Merge branch 'development' of https://github.com/kircherlab/MPRAsnake…

…flow into feature/assignment_exact_matches
kircherlab · Dec 4, 2023 · 225572c · 225572c
2 parents d6eae77 + d2b5fdb
commit 225572c
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -5,7 +5,7 @@ on:
   push:
     branches: [master]
   pull_request:
-    branches: [master]
+    branches: [master, development]
 
 jobs:
   docs:

diff --git a/config/sbatch.yml b/config/sbatch.yml
@@ -124,7 +124,7 @@ assigned_counts_createAssignmentPickleFile:
 assigned_counts_filterAssignment:
   time: "0-01:00"
   queue: "medium"
-  mem: 10G
+  mem: 15G
 
 #################
 ### Statistic ###

diff --git a/workflow/envs/python27.yaml b/workflow/envs/python27.yaml
@@ -5,6 +5,6 @@ channels:
   - conda-forge
 dependencies:
   - htslib
-  - pysam
+  - pysam>0.16.0
   - python=2.7
   - samtools
diff --git a/workflow/scripts/count/nucleotideCountPerPosition.py b/workflow/scripts/count/nucleotideCountPerPosition.py
@@ -58,7 +58,7 @@ def cli(input_file, column, use_header, output_file, chunksize):
 
             nucleotides = df["DNA"].apply(lambda x: pd.Series(list(x)))
 
-            for i, columns in nucleotides.iteritems():
+            for i, columns in nucleotides.items():
                 counts_column = "Position_%d_counts" % (i+1)
                 ratio_column = "Position_%d_ratio" % (i+1)
                 if counts_column not in output.columns: