Merge branch 'develop'

StanfordBioinformatics · Sep 9, 2017 · 98a6aa6 · 98a6aa6
2 parents b8d186a + fcce256
commit 98a6aa6
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Showing 2 changed files with 33 additions and 7 deletions.
diff --git a/scgpm_bcl2fastq/dxapp.json b/scgpm_bcl2fastq/dxapp.json
@@ -3,7 +3,7 @@
     "title": "SCGPM Bcl2fastq",
     "summary": "Convert raw Illumina sequencing data to FASTQ files",
     "dxapi": "1.0.0",
-    "version": "1.0.0",
+    "version": "1.1.0",
     "openSource": true,
     "inputSpec": [
         {
@@ -166,13 +166,36 @@
         "file": "src/code.py",
         "bundledDepends": [],
         "execDepends": [],
-        "systemRequirements": {
-            "*": {
-                "instanceType": "mem1_ssd1_x16"
+        "systemRequirementsByRegion": {
+            "azure:westus": {
+                "*": {
+                    "instanceType": "azure:mem2_ssd1_x16"
+                }
+            },
+            "aws:us-east-1": {
+                "*": {
+                    "instanceType": "mem1_ssd1_x16"
+                }
             }
         },
         "distribution": "Ubuntu",
-        "release": "12.04"
+        "release": "14.04"
+    },
+    "regionalOptions": {
+        "azure:westus": {
+          "systemRequirements": {
+            "*": {
+              "instanceType": "azure:mem2_ssd1_x16"
+            }
+          }
+        },
+        "aws:us-east-1": {
+          "systemRequirements": {
+            "*": {
+              "instanceType": "mem1_ssd1_x16"
+            }
+          }
+        }
     },
     "access": {
         "allProjects": "ADMINISTER",
@@ -184,7 +207,7 @@
         "upstreamUrl": "http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html",
         "upstreamVersion": "2.17.1.14",
         "upstreamLicenses": [],
-        "whatsNew": "* 1.0.0: Initial version"
+        "whatsNew": "* 1.1.0: Fixed base mask bug; added Azure region\n* 1.0.0: Initial version"
     },
     "categories": ["Read Manipulation"],
     "developers": ["org-scgpm"]

diff --git a/scgpm_bcl2fastq/src/code.py b/scgpm_bcl2fastq/src/code.py
@@ -428,7 +428,10 @@ def _get_use_bases_mask(self, run_info_file, index_lengths_list):
                 # RunInfo index numbers are 2 & 3. Corresponding index_length
                 # indices are 0 & 1. Subtract 2 to get corresponding index length.
                 index_length = int(index_lengths[number-2])
-                index_mask = 'I{}'.format(index_length)
+                if index_length > 0:
+                    index_mask = 'I{}'.format(index_length)
+                else:
+                    index_mask = ''
 
                 if read_length - index_length > 0:
                     n_mask = 'n{}'.format(read_length - index_length)