prj init

wc-params.nf

@@ -0,0 +1,65 @@
+#!/usr/bin/env nextflow
+
+
+
+/*
+========================================================================================
+    Workflow parameters are written as params.<parameter>
+    and can be initialised using the `=` operator.
+========================================================================================
+*/
+
+params.input = "data/yeast/reads/ref1_1.fq.gz"
+params.sleep = 2
+
+/*
+========================================================================================
+    Input data is received through channels
+========================================================================================
+*/
+
+input_ch = Channel.fromPath(params.input)
+
+/*
+========================================================================================
+   Main Workflow
+========================================================================================
+*/
+
+workflow {
+    //  The script to execute is called by it's process name, and input is provided between brackets.
+
+    NUM_LINES(input_ch)
+
+    /*  Process output is accessed using the `out` channel.
+        The channel operator view() is used to print process output to the terminal. */
+
+    NUM_LINES.out.view()
+
+}
+
+/*
+========================================================================================
+    A Nextflow process block. Process names are written, by convention, in uppercase.
+    This convention is used to enhance workflow readability.
+========================================================================================
+*/
+process NUM_LINES {
+
+    input:
+    path read
+
+    output:
+    stdout
+
+    script:
+    """
+    sleep ${params.sleep}
+
+    # Print file name
+    printf '${read}\\t'
+
+    # Unzip file and count number of lines
+    gunzip -c ${read} | wc -l
+    """
+}