IRMA: Edited config for plattform specific assembly

[aaronKol]

Default irma module is set to FLU-avian.

The user can now specify the sequencing platform used, such that minimap2 works best. The user can also decide if UTRs should be created or not.

Test data now consists of properly paired read files.

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• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
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[bgruening]

/usr/local/bin/IRMA_RES/scripts/parseSORTresults.pl ERROR: no classification output found! Aborting.
Traceback (most recent call last):
  File "/home/runner/work/tools-iuc/tools-iuc/tools/irma/createMissingFiles.py", line 78, in <module>
    bamHeader = getBamHeaderFromAnyFile()
                ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/tools-iuc/tools-iuc/tools/irma/createMissingFiles.py", line 27, in getBamHeaderFromAnyFile
    anyBamFile = glob.glob(dirPrefix + "*.bam")[0]
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range

[wm75]

@bgruening, yes, but the root of this error message seems to be that the irma LABEL step doesn't produce the expected output. The current working hypothesis is that this script has a lot of dependencies and at least one of them might be missing from the biocontainer (tests succeed when run locally non-containerized).

[bgruening]

sed or awk?

[wm75]

@aaronKol reading through the original IRMA publication it seems that read sorting with LABEL instead / in addition to BLAT comes with only a very small benefit in terms of accuracy, but we know it has a big runtime overhead.
Given the difficulty here to get this mode running in a container why not just stick to BLAT only for now (essentially what you had working in 42056e3)?

[wm75]

So, now that we know that we don't support LABEL you need to eliminate the advanced_config.sort_step section.

[wm75]

... and because we are always using minimap I would rename all the SSW_ options in advanced_config.assembly to their MM2 counterparts for clarity, and if set, apply them also in Illumina mode (instead of the -x sr defaults).