From c1efacac9631e99f4b6bb6f4efd6e305fa5e1024 Mon Sep 17 00:00:00 2001
From: Nathan Gaddis <ngaddis@rti.org>
Date: Wed, 25 Sep 2024 14:30:00 -0400
Subject: [PATCH] Updated t1dgrs2 v2 pipeline so that different yml files can
 be specified for t1dgrs2 tool

---
 t1dgrs2_pipeline/v2.0/Dockerfile                     |  1 +
 .../entrypoint_calculate_t1dgrs2.json                |  6 +-----
 .../v2.0/pipeline_config/t1dgrs2_settings_mod001.yml | 12 ++++++++++++
 ...s2_settings.yml => t1dgrs2_settings_original.yml} |  0
 .../v2.0/pipeline_config/t1dgrs2_tasks.json          |  5 ++++-
 .../pipeline_inputs/t1dgrs2_hg19_variants_mod001.tsv |  2 +-
 6 files changed, 19 insertions(+), 7 deletions(-)
 create mode 100644 t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings_mod001.yml
 rename t1dgrs2_pipeline/v2.0/pipeline_config/{t1dgrs2_settings.yml => t1dgrs2_settings_original.yml} (100%)

diff --git a/t1dgrs2_pipeline/v2.0/Dockerfile b/t1dgrs2_pipeline/v2.0/Dockerfile
index 61730d1..9e54050 100644
--- a/t1dgrs2_pipeline/v2.0/Dockerfile
+++ b/t1dgrs2_pipeline/v2.0/Dockerfile
@@ -83,3 +83,4 @@ WORKDIR /data
 RUN chown -R docker:staff /data
 
 ENTRYPOINT [ "/opt/entrypoint.sh" ]
+
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_calculate_t1dgrs2.json b/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_calculate_t1dgrs2.json
index 8594ee5..5552028 100644
--- a/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_calculate_t1dgrs2.json
+++ b/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_calculate_t1dgrs2.json
@@ -31,11 +31,6 @@
             "default": "",
             "required": true
         },
-        "control_samples": {
-            "type": "file",
-            "default": "",
-            "required": true
-        },
         "variant_list_version": {
             "type": "str",
             "default": "mod001",
@@ -76,6 +71,7 @@
                         "working_dir": "<inputs.working_dir>calculate_t1dgrs2",
                         "output_dir": "<inputs.output_dir>calculate_t1dgrs2",
                         "bfile": "<steps.merge_sample_bfiles_and_controls.bfile>",
+                        "yml": "/pipeline/config/t1dgrs2_settings_<inputs.variant_list_version>.yml",
                         "out_prefix": "<inputs.output_dir>calculate_t1dgrs2/samples_with_controls"
                     }
                 },
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings_mod001.yml b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings_mod001.yml
new file mode 100644
index 0000000..6342d3e
--- /dev/null
+++ b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings_mod001.yml
@@ -0,0 +1,12 @@
+---
+input: # mandatory, all files in here are tab-delimited tabular data
+  hla_map: "/pipeline/inputs/T1D67_mapping.tsv"
+  dq_rank: "/pipeline/inputs/HLADQ_USAEuropean_Klitz.tsv"
+  max_dq_calls: 2 # not implemented yet
+scores: # mandatory
+  interaction: "/pipeline/inputs/T1D67_interaction_scores.tsv"
+  all_variants: "/pipeline/inputs/T1D67_plink_all_scores_mod001.tsv"
+  hla_variants: "/pipeline/inputs/T1D67_plink_hla_scores.tsv" # optional, will automatically exclude HLA BETAs from final calculation if this key-value pair is removed
+metrics: # optional, will not compute centiles, PPV or case probability if this key (and child key-value pairs) is removed
+  centiles_file: "/pipeline/inputs/UKBB_T1D67_ROC.tsv"
+  params_file: "/pipeline/inputs/UKBB_T1D67_Fit.tsv"
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings.yml b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings_original.yml
similarity index 100%
rename from t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings.yml
rename to t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_settings_original.yml
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
index c5f306f..95e6808 100644
--- a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
+++ b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
@@ -370,6 +370,9 @@
             "bfile": {
                 "type": "str"
             },
+            "yml": {
+                "type": "file"
+            },
             "out_prefix": {
                 "type": "str"
             }
@@ -381,7 +384,7 @@
             "-b",
             "<inputs.bfile>",
             "-c",
-            "/pipeline/config/t1dgrs2_settings.yml",
+            "<inputs.yml>",
             "-o",
             "<inputs.out_prefix>"
         ],
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_inputs/t1dgrs2_hg19_variants_mod001.tsv b/t1dgrs2_pipeline/v2.0/pipeline_inputs/t1dgrs2_hg19_variants_mod001.tsv
index b84dc56..406be8e 100644
--- a/t1dgrs2_pipeline/v2.0/pipeline_inputs/t1dgrs2_hg19_variants_mod001.tsv
+++ b/t1dgrs2_pipeline/v2.0/pipeline_inputs/t1dgrs2_hg19_variants_mod001.tsv
@@ -79,8 +79,8 @@
 18:12809340	rs1893217	A	G
 18:67526644	rs1615504	T	C
 19:10492274	rs144309607	C	T
-19:47208481	rs425105	T	C
 19:47205707	rs60652743	A	G
+19:47208481	rs425105	T	C
 20:1610551	rs2281808	T	C
 21:43825722	rs9981624	G	C
 22:30504652	rs5763779	A	G