From 7479fe44fd6d4432d7fa391373cd727a7c482f2b Mon Sep 17 00:00:00 2001 From: Guoyi Zhang Date: Mon, 9 Dec 2024 17:45:12 +1100 Subject: [PATCH] polish: the begin tab --- README.md | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 54d05f6..ff35bcb 100644 --- a/README.md +++ b/README.md @@ -31,28 +31,28 @@ Author: Guoyi Zhang ### Details ``` - -c --config config file for software path (optional) - -g --genes gene file path (optional, if -r is specified) - -f --functions functions type (optional): all clean assembly - map postmap varcall consen codon align trim - -h --help show this information - -l --list list file path - -m --memory memory settings (optional, default 16 GB) - -r --reference reference genome path - -t --threads threads setting (optional, default 8 threads) - --codon Only use the codon region (optional) - --fastp Fastp path (optional) - --spades Spades python path (optional) - --diamond Diamond python path (optional) - --sortdiamond SortDiamond python path (optional) - --bowtie2 Bowtie2 path (optional) - --samtools Samtools path (optional) - --bcftools Bcftools path (optional) - --exonerate Exonerate path (optional) - --macse Macse jarfile path (optional) - --delstop Delstop path (optional) - --trimal Trimal path (optional) - for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta + -c --config config file for software path (optional) + -g --genes gene file path (optional, if -r is specified) + -f --functions functions type (optional): all clean assembly + map postmap varcall consen codon align trim + -h --help show this information + -l --list list file path + -m --memory memory settings (optional, default 16 GB) + -r --reference reference genome path + -t --threads threads setting (optional, default 8 threads) + --codon Only use the codon region (optional) + --fastp Fastp path (optional) + --spades Spades python path (optional) + --diamond Diamond python path (optional) + --sortdiamond SortDiamond python path (optional) + --bowtie2 Bowtie2 path (optional) + --samtools Samtools path (optional) + --bcftools Bcftools path (optional) + --exonerate Exonerate path (optional) + --macse Macse jarfile path (optional) + --delstop Delstop path (optional) + --trimal Trimal path (optional) + for example: ./RGBEPP -f all -l list -t 8 -r reference.fasta ``` ### Directories Design