refactor pipestat example to use sample_modifiers

pepkit · Feb 26, 2024 · 0927058 · 0927058
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commit 0927058
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Showing 5 changed files with 11 additions and 6 deletions.
diff --git a/pipestat/data/frog1_data.txt → pipestat/data/frog_1.txt b/pipestat/data/frog1_data.txt → pipestat/data/frog_1.txt
diff --git a/pipestat/data/frog2_data.txt → pipestat/data/frog_2.txt b/pipestat/data/frog2_data.txt → pipestat/data/frog_2.txt
diff --git a/pipestat/looper_pipestat_config.yaml b/pipestat/looper_pipestat_config.yaml
@@ -1,7 +1,7 @@
-results_file_path: /home/nsheff/code/hello_looper/basic-pipestat/./results.yaml
-flag_file_dir: /home/nsheff/code/hello_looper/basic-pipestat/./results/flags
-output_dir: /home/nsheff/code/hello_looper/basic-pipestat/./results
+results_file_path: /home/drc/GITHUB/hello_looper/hello_looper/pipestat/./results.yaml
+flag_file_dir: /home/drc/GITHUB/hello_looper/hello_looper/pipestat/./results/flags
+output_dir: /home/drc/GITHUB/hello_looper/hello_looper/pipestat/./results
 record_identifier: frog_2
-schema_path: /home/nsheff/code/hello_looper/basic-pipestat/./pipeline_pipestat/pipestat_output_schema.yaml
+schema_path: /home/drc/GITHUB/hello_looper/hello_looper/pipestat/./pipeline_pipestat/pipestat_output_schema.yaml
 pipeline_name: test_pipe
 pipeline_type: sample
diff --git a/pipestat/project/project_config.yaml b/pipestat/project/project_config.yaml
@@ -1,2 +1,7 @@
 pep_version: 2.0.0
 sample_table: sample_annotation.csv
+sample_modifiers:
+  derive:
+    attributes: [file]
+    sources:
+      source1: "data/{sample_name}.txt"
diff --git a/pipestat/project/sample_annotation.csv b/pipestat/project/sample_annotation.csv
@@ -1,3 +1,3 @@
 sample_name,library,file,toggle
-frog_1,anySampleType,data/frog1_data.txt,1
-frog_2,anySampleType,data/frog2_data.txt,1
+frog_1,anySampleType,source1,1
+frog_2,anySampleType,source1,1