fastq naming scheme is hard-coded

[messersc]

Hi,

this one is not urgent, but it's probably not a good idea to hard code the fastq naming scheme clinker expects.

================================== Stage plot_fusion (SRR) ==================================
ERROR: Unable to locate one or more specified inputs from pipeline with the following extension(s):

(.*)_R1.fastq.gz 

Quick workaround in case someone needs to change this, make sure to put a pattern that matches your files.

diff --git a/workflow/clinker.pipe b/workflow/clinker.pipe
index de19687..2eaa405 100644
--- a/workflow/clinker.pipe
+++ b/workflow/clinker.pipe
@@ -451,7 +451,8 @@ prepare_plot = {

        for(fusion_name in fusion){
                from("*.fastq.gz") {
-                       transform("(.*)_R1.fastq.gz","(.*)_R2.fastq.gz") {
+                       transform("(.*)_1.fastq.gz","(.*)_2.fastq.gz") {
+                       // transform("(.*)_R1.fastq.gz","(.*)_R2.fastq.gz") {

                                // Setup Stage 
                                fusion_friendly = fusion_name.replaceAll(":", "_") // allows for windows compatiability
@@ -473,7 +474,8 @@ plot_fusion = {

        for(fusion_name in fusion){
                from("*.fastq.gz") {
-                       transform("(.*)_R1.fastq.gz","(.*)_R2.fastq.gz") to ("${fusion_friendly}.pdf") {
+                       transform("(.*)_1.fastq.gz","(.*)_2.fastq.gz") {
+                       // transform("(.*)_R1.fastq.gz","(.*)_R2.fastq.gz") {

                                // Setup Stage
                                fusion_friendly = fusion_name.replaceAll(":", "_") //allows for windows compatiability

[breons]

Thanks Clemens, I'll work this in to the next release.