fix: CSV back in CI tests

nf-core · Jul 19, 2021 · c301e74 · c301e74
1 parent 09c4b75
commit c301e74
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Showing 5 changed files with 33 additions and 33 deletions.
diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml
@@ -10,12 +10,12 @@
     - path: results/preprocessing/1234N/recal_table/1234N.recal.table
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram.crai
-    # - path: results/preprocessing/csv/markduplicates.csv
-    # - path: results/preprocessing/csv/markduplicates_1234N.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
-    # - path: results/preprocessing/csv/recalibrated.csv
-    # - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
     - path: results/reports/fastqc/1234N-1234N_M1
     - path: results/reports/fastqc/1234N-1234N_M2
     - path: results/reports/fastqc/1234N-1234N_M4

diff --git a/tests/test_default.yml b/tests/test_default.yml
@@ -10,12 +10,12 @@
     - path: results/preprocessing/1234N/recal_table/1234N.recal.table
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram.crai
-    # - path: results/preprocessing/csv/markduplicates.csv
-    # - path: results/preprocessing/csv/markduplicates_1234N.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
-    # - path: results/preprocessing/csv/recalibrated.csv
-    # - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
     - path: results/reports/fastqc/1234N-1234N_M1
     - path: results/reports/fastqc/1234N-1234N_M2
     - path: results/reports/fastqc/1234N-1234N_M4

diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml
@@ -11,12 +11,12 @@
     - path: results/preprocessing/1234N/recal_table/1234N.recal.table
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram.crai
-    # - path: results/preprocessing/csv/markduplicates.csv
-    # - path: results/preprocessing/csv/markduplicates_1234N.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
-    # - path: results/preprocessing/csv/recalibrated.csv
-    # - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
     - path: results/reports/fastqc/1234N-1234N_M1
     - path: results/reports/fastqc/1234N-1234N_M2
     - path: results/reports/fastqc/1234N-1234N_M4

diff --git a/tests/test_pair.yml b/tests/test_pair.yml
@@ -15,15 +15,15 @@
     - path: results/preprocessing/9876T/recal_table/9876T.recal.table
     - path: results/preprocessing/9876T/recalibrated/9876T.recal.cram
     - path: results/preprocessing/9876T/recalibrated/9876T.recal.cram.crai
-    # - path: results/preprocessing/csv/markduplicates.csv
-    # - path: results/preprocessing/csv/markduplicates_1234N.csv
-    # - path: results/preprocessing/csv/markduplicates_9876T.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table_9876T.csv
-    # - path: results/preprocessing/csv/recalibrated.csv
-    # - path: results/preprocessing/csv/recalibrated_1234N.csv
-    # - path: results/preprocessing/csv/recalibrated_9876T.csv
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_9876T.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_9876T.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/preprocessing/csv/recalibrated_9876T.csv
     - path: results/reports/fastqc/1234N-1234N_M1
     - path: results/reports/fastqc/1234N-1234N_M2
     - path: results/reports/fastqc/1234N-1234N_M4

diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
@@ -10,12 +10,12 @@
     - path: results/preprocessing/1234N/recal_table/1234N.recal.table
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram
     - path: results/preprocessing/1234N/recalibrated/1234N.recal.cram.crai
-    # - path: results/preprocessing/csv/markduplicates.csv
-    # - path: results/preprocessing/csv/markduplicates_1234N.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table.csv
-    # - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
-    # - path: results/preprocessing/csv/recalibrated.csv
-    # - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
     - path: results/reports/fastqc/1234N-1234N_M1
     - path: results/reports/fastqc/1234N-1234N_M2
     - path: results/reports/fastqc/1234N-1234N_M4