From e90a7a5642e7096b872890203f8233a9f30ec0bf Mon Sep 17 00:00:00 2001
From: Thomas Weber <thomas.weber@embl.de>
Date: Mon, 4 Dec 2023 14:00:43 +0000
Subject: [PATCH] Linting, fmt, config update

---
 config/config.yaml        |  4 ++--
 workflow/Snakefile        | 12 ++++++------
 workflow/rules/common.smk |  4 +++-
 workflow/rules/plots.smk  |  3 ++-
 workflow/rules/setup.smk  |  6 ++++--
 5 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/config/config.yaml b/config/config.yaml
index 3809643d..017cd8bd 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.2.2
+version: 2.2.3
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.2.2
+ashleys_pipeline_version: 2.2.3
 
 # Email for notifications about the pipeline's status
 email: ""
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 4262bd44..652acaaa 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -19,12 +19,12 @@ if config["ashleys_pipeline"] is True:
 
     module ashleys_qc:
         snakefile:
-            "../../ashleys-qc-pipeline/workflow/Snakefile"
-            # github(
-            #     "friendsofstrandseq/ashleys-qc-pipeline",
-            #     path="workflow/Snakefile",
-            #     tag=str(config["ashleys_pipeline_version"]),
-            # )
+            # "../../ashleys-qc-pipeline/workflow/Snakefile"
+            github(
+                "friendsofstrandseq/ashleys-qc-pipeline",
+                path="workflow/Snakefile",
+                tag=str(config["ashleys_pipeline_version"]),
+            )
         config:
             config
 
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 7af4b6b4..8acedf9f 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -14,7 +14,9 @@ os.environ["LC_CTYPE"] = "C"
 # print(config["data_location"])
 
 if config["ashleys_pipeline"] is True and config["genecore"] is True:
-    config["data_location"] = "/".join(config["data_location"].split("/")[:-1])
+    config["data_location"] = config["abs_path"].join(
+        config["data_location"].split("/")[:-1]
+    )
 
 
 envvars:
diff --git a/workflow/rules/plots.smk b/workflow/rules/plots.smk
index 221c8610..23d35f3a 100644
--- a/workflow/rules/plots.smk
+++ b/workflow/rules/plots.smk
@@ -315,7 +315,8 @@ rule scTRIP_multiplot:
         "{folder}/log/scTRIP_multiplot/{sample}/{cell}/{chrom}.log",
     conda:
         "../envs/rtools.yaml"
-    container: None
+    container:
+        None
     resources:
         mem_mb=get_mem_mb,
     shell:
diff --git a/workflow/rules/setup.smk b/workflow/rules/setup.smk
index e59889ec..93ed6847 100644
--- a/workflow/rules/setup.smk
+++ b/workflow/rules/setup.smk
@@ -20,8 +20,10 @@ rule install_BSgenome_package:
     params:
         selected_package=lambda wc, input: "BSgenome.{}.UCSC.{}".format(
             "Mmusculus" if config["reference"] == "mm10" else "Hsapiens",
-            config["reference"]
-        ) if config["reference"] in ["hg38", "hg19", "mm10"] else input.package,
+            config["reference"],
+        )
+        if config["reference"] in ["hg38", "hg19", "mm10"]
+        else input.package,
     conda:
         "../envs/rtools.yaml"
     resources: