add simple pipeline

main.nf

+#!/usr/bin/env nextflow
+/*
+========================================================================================
+                         GeT/template
+========================================================================================
+ GeT/template Analysis Pipeline.
+ #### Homepage / Documentation
+ https://github.com/nf-core/template
+----------------------------------------------------------------------------------------
+*/
+
+def helpMessage() {
+    log.info"""
+
+    Usage:
+
+    The typical command for running the pipeline is as follows:
+
+    nextflow run nf-core/template --reads '*_R{1,2}.fastq.gz' -profile docker
+
+    Mandatory arguments:
+      --reads                       Path to input data (must be surrounded with quotes)
+      -profile                      Configuration profile to use. Can use multiple (comma separated)
+                                    Available: conda, docker, singularity, genotoul, test and more.
+
+    Options:
+      --genome                      Name of iGenomes reference
+      --singleEnd                   Specifies that the input is single end reads
+
+    References                      If not specified in the configuration file or you wish to overwrite any of the references.
+      --fasta                       Path to Fasta reference
+
+    Other options:
+      --genome_base                 Path to databases
+      --outdir                      The output directory where the results will be saved
+      --email                       Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
+      --email_on_fail               Same as --email, except only send mail if the workflow is not successful
+      --maxMultiqcEmailFileSize     Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
+      -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+
+    """.stripIndent()
+}
+
+// Show help message
+if (params.help) {
+    helpMessage()
+    exit 0
+}
+
+// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
+// If you want to use the channel below in a process, define the following:
+//   input:
+//   file fasta from ch_fasta
+//
+if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) }
+
+
+/*
+ * Create a channel for input read files
+ */
+if (params.readPaths) {
+    if (params.singleEnd) {
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true) ] ] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .into { read_files_fastqc; read_files_trimming }
+    } else {
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true), file(row[1][1], checkIfExists: true) ] ] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .into { read_files_fastqc; read_files_trimming }
+    }
+} else {
+    Channel
+        .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
+        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --singleEnd on the command line." }
+        .into { read_files_fastqc; read_files_trimming }
+}
+
+/*
+ * STEP 1 - FastQC
+ */
+process fastqc {
+    tag "$name"
+    label 'process_medium'
+    publishDir "${params.outdir}/fastqc", mode: 'copy',
+        saveAs: { filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename" }
+
+    input:
+    set val(name), file(reads) from read_files_fastqc
+
+    output:
+    file "*_fastqc.{zip,html}" into fastqc_results
+
+    script:
+    """
+    fastqc --quiet --threads $task.cpus $reads
+    """
+}
+