From 031dba4d5eb5a15b635f38fcb6d538ad0414ce78 Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Tue, 31 Mar 2020 12:44:56 -0400
Subject: [PATCH 1/2] update config and piface to comply with pep2 spec

---
 pipeline_interface.yaml | 30 +++++++++---------------------
 project/cfg.yaml        | 19 ++++++++++---------
 2 files changed, 19 insertions(+), 30 deletions(-)

diff --git a/pipeline_interface.yaml b/pipeline_interface.yaml
index e5e57a4..8ec20a6 100644
--- a/pipeline_interface.yaml
+++ b/pipeline_interface.yaml
@@ -3,24 +3,12 @@ protocol_mapping:
 
 pipelines:
   bedbuncher:
-    name: bedbuncher
-    path: bedbuncher.py
-    looper_args: True
-    arguments:
-      "--JSON-query-path": JSONquery_path
-      "--bedset-name": bedset_name
-    optional_arguments:
-      "--bedbase-config": bbconfig_path
-    resources:
-      default: 
-        file_size: "0"
-        cores: "1"
-        mem: "12000"
-        time: "00-18:00:00"
-    
-
-
-
-
-
-
+    name: BEDBUNCHER
+    path: pipelines/bedbuncher.py
+    command_template: >
+      {pipeline.path}
+      --JSON-query-path {sample.JSONquery_path}
+      --bedset-name {sample.bedset_name}
+      {% if sample.bbconfig_path is defined %} --bedbase-config {sample.bbconfig_path} {% endif %}
+    compute:
+      size_dependent_variables: resources.tsv
diff --git a/project/cfg.yaml b/project/cfg.yaml
index 18095ae..923b292 100644
--- a/project/cfg.yaml
+++ b/project/cfg.yaml
@@ -1,12 +1,13 @@
-metadata:
-  sample_table: bedset_query.csv
+sample_table: bedset_query.csv
+looper:
   output_dir: . 
   pipeline_interfaces: ../pipeline_interface.yaml 
 
-derived_attributes: [JSONquery_path, output_folder_path]
-data_sources:
-  source1: ../tests/{JSONquery_name}.json
-  source2: ../tests/BEDset_output/
- 
-constant_attributes:
-  protocol: "bedbuncher"
\ No newline at end of file
+sample_modifiers:
+  derive:
+    attributes: [JSONquery_path, output_folder_path]
+    sources:
+      source1: ../tests/{JSONquery_name}.json
+      source2: ../tests/BEDset_output/
+  append:
+    protocol: "bedbuncher"
\ No newline at end of file

From e8be298d46d88dc5122b17a0dbc8049d8ad5bbc9 Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Tue, 31 Mar 2020 12:45:38 -0400
Subject: [PATCH 2/2] add resources tsv

---
 resources.tsv | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 resources.tsv

diff --git a/resources.tsv b/resources.tsv
new file mode 100644
index 0000000..2c2c10d
--- /dev/null
+++ b/resources.tsv
@@ -0,0 +1,6 @@
+max_file_size	cores	mem	time
+NaN	1	8000	00-04:00:00
+0.05	2	12000	00-08:00:00
+0.5	4	16000	00-12:00:00
+1	8	16000	00-24:00:00
+10	16	32000	02-00:00:00
\ No newline at end of file