Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
comparison fastq_dump_pe_render.R @ 19:42e154ba2d35 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c4beda20972367ab7d47a058a01a5f6fe492255d-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 27 Sep 2017 21:15:56 -0400 |
| parents | 883f102eb227 |
| children | 3c859d094074 |
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| 18:dcd0e0b6fcaf | 19:42e154ba2d35 |
|---|---|
| 52 library(rmarkdown) | 52 library(rmarkdown) |
| 53 library(htmltools) | 53 library(htmltools) |
| 54 library(dplyr) | 54 library(dplyr) |
| 55 | 55 |
| 56 #----- 1. create the report directory ------------------------ | 56 #----- 1. create the report directory ------------------------ |
| 57 # system(paste0('mkdir -p ', opt$output_dir)) | |
| 58 dir.create(opt$output_dir) | 57 dir.create(opt$output_dir) |
| 59 | 58 |
| 60 #----- 2. generate Rmd files with Rmd templates -------------- | 59 #----- 2. generate Rmd files with Rmd templates -------------- |
| 61 # a. templates without placeholder variables: | 60 # a. templates without placeholder variables: |
| 62 # copy templates from tool directory to the working directory. | 61 # copy templates from tool directory to the working directory. |