annotate 02_mapping.Rmd @ 1:c8c0b708c221 draft

planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
author mingchen0919
date Tue, 01 May 2018 11:07:53 -0400
parents c12e291895ff
children c04ef267c2c9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
1 ---
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
2 title: 'Mapping'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
3 output:
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
4 html_document:
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
5 highlight: pygments
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
6 ---
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
7
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
10 ```
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
11
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
12 ### Mapping
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
13
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
14 ```{r echo=FALSE,results='asis'}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
15 # display content of the job-script.sh file.
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
16 cat('```bash\n')
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
17 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/mapping.sh')), sep = '\n')
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
18 cat('\n```')
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
19 ```