70 lines
1.9 KiB
Plaintext
70 lines
1.9 KiB
Plaintext
#!/usr/bin/env nextflow
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/*
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========================================================================================
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Workflow parameters are written as params.<parameter>
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and can be initialised using the `=` operator.
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========================================================================================
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*/
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params.input = "data/yeast/reads/ref1_1.fq.gz"
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ch1 = Channel.value( 'GRCh38' )
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ch2 = Channel.value( ['chr1', 'chr2', 'chr3', 'chr4', 'chr5'] )
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ch3 = Channel.value( ['chr1' : 248956422, 'chr2' : 242193529, 'chr3' : 198295559] )
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ch1.view()
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ch2.view()
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ch3.view()
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/*
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========================================================================================
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Input data is received through channels
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========================================================================================
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*/
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input_ch = Channel.fromPath(params.input)
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/*
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========================================================================================
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Main Workflow
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========================================================================================
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*/
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workflow {
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// The script to execute is called by it's process name, and input is provided between brackets.
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NUM_LINES(input_ch)
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/* Process output is accessed using the `out` channel.
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The channel operator view() is used to print process output to the terminal. */
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NUM_LINES.out.view()
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}
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/*
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========================================================================================
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A Nextflow process block. Process names are written, by convention, in uppercase.
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This convention is used to enhance workflow readability.
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========================================================================================
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*/
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process NUM_LINES {
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input:
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path read
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output:
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stdout
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script:
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"""
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# Print file name
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printf '${read}\\t'
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# Unzip file and count number of lines
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gunzip -c ${read} | wc -l
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"""
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} |