From 18b9d0e6e20abac7211842d9fbd5f1b7cf0b6899 Mon Sep 17 00:00:00 2001
From: marvin-jens <marvin.jens@mdc-berlin.de>
Date: Fri, 21 Apr 2023 15:53:08 +0200
Subject: [PATCH] * removed polyA_adapter_trimming=false support throughout. If
 it's present in a user's config.yaml, this will trigger a warning and be
 overriden with 'true'

---
 spacemake/config.py                           | 31 +++++++++++++------
 spacemake/data/config/config.yaml             |  2 --
 .../scripts/snakemake_helper_functions.py     |  1 -
 3 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/spacemake/config.py b/spacemake/config.py
index 339faa61..cfdd76b3 100644
--- a/spacemake/config.py
+++ b/spacemake/config.py
@@ -76,14 +76,14 @@ def get_run_mode_parser(required=True):
         + "parameter is set, contiguous islands within umi_cutoff passing beads will "
         + "also be included in the analysis",
     )
-    parser.add_argument(
-        "--polyA_adapter_trimming",
-        required=False,
-        choices=bool_in_str,
-        type=str,
-        help="if set, reads will have polyA stretches and adapter sequence overlaps trimmed "
-        + "BEFORE mapping.",
-    )
+    # parser.add_argument(
+    #     "--polyA_adapter_trimming",
+    #     required=False,
+    #     choices=bool_in_str,
+    #     type=str,
+    #     help="if set, reads will have polyA stretches and adapter sequence overlaps trimmed "
+    #     + "BEFORE mapping.",
+    # )
     parser.add_argument(
         "--count_intronic_reads",
         required=False,
@@ -581,6 +581,18 @@ def correct(self):
                 if not var in RunMode.variable_types:
                     del variables[var]
 
+            if ("polyA_adapter_trimming" in variables) and (
+                variables["polyA_adapter_trimming"] == False
+            ):
+                import logging
+
+                logger = logging.getLogger("spacemake.config")
+                logger.warning(
+                    f"WARNING: run_mode {run_mode_name} lists polyA_adapter_trimming=false. This is no longer supported and will be overriden with true"
+                )
+                variables["polyA_adapter_trimming"] = True
+
+            # print(f"assigning run mode {run_mode_name}: {variables}")
             self.variables["run_modes"][run_mode_name] = variables
 
     def dump(self):
@@ -723,7 +735,7 @@ def add_variable(self, variable, name, **kwargs):
         # --name is absolutely REQUIRED and its value has to map somehow onto
         # an internal function name
         # @TAMAS: can you help?
-        print(f"add_variable() called with variable={variable} name={name} kw={kwargs}")
+        # print(f"add_variable() called with variable={variable} name={name} kw={kwargs}")
 
         if variable == "species":
             # for the species command, collision check is on the reference name, not the species name
@@ -769,6 +781,7 @@ def update_variable(self, variable, name, **kwargs):
         return variable_data
 
     def get_variable(self, variable, name):
+        # print(f"config.get_variable({variable}, {name})")
         if not self.variable_exists(variable, name):
             raise ConfigVariableNotFoundError(variable, name)
         else:
diff --git a/spacemake/data/config/config.yaml b/spacemake/data/config/config.yaml
index 802f8806..4a2ae45a 100644
--- a/spacemake/data/config/config.yaml
+++ b/spacemake/data/config/config.yaml
@@ -35,7 +35,6 @@ run_modes:
         umi_cutoff: [1000]
         clean_dge: False
         detect_tissue: True
-        polyA_adapter_trimming: False
         count_intronic_reads: False
         count_mm_reads: True
     slide_seq:
@@ -47,7 +46,6 @@ run_modes:
         n_beads: 10000
         umi_cutoff: [500]
         detect_tissue: False
-        polyA_adapter_trimming: True
         count_intronic_reads: True
         count_mm_reads: False
     seq_scope:
diff --git a/spacemake/snakemake/scripts/snakemake_helper_functions.py b/spacemake/snakemake/scripts/snakemake_helper_functions.py
index bc3e56b4..9a8adff1 100644
--- a/spacemake/snakemake/scripts/snakemake_helper_functions.py
+++ b/spacemake/snakemake/scripts/snakemake_helper_functions.py
@@ -65,7 +65,6 @@ def get_output_files(
 
         for run_mode in row["run_mode"]:
             run_mode_variables = project_df.config.get_run_mode(run_mode).variables
-
             if "polyA_adapter_trimmed" in kwargs:
                 polyA_adapter_trimmed = kwargs["polyA_adapter_trimmed"]
             else: