Merge pull request #44 from vyepez88/code_cleaning

Code cleaning
gagneurlab · May 21, 2020 · 53d09ad · 53d09ad
2 parents 90ef0ee + 0ac8fad
commit 53d09ad
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Showing 6 changed files with 11 additions and 6 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -42,8 +42,7 @@ addons:
 
 install:
   - cd $DROP_DIR
-  - R -e "if ('FRASER' %in% rownames(installed.packages())) remove.packages('FRASER')"
-  - R -e "install.packages('BiocManager'); BiocManager::install('remotes'); BiocManager::install('c-mertes/FRASER')"
+#  - R -e "if ('FRASER' %in% rownames(installed.packages())) remove.packages('FRASER')"
 #  - R -e "if ('tMAE' %in% rownames(installed.packages())) remove.packages('tMAE')"
   - Rscript travis/installRPackages.R drop/requirementsR.txt
   - bash travis/install_bcftools.sh
@@ -59,7 +58,7 @@ before_script:
   - cd $PROJECT_DIR
   - drop demo
 
-script:
+script: 
  - cd $PROJECT_DIR
  - snakemake -n
  - snakemake aberrantExpression --cores 2

diff --git a/drop/configHelper.py b/drop/configHelper.py
@@ -186,6 +186,11 @@ def getSampleAnnotation(self, filename, sep='\t'):
         col = col.str.replace(" ", "").str.replace("(|)", "", regex=True)
         sample_annotation["DROP_GROUP"] = col
 
+        # set ID type as string
+        sample_annotation = sample_annotation.astype({
+            "RNA_ID": str, "DNA_ID": str
+        })
+
         return sample_annotation
 
     def createSampleFileMapping(self, sample_annotation):

diff --git a/drop/modules/aberrant-expression-pipeline b/drop/modules/aberrant-expression-pipeline
diff --git a/drop/modules/aberrant-splicing-pipeline b/drop/modules/aberrant-splicing-pipeline
diff --git a/drop/modules/mae-pipeline b/drop/modules/mae-pipeline
diff --git a/drop/template/config.yaml b/drop/template/config.yaml
@@ -31,6 +31,7 @@ aberrantSplicing:
         - group1
     recount: false
     longRead: false
+    keepNonStandardChrs: true
     filter: true
     minExpressionInOneSample: 20
     minDeltaPsi: 0