From 905046e37c00c0b279144c33b813d7f01e52ca54 Mon Sep 17 00:00:00 2001
From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com>
Date: Wed, 24 Jan 2024 15:06:54 +0000
Subject: [PATCH] Fix slurm preset (#118)

* require snakemake<8

* fix escape character and whitespace errors
---
 pyproject.toml                                       | 2 +-
 seqnado/workflow/rules/alignment_post_processing.smk | 4 ++--
 seqnado/workflow/rules/hub.smk                       | 2 +-
 seqnado/workflow/snakefile_atac                      | 2 +-
 seqnado/workflow/snakefile_chip                      | 2 +-
 seqnado/workflow/snakefile_rna                       | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 33f84728..90efb950 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     "seaborn",
     "setuptools_scm",
     "snakemake-wrapper-utils",
-    "snakemake<=9.0.0",
+    "snakemake<8.0.0",
     "tracknado",
     "wget",
 ]
diff --git a/seqnado/workflow/rules/alignment_post_processing.smk b/seqnado/workflow/rules/alignment_post_processing.smk
index 09097ce8..ea8c1354 100644
--- a/seqnado/workflow/rules/alignment_post_processing.smk
+++ b/seqnado/workflow/rules/alignment_post_processing.smk
@@ -159,8 +159,8 @@ rule move_bam_to_final_location:
         bam="seqnado_output/aligned/shifted_for_tn5_insertion/{sample}.bam",
         bai="seqnado_output/aligned/shifted_for_tn5_insertion/{sample}.bam.bai",
     output:
-        bam="seqnado_output/aligned/{sample,[A-Za-z0-9_\-]+}.bam",
-        bai="seqnado_output/aligned/{sample,[A-Za-z0-9_\-]+}.bam.bai",
+        bam="seqnado_output/aligned/{sample,[A-Za-z0-9_-]+}.bam",
+        bai="seqnado_output/aligned/{sample,[A-Za-z0-9_-]+}.bam.bai",
     log:
         "seqnado_output/logs/move_bam/{sample}.log",
     shell:"""
diff --git a/seqnado/workflow/rules/hub.smk b/seqnado/workflow/rules/hub.smk
index fbd87868..8344728b 100644
--- a/seqnado/workflow/rules/hub.smk
+++ b/seqnado/workflow/rules/hub.smk
@@ -137,7 +137,7 @@ rule generate_hub:
     output:
         hub=get_hub_txt_path(),
     log:
-        log=f"seqnado_output/logs/{config['ucsc_hub_details']['name']}.hub.log",
+        log=f"seqnado_output/logs/{config['ucsc_hub_details']['name']}.hub.log".strip(),
     container:
         None
     params:
diff --git a/seqnado/workflow/snakefile_atac b/seqnado/workflow/snakefile_atac
index f3ce29ef..ce799548 100644
--- a/seqnado/workflow/snakefile_atac
+++ b/seqnado/workflow/snakefile_atac
@@ -25,7 +25,7 @@ utils.format_config_dict(config)
 
 # Generate design
 if os.path.exists(config["design"]):
-    df = pd.read_csv(config["design"], sep="[\s+,\t]", engine="python")
+    df = pd.read_csv(config["design"], sep=r"\s+|,|\t", engine="python", index_col=0)
     DESIGN = Design.from_dataframe(df)
 else:
     DESIGN = Design.from_directory(".")
diff --git a/seqnado/workflow/snakefile_chip b/seqnado/workflow/snakefile_chip
index 8f48e9a3..8beb22bb 100644
--- a/seqnado/workflow/snakefile_chip
+++ b/seqnado/workflow/snakefile_chip
@@ -24,7 +24,7 @@ utils.format_config_dict(config)
 
 # Generate design
 if os.path.exists(config["design"]):
-    df = pd.read_csv(config["design"], sep="[\s+,\t]", engine="python")
+    df = pd.read_csv(config["design"], sep=r"\s+|,|\t", engine="python")
     DESIGN = DesignIP.from_dataframe(df)
 else:
     DESIGN = DesignIP.from_directory(".")
diff --git a/seqnado/workflow/snakefile_rna b/seqnado/workflow/snakefile_rna
index dd3d6849..6cafa0c3 100644
--- a/seqnado/workflow/snakefile_rna
+++ b/seqnado/workflow/snakefile_rna
@@ -29,7 +29,7 @@ utils.format_config_dict(config)
 
 # Generate design
 if os.path.exists(config["design"]):
-    df = pd.read_csv(config["design"], sep="[\s+,\t]", engine="python", index_col=0)
+    df = pd.read_csv(config["design"], sep=r"\s+|,|\t", engine="python", index_col=0)
     DESIGN = Design.from_dataframe(df)
 else:
     DESIGN = Design.from_directory(".")