Merge pull request #10 from moka-guys/development

Install networkx v1.1 with conda. Fixes #8
moka-guys · Aug 22, 2017 · 5bbcebc · 5bbcebc
2 parents 65c728d + f4d7fdd
commit 5bbcebc
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# dnanexus_multiqc v 1.1
+# dnanexus_multiqc v 1.2
 
 ## What does this app do?
 This app runs MultiQC to generate run wide QC using the outputs from Picard CalculateHsMetrics, MarkDuplicates and CollectMultipleMetrics and FastQC

diff --git a/dxapp.json b/dxapp.json
@@ -1,13 +1,13 @@
 {
   "name": "multiqc",
   "title": "MultiQC",
-  "summary": "v1.1 - Generates a run-wide QC report on various QC data files",
+  "summary": "v1.2 - Generates a run-wide QC report on various QC data files",
   "tags": [
     "Read QC",
     "Statistics"
   ],
-        "properties": {
-    "github release": "v1.1"
+  "properties": {
+    "github release": "v1.2"
   },
   "dxapi": "1.0.0",
   "inputSpec": [
@@ -32,9 +32,16 @@
         "name": "openjdk-7-jre-headless"
       },
       {
-        "name":"git"
+        "name": "git"
       }
     ],
+    "systemRequirementsByRegion": {
+      "aws:us-east-1": {
+        "main": {
+          "instanceType": "mem1_ssd1_x2"
+        }
+      }
+    },
     "systemRequirements": {
       "main": {
         "instanceType": "mem1_ssd1_x2"
@@ -43,9 +50,9 @@
     "file": "src/code.sh",
     "interpreter": "bash"
   },
-   "access": {
-    "network": [  
-    "*"
+  "access": {
+    "network": [
+      "*"
     ]
   }
 }
diff --git a/resources/home/dnanexus/multiqc_config_20X.yaml b/resources/home/dnanexus/multiqc_config_20X.yaml
@@ -39,7 +39,7 @@ make_data_dir: True
 extra_fn_clean_exts:
 #    - type: 'replace'
 #      pattern: 'NGS95a_'
-    - type: 'replace'
+    - type: remove
       pattern: '_001'      
     # - .gz
     # - .fastq
@@ -88,36 +88,23 @@ max_table_rows: 500              # Swap tables for a beeswarm plot above this
 # Overwrite module filename search patterns. See multiqc/utils/search_patterns.yaml
 # for the defaults. Remove a default by setting it to null.
 sp:
-    fastqc:
-        data:
-            fn: '*.stats-fastqc.txt'
-        zip:
-            fn: '*_fastqc.zip'
-        theoretical_gc:
-            fn: '*fastqc_theoretical_gc*'
-    picard:
-        alignment_metrics:
-            contents: 'picard.analysis.AlignmentSummaryMetrics'
-        basedistributionbycycle:
-            contents: 'picard.analysis.BaseDistributionByCycleMetrics'
-        gcbias:
-            contents: 'picard.analysis.GcBiasDetailMetrics'
-        hsmetrics:
-            contents: 'picard.analysis.directed.HsMetrics'
-        insertsize:
-            contents: 'picard.analysis.InsertSizeMetrics'
-        markdups:
-            contents: 'picard.sam.DuplicationMetrics'
-        oxogmetrics:
-            contents: 'picard.analysis.CollectOxoGMetrics'
-        rnaseqmetrics:
-            contents:
-              - 'picard.analysis.CollectRnaSeqMetrics'
-              - 'picard.analysis.Collectrnaseqmetrics'
-        rrbs_metrics:
-            contents: 'picard.analysis.RrbsSummaryMetrics'
-        wgs_metrics:
-            contents: 'picard.analysis.CollectWgsMetrics$WgsMetrics'
+    fastqc/data:
+        fn: '*.stats-fastqc.txt'
+    picard/alignment_metrics:
+        contents: 'picard.analysis.AlignmentSummaryMetrics'
+        shared: true
+    picard/basedistributionbycycle:
+        contents: 'picard.analysis.BaseDistributionByCycleMetrics'
+        shared: true
+    picard/hsmetrics:
+        contents: 'picard.analysis.directed.HsMetrics'
+        shared: true
+    picard/insertsize:
+        contents: 'picard.analysis.InsertSizeMetrics'
+        shared: true
+    picard/markdups:
+        contents: 'picard.sam.DuplicationMetrics'
+        shared: true
 
 
 # # Specify a custom logo to add to reports (uncomment to use)

diff --git a/resources/home/dnanexus/multiqc_config_30X.yaml b/resources/home/dnanexus/multiqc_config_30X.yaml
@@ -39,7 +39,7 @@ make_data_dir: True
 extra_fn_clean_exts:
 #    - type: 'replace'
 #      pattern: 'NGS95a_'
-    - type: 'replace'
+    - type: remove
       pattern: '_001'      
     # - .gz
     # - .fastq
@@ -88,36 +88,23 @@ max_table_rows: 500              # Swap tables for a beeswarm plot above this
 # Overwrite module filename search patterns. See multiqc/utils/search_patterns.yaml
 # for the defaults. Remove a default by setting it to null.
 sp:
-    fastqc:
-        data:
-            fn: '*.stats-fastqc.txt'
-        zip:
-            fn: '*_fastqc.zip'
-        theoretical_gc:
-            fn: '*fastqc_theoretical_gc*'
-    picard:
-        alignment_metrics:
-            contents: 'picard.analysis.AlignmentSummaryMetrics'
-        basedistributionbycycle:
-            contents: 'picard.analysis.BaseDistributionByCycleMetrics'
-        gcbias:
-            contents: 'picard.analysis.GcBiasDetailMetrics'
-        hsmetrics:
-            contents: 'picard.analysis.directed.HsMetrics'
-        insertsize:
-            contents: 'picard.analysis.InsertSizeMetrics'
-        markdups:
-            contents: 'picard.sam.DuplicationMetrics'
-        oxogmetrics:
-            contents: 'picard.analysis.CollectOxoGMetrics'
-        rnaseqmetrics:
-            contents:
-              - 'picard.analysis.CollectRnaSeqMetrics'
-              - 'picard.analysis.Collectrnaseqmetrics'
-        rrbs_metrics:
-            contents: 'picard.analysis.RrbsSummaryMetrics'
-        wgs_metrics:
-            contents: 'picard.analysis.CollectWgsMetrics$WgsMetrics'
+    fastqc/data:
+        fn: '*.stats-fastqc.txt'
+    picard/alignment_metrics:
+        contents: 'picard.analysis.AlignmentSummaryMetrics'
+        shared: true
+    picard/basedistributionbycycle:
+        contents: 'picard.analysis.BaseDistributionByCycleMetrics'
+        shared: true
+    picard/hsmetrics:
+        contents: 'picard.analysis.directed.HsMetrics'
+        shared: true
+    picard/insertsize:
+        contents: 'picard.analysis.InsertSizeMetrics'
+        shared: true
+    picard/markdups:
+        contents: 'picard.sam.DuplicationMetrics'
+        shared: true
 
 
 # # Specify a custom logo to add to reports (uncomment to use)

diff --git a/src/code.sh b/src/code.sh
@@ -30,7 +30,7 @@ bash ~/Miniconda2-latest-Linux-x86_64.sh -b -p $HOME/Miniconda
 #export to path
 export PATH="$HOME/Miniconda/bin:$PATH"
 
-conda install jinja2 click markupsafe simplejson freetype -y
+conda install jinja2 click markupsafe simplejson freetype networkx=1.11 -y
 
 WES=FALSE
 #determine if need to use multiqc @ 20X or 30X