malacology/RGBEPP
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

polish: the begin tab

Browse source
This commit is contained in:
kuoi 2024-12-09 17:45:12 +11:00
parent b3429e9d74
commit 7479fe44fd
1 changed files with 22 additions and 22 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

44
README.md
View file

@ -31,28 +31,28 @@ Author: Guoyi Zhang
### Details ### Details
``` ```
-c --config config file for software path (optional) -c --config config file for software path (optional)
-g --genes gene file path (optional, if -r is specified) -g --genes gene file path (optional, if -r is specified)
-f --functions functions type (optional): all clean assembly -f --functions functions type (optional): all clean assembly
map postmap varcall consen codon align trim map postmap varcall consen codon align trim
-h --help show this information -h --help show this information
-l --list list file path -l --list list file path
-m --memory memory settings (optional, default 16 GB) -m --memory memory settings (optional, default 16 GB)
-r --reference reference genome path -r --reference reference genome path
-t --threads threads setting (optional, default 8 threads) -t --threads threads setting (optional, default 8 threads)
--codon Only use the codon region (optional) --codon Only use the codon region (optional)
--fastp Fastp path (optional) --fastp Fastp path (optional)
--spades Spades python path (optional) --spades Spades python path (optional)
--diamond Diamond python path (optional) --diamond Diamond python path (optional)
--sortdiamond SortDiamond python path (optional) --sortdiamond SortDiamond python path (optional)
--bowtie2 Bowtie2 path (optional) --bowtie2 Bowtie2 path (optional)
--samtools Samtools path (optional) --samtools Samtools path (optional)
--bcftools Bcftools path (optional) --bcftools Bcftools path (optional)
--exonerate Exonerate path (optional) --exonerate Exonerate path (optional)
--macse Macse jarfile path (optional) --macse Macse jarfile path (optional)
--delstop Delstop path (optional) --delstop Delstop path (optional)
--trimal Trimal path (optional) --trimal Trimal path (optional)
for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta
``` ```
### Directories Design ### Directories Design