Paired end parameter + fixing samtools index issue

config/config.yaml

@@ -46,6 +46,8 @@ MultiQC: False
 # Enable or disable ashleys-qc automatic classification
 bypass_ashleys: False
 
+paired_end: True
+
 # --------------------------------------------------------
 # Other modules
 # --------------------------------------------------------

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

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"),