Mercurial > repos > petr-novak > re_utils
comparison paired_fastq_filtering.R @ 33:f1738f8649b0 draft
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
| author | petr-novak |
|---|---|
| date | Fri, 04 Aug 2023 08:09:40 +0000 |
| parents | 378565f5a875 |
| children |
comparison
equal
deleted
inserted
replaced
| 32:628b235d76c7 | 33:f1738f8649b0 |
|---|---|
| 180 } | 180 } |
| 181 | 181 |
| 182 | 182 |
| 183 | 183 |
| 184 cutadapt_cmd = function(input, output, cutadapt_arguments) { | 184 cutadapt_cmd = function(input, output, cutadapt_arguments) { |
| 185 cmds = paste("cutadapt --format=", "fastq", cutadapt_arguments, " ", c(input), | 185 cmds = paste("cutadapt ", cutadapt_arguments, " ", c(input), |
| 186 " -o ", c(output), sep = "") | 186 " -o ", c(output), sep = "") |
| 187 } | 187 } |
| 188 | 188 |
| 189 set.seed(opt$rnd_seed) | 189 set.seed(opt$rnd_seed) |
| 190 PROP = opt$percent_above/100 | 190 PROP = opt$percent_above/100 |