Merge branch 'master' into 'public'

merge master into public for v1.3.2

See merge request icbi-lab/pipelines/rnaseq-nf!38

README.html

@@ -480,6 +480,7 @@ <h2 id="2-usage">2. Usage</h2>
 <p><strong>Mandatory arguments:</strong></p>
 <p><code>-config</code> nextNEOpi config file, e.g. <code>-config conf/params.config</code></p>
 <p><code>--accept_license</code> accept the license terms</p>
+<p><code>--MIXCR_lic /path/to/mi.license</code> OR <code>--TCR false</code> : a MiXCR license may be requested at https://licensing.milaboratories.com</p>
 <p><code>--batchFile</code></p>
 <p>Make sure that your batchFile CSV includes the column names as shown in the examples below as header line. See also <code>example_batchFile_FASTQ.csv</code> or <code>example_batchFile_BAM.csv</code></p>
 <p><strong>FASTQ raw reads</strong></p>

README.md

@@ -158,6 +158,8 @@ Besides raw reads in **FASTQ** fromated files, input data may also be provided i
 
 ```--accept_license``` accept the license terms
 
+```--MIXCR_lic /path/to/mi.license``` OR ```--TCR false``` : a MiXCR license may be requested at https://licensing.milaboratories.com
+
 ```--batchFile```
 
 Make sure that your batchFile CSV includes the column names as shown in the examples below as header line. See also `example_batchFile_FASTQ.csv` or `example_batchFile_BAM.csv`

nextNEOpi.nf

@@ -406,7 +406,7 @@ if (params.GATK3 != "" && file(params.GATK3) && params.JAVA8 != "" && file(param
 if (params.TCR && params.MIXCR_lic != "") {
     checkToolAvailable(params.MIXCR_lic, "exists", "error")
 } else if (params.TCR && params.MIXCR_lic == "") {
-    exit 1, "ERROR: no MiXCR license file specified, please provide a MiXCR license file in params.config or by using the --MIXCR_lic option. If you do not have a MiXCR license, please run nextNEOpi with --TCR false"
+    exit 1, "ERROR: no MiXCR license file specified, please provide a MiXCR license file in params.config or by using the --MIXCR_lic option.\nIf you do not have a MiXCR license you may:\n\ta) run nextNEOpi with --TCR false\n\tb) request one at https://licensing.milaboratories.com"
 }
 
 /*