add data_subtypes, default to null

junjun-zhang · junjun-zhang · commit b0971f4ac70d · 2021-04-28T10:46:19.000-04:00
diff --git a/payload-gen-dna-alignment/main.nf b/payload-gen-dna-alignment/main.nf
@@ -17,6 +17,7 @@
   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
   Authors:
+    Linda Xiang
     Junjun Zhang
 */
 
diff --git a/payload-gen-dna-alignment/main.py b/payload-gen-dna-alignment/main.py
@@ -109,6 +109,7 @@ def get_files_info(file_to_upload):
         'dataType': 'Aligned Reads' if file_to_upload.split(".")[-1] in ('bam', 'cram') else 'Aligned Reads Index',
         'info': {
             'data_category': 'Sequencing Reads',
+            'data_subtypes': None,
             'analysis_tools': ["BWA-MEM", "biobambam2:bammarkduplicates2"]
         }
     }
diff --git a/payload-gen-dna-alignment/pkg.json b/payload-gen-dna-alignment/pkg.json
@@ -27,6 +27,9 @@
     "dependencies": [],
     "devDependencies": [],
     "contributors": [
+        {
+            "name": "Linda Xiang"
+        },
         {
             "name": "Junjun Zhang"
         }
diff --git a/tests/data/635bad16-25b7-4143-81a4-c4f6f3661e7d.dna_alignment.payload.json b/tests/data/635bad16-25b7-4143-81a4-c4f6f3661e7d.dna_alignment.payload.json
@@ -26,6 +26,7 @@
       "dataType": "Aligned Reads",
       "info": {
         "data_category": "Sequencing Reads",
+        "data_subtypes": null,
         "analysis_tools": [
           "BWA-MEM",
           "biobambam2:bammarkduplicates2"
@@ -41,6 +42,7 @@
       "dataType": "Aligned Reads Index",
       "info": {
         "data_category": "Sequencing Reads",
+        "data_subtypes": null,
         "analysis_tools": [
           "BWA-MEM",
           "biobambam2:bammarkduplicates2"
diff --git a/tests/data/dc934840-98a2-4471-8655-deaaad226180.dna_alignment.payload.json b/tests/data/dc934840-98a2-4471-8655-deaaad226180.dna_alignment.payload.json
@@ -26,6 +26,7 @@
       "dataType": "Aligned Reads",
       "info": {
         "data_category": "Sequencing Reads",
+        "data_subtypes": null,
         "analysis_tools": [
           "BWA-MEM",
           "biobambam2:bammarkduplicates2"
@@ -41,6 +42,7 @@
       "dataType": "Aligned Reads Index",
       "info": {
         "data_category": "Sequencing Reads",
+        "data_subtypes": null,
         "analysis_tools": [
           "BWA-MEM",
           "biobambam2:bammarkduplicates2"
diff --git a/tests/data/ebf6a3ab-05d5-4a19-bc36-5fd4abac58ff.dna_alignment.payload.json b/tests/data/ebf6a3ab-05d5-4a19-bc36-5fd4abac58ff.dna_alignment.payload.json
@@ -38,6 +38,7 @@
       "dataType": "Aligned Reads",
       "info": {
         "data_category": "Sequencing Reads",
+        "data_subtypes": null,
         "analysis_tools": [
           "BWA-MEM",
           "biobambam2:bammarkduplicates2"
@@ -53,6 +54,7 @@
       "dataType": "Aligned Reads Index",
       "info": {
         "data_category": "Sequencing Reads",
+        "data_subtypes": null,
         "analysis_tools": [
           "BWA-MEM",
           "biobambam2:bammarkduplicates2"

Original file line number	Diff line number	Diff line change
`@@ -109,6 +109,7 @@ def get_files_info(file_to_upload):`
`109`	`109`	`'dataType': 'Aligned Reads' if file_to_upload.split(".")[-1] in ('bam', 'cram') else 'Aligned Reads Index',`
`110`	`110`	`'info': {`
`111`	`111`	`'data_category': 'Sequencing Reads',`
	`112`	`+ 'data_subtypes': None,`
`112`	`113`	`'analysis_tools': ["BWA-MEM", "biobambam2:bammarkduplicates2"]`
`113`	`114`	`}`
`114`	`115`	`}`
Original file line number	Diff line number	Diff line change
`@@ -27,6 +27,9 @@`
`27`	`27`	`"dependencies": [],`
`28`	`28`	`"devDependencies": [],`
`29`	`29`	`"contributors": [`
	`30`	`+ {`
	`31`	`+ "name": "Linda Xiang"`
	`32`	`+ },`
`30`	`33`	`{`
`31`	`34`	`"name": "Junjun Zhang"`
`32`	`35`	`}`