract the necessary characteristics of the samples for the bioinformatics analysis like filenames, reference, paired-end or single-end, long or short-reads and generate a template to run viralrecon with the correspondent parameters (or IRMA if necessary) depending on key points.
On the other hand, #245 just mentions the necessity to process the log file created using --log to generate a summary report of the execution and maybe combine it with an automatic email to the submitter

[Shettland]

Ok you are refering to #244 . Its an extension of this one so yeah, I'll delete it.

[saramonzon]

yes, it was #244 sorry xD, add the extended description here so we don't loose it :)

[Shettland]

A new module could be implemented to do the following tasks:

1. Create folder structure to launch viralrecon/IRMA in the desired folder (HPC), taking support from buisciii-tools
2. Copy/move the fastq files to RAW
3. Extract metadata from json with .get("r1/r2_fastq_filepath") to create the samplesheet
4. Extract necessary metadata for configuration files (paired/single-end, flu/RSV/SARS...)
5. Load the necessary modules
6. Launch viralrecon if possible

[Shettland]

Friendly reminder: read_bioinfo_metadata.py should try to find the files for each sample from the bioinformatic analysis results using the same "search" process as the one used to create the samplesheet for either viralrecon or IRMA. Right now it uses "sequencing_sample_id" which is definitely not the best option

[Shettland]

This issue was adressed in #286