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apeltzer / EAGER-links

Preformatted execution scripts for EAGER, making installation easier for end users.
GNU General Public License v3.0
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mttonucratiocalculator 0.7 does not work with EAGER-CLI 1.92.55 #1

Open alexreg opened 2 months ago

alexreg commented 2 months ago

I'm not clear about which version of mttonucratiocalculator that EAGER-CLI 1.92.55 expects, since EAGER it seems to pass it 3 arguments, whereas mttonucratiocalculator only expects two.

$ mttonucratiocalculator /tmp/ArzelierEtAl2024/eager/BOU13/results/5-DeDup/BOU13_S8_R1_001.fastq.merged.fq.mappedonly.sorted.cleaned_rmdup.sorted.bam /tmp/ArzelierEtAl2024/eager/BOU13/results/5-DeDup MT
Version: 0.7
Please provide the (coordinate) sorted input SAM File, as well as the MT identifier. No further parameters are necessary! 

Make sure that your input file has an appropriate SAM/BAM file header, or the SAMRecords will be set to '*'!

Furthermore, if I manually run this command but remove the second argument, I get an error.

Exception in thread "main" java.lang.NullPointerException
    at MTtoNucCalculator.getMTLength(MTtoNucCalculator.java:138)
    at MTtoNucCalculator.<init>(MTtoNucCalculator.java:52)
    at MTtoNucCalculator.main(MTtoNucCalculator.java:71)

Any clarification would be appreciated.

alexreg commented 2 months ago

Okay, well the second problem at least is now fixed in my PR here.

apeltzer commented 2 months ago

I would also advise to using https://nf-co.re/eager these days instead of the old EAGERv1 pipeline.