WIP add licence

main.nf

 #!/usr/bin/env nextflow
+
+
+/*
+Copyright INRAE 2021
+
+This software is a computer program whose purpose is to
+analyze high-throughput sequencing data.
+You can use, modify and/ or redistribute the software under the terms
+of license (see the LICENSE file for more details).
+The software is distributed in the hope that it will be useful,
+but "AS IS" WITHOUT ANY WARRANTY OF ANY KIND.
+Users are therefore encouraged to test the software's suitability as regards
+their requirements in conditions enabling the security of their systems and/or data.
+The fact that you are presently reading this means that you have had knowledge
+of the license and that you accept its terms.
+This script is based on : 
+ - the nf-core guidelines . See https://nf-co.re/ for more information
+ - the institut cury template https://github.com/bioinfo-pf-curie/geniac-template/
+
+*/
+
+
 /*
 ========================================================================================
                          GeT/template
@@ -16,27 +38,31 @@ def helpMessage() {
 
     The typical command for running the pipeline is as follows:
 
-    nextflow run nf-core/template --reads '*_R{1,2}.fastq.gz' -profile docker
+    nextflow run nf-core/template --inputdir '/path/to/data' --samplesheet 'samples.csv' -profile docker
 
     Mandatory arguments:
-      --reads                       Path to input data (must be surrounded with quotes)
+      --inputdir                    Path to input directory 
       -profile                      Configuration profile to use. Can use multiple (comma separated)
-                                    Available: conda, docker, singularity, genotoul, test and more.
+                                    Available: conda, docker, singularity, path, 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
+      --samplesheet                 Default inputdir/samples.csv eg: SAMPLE_ID,SAMPLE_NAME,path/to/R1/fastq/file,path/to/R2/fastq/file (for paired-end only)
+      --contaminant                 Name of iGenomes // To be discussed ????
       --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.
+      -name [str]                   Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+
+
+    =======================================================
+    Available profiles
+    -profile test                    Run the test dataset
+    -profile conda                   Build a new conda environment before running the pipeline. Use `--condaCacheDir` to define the conda cache path
+    -profile path                    Use the installation path defined for all tools. Use `--globalPath` to define the installation path
+    -profile docker                  Use the Docker images for each process
+    -profile singularity             Use the singularity images for each process
+    -profile genologin               Run the workflow on the cluster, instead of locally
 
     """.stripIndent()
 }
@@ -49,35 +75,60 @@ if (params.help) {
 
 
 // NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
+
+/*
+ * Create a channel for input read files
+ */
 // If you want to use the channel below in a process, define the following:
 //   input:
-//   file fasta from ch_fasta
+//   file dir from inputDirCh
 //
-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 ; raw_reads_fastqc; raw_reads_assembly}
-    } 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; raw_reads_fastqc; raw_reads_assembly}
-    }
-} else {
+inputDirCh = Channel.fromPath(params.inputdir, checkIfExists: true) : Channel.empty()
+if (! params.samplesheet){
+    params.samplesheet = params.inputdir + "/samples.csv"
+}
+
+samplesheetCh = Channel.fromPath(params.samplesheet, checkIfExists: true) : Channel.empty()
+
+
+// Create a channel for input read files
+if(params.samplesheet){
+  if(params.singleEnd){
     Channel
-        .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
-        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --singleEnd on the command line." }
-        .into { read_files_fastqc; read_files_trimming; raw_reads_fastqc; raw_reads_assembly }
+      .from(file("${params.samplePlan}"))
+      .splitCsv(header: false)
+      .map{ row -> [ row[0], [file(row[2])]] }
+      .set { rawReadsFastqcCh }
+  }else{
+    Channel
+      .from(file("${params.samplePlan}"))
+      .splitCsv(header: false)
+      .map{ row -> [ row[0], [file(row[2]), file(row[3])]] }
+      .set { rawReadsFastqcCh }
+   }
+  params.reads=false
+}
+else if(params.readPaths){
+  if(params.singleEnd){
+    Channel
+      .from(params.readPaths)
+      .map { row -> [ row[0], [file(row[1][0])]] }
+      .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied." }
+      .set { rawReadsFastqcCh }
+  } else {
+    Channel
+      .from(params.readPaths)
+      .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
+      .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied." }
+      .set { rawReadsFastqcCh }
+  }
+} 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!\nNB: Path requires at least one * wildcard!\nIf this is single-end data, please specify --singleEnd on the command line." }
+    .set { rawReadsFastqcCh }
 }
 
 /* In case of modular pipeline*/