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nf-core / hic

Analysis of Chromosome Conformation Capture data (Hi-C)
https://nf-co.re/hic
MIT License
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Wrong restriction sites for the Arima Kit => incorrect "--digestion 'arima'" option #127

Closed syfobfx closed 1 year ago

syfobfx commented 2 years ago

Description of the bug

An old issue that came back: the default Arima restriction and religation sites are incorrect, which makes the --digestion 'arima' option fail.

Precisely, the file https://github.com/nf-core/hic/blob/master/nextflow.config indicates

'arima' {
   restriction_site='^GATC,G^ANT'
   ligation_site='GATCGATC,GATCGANT,GANTGATC,GANTGANT'
}

while it should be

'arima' {
   restriction_site='^GATC,G^ANTC'
   ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
}

instead, as already rectified in the doc: https://nf-co.re/hic/usage#ligation_site

See https://github.com/nservant/HiC-Pro/issues/328

nservant commented 1 year ago

Thanks !