From cf38ed9de68367d0d1700ccff262e91ad6f1fbc0 Mon Sep 17 00:00:00 2001
From: Max Schubach <max.schubach@bih-charite.de>
Date: Tue, 11 Jun 2024 14:26:32 +0200
Subject: [PATCH] feat: snakemake 8 compatibility

---
 workflow/rules/common.smk                           | 11 ++---------
 workflow/rules/counts/counts_noUMI.smk              |  2 ++
 workflow/rules/counts/counts_umi.smk                |  2 ++
 workflow/scripts/count/MergeTrimReadsBAM_python3.py |  3 ---
 workflow/scripts/count/MergeTrimReads_python3.py    |  3 +--
 5 files changed, 7 insertions(+), 14 deletions(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 5e4dbbf..eeffe8a 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -1,18 +1,11 @@
 ################################
 #### Global functions       ####
 ################################
-from snakemake.workflow import srcdir
-
-SCRIPTS_DIR = srcdir("../scripts")
 
+SCRIPTS_DIR = "../scripts"
 
 def getScript(name):
-    return "%s/%s" % (SCRIPTS_DIR, name)
-
-
-# this container defines the underlying OS for each job when using the workflow
-# with --use-conda --use-singularity
-container: "docker://continuumio/miniconda3"
+    return workflow.source_path("%s/%s" % (SCRIPTS_DIR, name))
 
 
 ##### load config and sample sheets #####
diff --git a/workflow/rules/counts/counts_noUMI.smk b/workflow/rules/counts/counts_noUMI.smk
index 9f8f2c9..e0af257 100644
--- a/workflow/rules/counts/counts_noUMI.smk
+++ b/workflow/rules/counts/counts_noUMI.smk
@@ -14,7 +14,9 @@ rule counts_noUMI_create_BAM:
         fw_fastq=lambda wc: getFW(wc.project, wc.condition, wc.replicate, wc.type),
         rev_fastq=lambda wc: getRev(wc.project, wc.condition, wc.replicate, wc.type),
         script_FastQ2doubleIndexBAM=getScript("count/FastQ2doubleIndexBAM_python3.py"),
+        module_FastQ2doubleIndexBAM=getScript("count/library_python3.py"),
         script_MergeTrimReadsBAM=getScript("count/MergeTrimReadsBAM_python3.py"),
+        module_MergeTrimReadsBAM=getScript("count/MergeTrimReads_python3.py"),
     output:
         "results/experiments/{project}/counts/noUMI.{condition}_{replicate}_{type}.bam",
     params:
diff --git a/workflow/rules/counts/counts_umi.smk b/workflow/rules/counts/counts_umi.smk
index 5a86e6d..5f4b1b7 100644
--- a/workflow/rules/counts/counts_umi.smk
+++ b/workflow/rules/counts/counts_umi.smk
@@ -15,7 +15,9 @@ rule counts_umi_create_BAM:
         rev_fastq=lambda wc: getRev(wc.project, wc.condition, wc.replicate, wc.type),
         umi_fastq=lambda wc: getUMI(wc.project, wc.condition, wc.replicate, wc.type),
         script_FastQ2doubleIndexBAM=getScript("count/FastQ2doubleIndexBAM_python3.py"),
+        module_FastQ2doubleIndexBAM=getScript("count/library_python3.py"),
         script_MergeTrimReadsBAM=getScript("count/MergeTrimReadsBAM_python3.py"),
+        module_MergeTrimReadsBAM=getScript("count/MergeTrimReads_python3.py"),
     output:
         "results/experiments/{project}/counts/useUMI.{condition}_{replicate}_{type}.bam",
     params:
diff --git a/workflow/scripts/count/MergeTrimReadsBAM_python3.py b/workflow/scripts/count/MergeTrimReadsBAM_python3.py
index fd86182..46fe94e 100644
--- a/workflow/scripts/count/MergeTrimReadsBAM_python3.py
+++ b/workflow/scripts/count/MergeTrimReadsBAM_python3.py
@@ -21,12 +21,9 @@
 """
 
 import sys, os
-import math
-import random
 
 import pysam
 from optparse import OptionParser,OptionGroup
-import string
 
 from MergeTrimReads_python3 import set_adapter_sequences, set_options, set_keys, process_SR, process_PE
 table = str.maketrans('TGCA','ACGT') # COMPLEMENT DNA
diff --git a/workflow/scripts/count/MergeTrimReads_python3.py b/workflow/scripts/count/MergeTrimReads_python3.py
index e5b55a9..c08d063 100644
--- a/workflow/scripts/count/MergeTrimReads_python3.py
+++ b/workflow/scripts/count/MergeTrimReads_python3.py
@@ -18,10 +18,9 @@
 
 """
 
-import sys, os
+import sys
 import math
 import random
-import string
 
 table = str.maketrans('TGCA','ACGT') # COMPLEMENT DNA