Fix #170

vib-singlecell-nf · Mar 16, 2020 · a02ee0a · a02ee0a
1 parent 5bfb615
commit a02ee0a
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/src/utils/bin/sc_file_converter.py b/src/utils/bin/sc_file_converter.py
@@ -155,6 +155,15 @@ def add_sample_id(adata, args):
     adata = adata[:, np.sort(adata.var.index)]
     adata.write_h5ad(filename="{}.h5ad".format(FILE_PATH_OUT_BASENAME))
 
+elif INPUT_FORMAT == 'h5ad' and OUTPUT_FORMAT == 'h5ad':
+    adata = sc.read_h5ad(
+        FILE_PATH_IN
+    )
+    adata = add_sample_id(
+        adata=adata,
+        args=args
+    )
+    adata.write_h5ad(filename="{}.h5ad".format(FILE_PATH_OUT_BASENAME))
 else:
     raise Exception(
         "File format conversion {0} --> {1} hasn't been implemented yet.".format(INPUT_FORMAT, OUTPUT_FORMAT))

diff --git a/src/utils/processes/utils.nf b/src/utils/processes/utils.nf
@@ -100,11 +100,7 @@ process SC__FILE_CONVERTER {
             break;
         }
 
-        if(inputDataType == "h5ad")
-            """
-            cp ${f} "${sampleId}.SC__FILE_CONVERTER.h5ad"
-            """
-        else if(inputDataType == "10x_atac_cellranger_mex" && outputDataType == "cistopic_rds")
+        if(inputDataType == "10x_atac_cellranger_mex" && outputDataType == "cistopic_rds")
             """
             ${binDir}create_cistopic_object.R \
                 --tenx_path ${f} \