In [1]:

    

%run --excel-file data/DEG.xlsx

[global]
parameter: excel_file = path
parameter: figure_file = 'output.pdf'

csv_file = excel_file.with_suffix('.csv')

[plot_1 (convert)]
sh: expand=True
    xlsx2csv {excel_file} > {csv_file}
    
[plot_2 (plot)]
R: expand=True
    data <- read.csv('{csv_file}')
    pdf('{figure_file}')
    plot(data$log2FoldChange, data$stat)
    dev.off()


    

    




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          1 

In [2]:

    

%run --excel-file data/DEG.xlsx

[global]
parameter: excel_file = path
parameter: figure_file = 'output.pdf'

csv_file = excel_file.with_suffix('.csv')

[plot_1 (convert)]
input: excel_file
output: csv_file
sh: expand=True
    xlsx2csv {_input} > {_output}
    
[plot_2 (plot)]
output: figure_file
R: expand=True
    data <- read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()


    

    




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          1 

In [3]:

    

%run

[plot_1 (convert)]
input:  'data/DEG.xlsx'
output: 'DEG.csv'
sh: expand=True
    xlsx2csv {_input} > {_output}
    
[plot_2 (plot)]
input:  'DEG.csv'
output: 'DEG.pdf'
R: expand=True
    data <- read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()


    

    




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          1 

In [4]:

    

!rm -f data/DEG.csv DEG.pdf
%run -t DEG.pdf

[convert: provides='{filename}.csv']
input:  f'{filename}.xlsx'
sh: expand=True
    xlsx2csv {_input} > {_output}
    
[plot]
input:  'data/DEG.csv'
output: 'DEG.pdf'
R: expand=True
    data <- read.csv('{_input}')
    pdf('{_output}')
    plot(data$log2FoldChange, data$stat)
    dev.off()


    

    




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          1 

In [5]:

    

!rm hg19.fa dbsnp.vcf


    

    




rm: hg19.fa: No such file or directory
rm: dbsnp.vcf: No such file or directory

In [6]:

    

%preview -n mixed.dot
%run align+call -d mixed.dot -p mixed.html

import time

[refseq: provides='hg19.fa']
time.sleep(1)
_output.touch()

[dbsnp: provides='dbsnp.vcf']
_output.touch()

[align_10]
depends: 'hg19.fa'
time.sleep(2)

[align_20]
time.sleep(4)

[call_10]
depends: 'dbsnp.vcf', 'hg19.fa'
time.sleep(2)

[call_20]
time.sleep(2)


    

    





INFO: Workflow align+call (ID=35f0aa01e07c827d) is executed successfully with 6 completed steps.






    





INFO: Workflow DAG saved to mixed.dot






    





INFO: Summary of workflow saved to mixed.html






    





%preview mixed.dot






    





> mixed.dot (4.0 KiB):