Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

annotate 02_fastqc_original_reports.Rmd @ 5:0ac073bef19d draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author mingchen0919
date Tue, 08 Aug 2017 11:45:41 -0400
parents d732d4526c6d
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d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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1 ---
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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2 title: "FastQC original reports"
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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3 output: html_document
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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4 ---
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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5
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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6 ```{r 'FastQC original reports', include=FALSE, warning=FALSE, message=FALSE}
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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7 knitr::opts_chunk$set(echo = ECHO)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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8 ```
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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9
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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11 Below are links to ***Fastqc*** original html reports.
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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13 ```{r 'html report links'}
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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14 html_report_list = list()
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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15 html_files = list.files('REPORT_OUTPUT_DIR', pattern = '.*html')
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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16 for (i in html_files) {
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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17 html_report_list[[i]] = tags$li(tags$a(href=i, i))
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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18 }
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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19 tags$ul(html_report_list)
d732d4526c6d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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20 ```