Adding tutorials

Author: JBris

.gitignore

@@ -0,0 +1,10 @@
+.DS_Store
+.cache
+.idea
+serve
+nextflow
+work
+.nextflow*
+nf-training/results
+transcript-index
+.vscode

README.md

@@ -0,0 +1,9 @@
+#!/bin/bash
+set -e
+set -u
+
+sample_id=${1}
+reads=${2}
+
+mkdir fastqc_${sample_id}_logs
+fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}

bin/fastqc.sh

@@ -0,0 +1,8 @@
+square = { num -> num * num }
+
+x = [ 1, 2, 3, 4 ].collect(square)
+println x
+
+printMap = { a, b -> println "$a with value $b" }
+values = [ "Yue" : "Wu", "Mark" : "Williams", "Sudha" : "Kumari" ]
+values.each(printMap)

closure.nf

@@ -0,0 +1,24 @@
+params.compress = 'gzip'
+params.file2compress = "$baseDir/data/ggal/transcriptome.fa"
+
+process FOO {
+
+  input:
+  path file
+
+  script:
+  if( params.compress == 'gzip' )
+    """
+    gzip -c $file > ${file}.gz
+    """
+  else if( params.compress == 'bzip2' )
+    """
+    bzip2 -c $file > ${file}.bz2
+    """
+  else
+    throw new IllegalArgumentException("Unknown aligner $params.compress")
+}
+
+workflow {
+  FOO(params.file2compress)
+}

conditional_compress.nf

@@ -0,0 +1,7 @@
+Lorem Ipsum is simply dummy text of the printing and typesetting industry.
+Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
+when an unknown printer took a galley of type and scrambled it to make a type specimen book.
+It has survived not only five centuries, but also the leap into electronic typesetting,
+remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset
+sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like
+Aldus PageMaker including versions of Lorem Ipsum

dag.png

@@ -0,0 +1,10 @@
+name: nf-tutorial
+channels:
+  - conda-forge
+  - defaults
+  - bioconda
+dependencies:
+  - bioconda::salmon=1.5.1
+  - bioconda::fastqc=0.11.9
+  - bioconda::multiqc=1.12
+  - conda-forge::tbb=2020.2

data/ggal/gut_1.fq

@@ -0,0 +1,32 @@
+ch1 = Channel.of(1,2,3)
+ch2 = Channel.of(1)
+
+process SUM {
+    input:
+    val x
+    val y
+
+    output:
+    stdout
+
+    script:
+    """
+    echo \$(($x+$y))
+    """
+}
+
+workflow {
+    SUM(ch1,ch2.first()).view()
+    
+    Channel.fromPath( './data/ggal/**.fq' , hidden:true)
+     	 .view()
+   
+    Channel
+     	.fromFilePairs('./data/ggal/*_{1,2}.fq')
+ 	.view()
+
+    Channel
+  	.fromPath('data/meta/random.txt')
+  	.splitText( by: 2 ) { it.toUpperCase() }
+  	.view()
+}

data/ggal/gut_2.fq

@@ -0,0 +1,6 @@
+process foo {
+  echo true
+  '''
+  env | egrep 'ALPHA|BETA'
+  '''
+}

data/ggal/liver_1.fq

@@ -0,0 +1,84 @@
+println "Hello, World!"
+
+// comment a single config file
+
+/*
+   a comment spanning
+   multiple lines
+*/
+
+x = 1
+println x
+
+x = new java.util.Date()
+println x
+
+x = -3.1499392
+println x
+
+x = false
+println x
+
+x = "Hi"
+println x
+
+
+
+def x = 'foo'
+
+
+list = [10,20,30,40]
+println list[0]
+println list.get(0)
+println list.size()
+
+
+
+map = [a:0, b:1, c:2]
+map['a'] = 'x'           
+map.b = 'y'              
+map.put('c', 'z')        
+assert map == [a:'x', b:'y', c:'z']
+
+
+
+foxtype = 'quick'
+foxcolor = ['b', 'r', 'o', 'w', 'n']
+println "The $foxtype ${foxcolor.join()} fox"
+
+x = 'Hello'
+println '$x + $y'
+
+text = """
+    Hello there James.
+    How are you today?
+    """
+println text
+
+
+
+
+list = [1,2,3]
+if( list != null && list.size() > 0 ) {
+  println list
+}
+else {
+  println 'The list is empty'
+}
+
+
+
+list = ['a','b','c']
+
+for( String elem : list ) {
+  println elem
+}
+
+
+
+int fib(int n) {
+    return n < 2 ? 1 : fib(n-1) + fib(n-2)
+}
+
+assert fib(10)==89
+

data/ggal/liver_2.fq

@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow     
+
+params.greeting  = 'Hello' 
+greeting_ch = Channel.of(params.greeting) 
+
+process SPLITLETTERS { 
+    input: 
+    val x 
+
+    output: 
+    path 'test_*' 
+
+    """ 
+    printf '$x' | split -b 6 - test_  
+    """ 
+} 
+
+process CONVERTTOUPPER { 
+    input:  
+    path y 
+
+    output: 
+    stdout 
+
+    """ 
+    rev $y  
+    """ 
+} 
+
+workflow { 
+    letters_ch = SPLITLETTERS(greeting_ch) 
+    results_ch = CONVERTTOUPPER(letters_ch.flatten()) 
+    results_ch.view{ it } 
+}

data/ggal/lung_1.fq

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+params.greeting  = 'Hello world!'
+greeting_ch = Channel.of(params.greeting)
+
+include { SPLITLETTERS   } from './modules.nf'
+include { CONVERTTOUPPER } from './modules.nf'
+
+workflow {
+    letters_ch = SPLITLETTERS(greeting_ch)
+    results_ch = CONVERTTOUPPER(letters_ch.flatten())
+    results_ch.view{ it }
+}

data/ggal/lung_2.fq

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+params.greeting = 'Hello world!'
+greeting_ch = Channel.of(params.greeting)
+
+include { SPLITLETTERS as SPLITLETTERS_one } from './modules.nf'
+include { SPLITLETTERS as SPLITLETTERS_two } from './modules.nf'
+
+include { CONVERTTOUPPER as CONVERTTOUPPER_one } from './modules.nf'
+include { CONVERTTOUPPER as CONVERTTOUPPER_two } from './modules.nf'
+
+workflow {
+    letters_ch1 = SPLITLETTERS_one(greeting_ch)
+    results_ch1 = CONVERTTOUPPER_one(letters_ch1.flatten())
+    results_ch1.view{ it }
+
+    letters_ch2 = SPLITLETTERS_two(greeting_ch)
+    results_ch2 = CONVERTTOUPPER_two(letters_ch2.flatten())
+    results_ch2.view{ it }
+}

data/ggal/transcriptome.fa

@@ -0,0 +1,25 @@
+process SPLITLETTERS {
+
+    input:
+    val x
+
+    output:
+    path 'chunk_*'
+
+    """
+    printf '$x' | split -b 6 - chunk_
+    """
+}
+
+process CONVERTTOUPPER {
+
+    input:
+    path y
+
+    output:
+    stdout
+
+    """
+    cat $y | tr '[a-z]' '[A-Z]'
+    """
+}

data/meta/random.txt

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+params.greeting = 'Hello world!'
+
+include { SPLITLETTERS as SL; CONVERTTOUPPER } from './modules.nf'
+
+workflow my_pipeline {
+        Channel.of(params.greeting) | SL | flatten() | CONVERTTOUPPER | view
+}
+
+workflow {
+    my_pipeline()
+}

environment.yml

@@ -0,0 +1,2 @@
+env.ALPHA = 'some value'
+env.BETA = "$HOME/some/path"

example.nf

@@ -0,0 +1,9 @@
+process.container = 'nextflow/rnaseq-nf'
+docker.runOptions = '-u $(id -u):$(id -g)'
+docker.enabled = true
+propertyOne = 'world'
+anotherProp = "Hello $propertyOne"
+
+params.greeting = "bonjour"
+
+

foo.nf

@@ -0,0 +1,27 @@
+Channel
+    .of(1,2,3,4)
+    .map { it -> it * it }
+    .mix(Channel.of( 1,2,3 )) 
+    .collect()
+    .flatten()
+    .view { "- $it" }
+
+left = Channel.of(['X', 1], ['Y', 2], ['Z', 3], ['P', 7])
+right = Channel.of(['Z', 6], ['Y', 5], ['X', 4])
+left.join(right).view()
+
+Channel
+    .of( [1,'A'], [1,'B'], [2,'C'], [3, 'B'], [1,'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple()
+    .view()
+
+Channel
+    .of(1,2,3,40,50)
+    .branch {
+        small: it < 10
+        large: it > 10
+    }
+    .set { result }
+
+result.small.view { "$it is small" }
+result.large.view { "$it is large" }