Dear all,
I would like to have a sorted bam from mapping to a custom reference. It seems that I'm using the wrong syntax. Could somebody please guide me? Using ngless v1.2 samtools module v 1.0
Best,
Ulrike
SARScov2_mapped = map(non_human_reads, fafile='allSARScov2variants210221.fna',allbest=true)
write(mapstats(SARScov2_mapped),ofile=RESULTS</> 'SARScov2.stats210221.txt')
counts = count(SARScov2_mapped,
features=['seqname'],
normalization={raw})
collect(counts,
current=current,
allneeded=samples,
ofile='SARScov2.raw.210221.txt')
sorted = samtools_sort(SARScov2_mapped)
write(sorted, ofile=RESULTS<\> 'SARScov2.sorted.bam')write(SARScov2_mapped, ofile=RESULTS<\> 'SARScov2.fastq.gz')
Exiting after fatal error while loading and running script
Script Error (there is likely an error in your script)
"human.ngl" (line 77, column 29):
unexpected '\\'
expecting "#", "//", "/*", "{", "'", "\"", digit, "0x", "_", letter, "!=", "==", "</>", "<=", "<", ">=", ">", "+", "*", " ", tab, ";", "\r", "\n" or end of input