add: more path args

This commit is contained in:
kuoi 2024-09-09 11:45:55 +10:00
parent 391dc5c17d
commit 51db2c767f

View file

@ -16,6 +16,7 @@ void show_help(string pkgver) {
Version: ", pkgver, " Version: ", pkgver, "
License: GPL-2.0-only License: GPL-2.0-only
Author: Guoyi Zhang Author: Guoyi Zhang
-c\t--config\tconfig file for software path (optional)
-g\t--genes\t\tgene file path (optional, if -r is specified) -g\t--genes\t\tgene file path (optional, if -r is specified)
-f\t--functions\tfunctions type (optional): all clean map -f\t--functions\tfunctions type (optional): all clean map
\t \tpostmap varcall consen align \t \tpostmap varcall consen align
@ -24,7 +25,12 @@ void show_help(string pkgver) {
-m\t--memory\tmemory settings (optional, default 16 GB) -m\t--memory\tmemory settings (optional, default 16 GB)
-r\t--reference\treference genome path -r\t--reference\treference genome path
-t\t--threads\tthreads setting (optional, default 8 threads) -t\t--threads\tthreads setting (optional, default 8 threads)
--macse\t\tMacse jarfile path --fastp\t\tFastp path (optional)
--bowtie2\t\tBowtie2 path (optional)
--samtools\t\tSamtools path (optional)
--bcftools\t\tBcftools path (optional)
--macse\t\tMacse jarfile path (optional)
--trimal\t\tTrimal path (optional)
for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n"); for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta \n");
} }
@ -385,10 +391,30 @@ void main(string[] args) {
i++; i++;
ARG_T = args[i].to!int; ARG_T = args[i].to!int;
break; break;
case "--fastp":
i++;
PathFastp = args[i];
break;
case "--bowtie2":
i++;
PathBowtie2 = args[i];
break;
case "--samtools":
i++;
PathSamtools = args[i];
break;
case "--bcftools":
i++;
PathBcftools = args[i];
break;
case "--macse": case "--macse":
i++; i++;
PathMacse = args[i]; PathMacse = args[i];
break; break;
case "--trimal":
i++;
PathTrimal = args[i];
break;
default: default:
break; break;
} }