From d0e5cf57459ffccdc190e5733a9505bc35bcbb4b Mon Sep 17 00:00:00 2001
From: Thomas Weber <thomas.weber@embl.de>
Date: Wed, 26 Jun 2024 10:37:29 +0000
Subject: [PATCH] Paired end parameter + fixing samtools index issue

---
 config/config.yaml        |  2 ++
 workflow/rules/common.smk |  7 ++++++-
 workflow/rules/utils.smk  | 15 +++++++++++++++
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/config/config.yaml b/config/config.yaml
index 6a25bcb9..846efcac 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -46,6 +46,8 @@ MultiQC: False
 # Enable or disable ashleys-qc automatic classification
 bypass_ashleys: False
 
+paired_end: True
+
 # --------------------------------------------------------
 # Other modules
 # --------------------------------------------------------
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index d85be96c..ca1ebb34 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -20,6 +20,11 @@ conda_envs += (
     else []
 )
 
+if config["paired_end"] is True:
+    pair = ["1", "2"]
+else:
+    pair = ["1"]
+
 # print(config["data_location"])
 
 if config["ashleys_pipeline"] is True and config["genecore"] is True:
@@ -284,7 +289,7 @@ class HandleInput:
                 regex_element=d_master[sample]["index_pattern"],
                 index=d_master[sample]["indexes"],
                 cell_nb=[str(e).zfill(2) for e in list(range(1, 97))],
-                pair=["1", "2"],
+                pair=pair,
             )
             for sample in d_master
             if sample in samples_to_process
diff --git a/workflow/rules/utils.smk b/workflow/rules/utils.smk
index 6f2f270d..ed94a3d1 100644
--- a/workflow/rules/utils.smk
+++ b/workflow/rules/utils.smk
@@ -126,6 +126,21 @@ rule index_merged_strandphaser_vcf:
         "tabix -p vcf {input.vcf} > {log} 2>&1"
 
 
+rule gunzip_fasta:
+    input:
+        ancient("{file}.fa.gz"),
+    output:
+        "{file}.fa",
+    log:
+        "{file}.log",
+    conda:
+        "../envs/mc_bioinfo_tools.yaml"
+    resources:
+        mem_mb=get_mem_mb_heavy,
+    shell:
+        "gunzip -cd {input} > {output}"
+
+
 rule samtools_faindex:
     input:
         ancient("{file}.fa"),