Using more processors to map and index.

Hopefully this will be more efficient on pisa.

CLIP/iCLIP.snakefile

@@ -233,7 +233,7 @@ rule trim_and_dedup:
         process_type = "iCLIP",
         trim5 = 8,
         trim3 = 4,
-    threads: 4 # Actually, to avoid too much IO
+    threads: 8 # Actually, to avoid too much IO
     message:
         "Trimming adaptor from raw data using {wildcards.trimmer}, deduplicating reads, and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
     benchmark:
@@ -470,7 +470,7 @@ rule sam2indexedbam:
         log = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
         err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
     threads:
-        4
+        8
     resources:
         mem_mb=4100
     wrapper:

Degradome-seq/Degradome-seq.snakefile

@@ -168,7 +168,7 @@ rule map_on_genome:
     resources:
         io=5
     threads:
-        4
+        8
     wrapper:
         f"file://{wrappers_dir}/map_on_genome"
 

PRO-seq/PRO-seq.snakefile

@@ -392,7 +392,7 @@ rule trim_and_dedup:
         process_type = "PRO-seq",
         trim5 = lambda wildcards : lib2UMI[wildcards.lib][0],
         trim3 = lambda wildcards : lib2UMI[wildcards.lib][1],
-    threads: 4 # Actually, to avoid too much IO
+    threads: 8 # Actually, to avoid too much IO
     message:
         "Trimming adaptor from raw data using {wildcards.trimmer}, deduplicating reads, and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
     benchmark:
@@ -429,7 +429,7 @@ rule trim_only:
         process_type = "PRO-seq",
         trim5 = lambda wildcards : lib2UMI[wildcards.lib][0],
         trim3 = lambda wildcards : lib2UMI[wildcards.lib][1],
-    threads: 4 # Actually, to avoid too much IO
+    threads: 8 # Actually, to avoid too much IO
     message:
         "Trimming adaptor from raw data using {wildcards.trimmer} and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
     benchmark:
@@ -481,6 +481,8 @@ rule map_on_genome:
     log:
         log = OPJ(log_dir, "{trimmer}", "map_{type}_on_genome", "{lib}_{rep}.log"),
         err = OPJ(log_dir, "{trimmer}", "map_{type}_on_genome", "{lib}_{rep}.err"),
+    threads:
+        8
 #    shell:
 #        """
 #        genome_dir="${{HOME}}/Genomes"
@@ -506,7 +508,7 @@ rule sam2indexedbam:
         log = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.log"),
         err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.err"),
     threads:
-        4
+        8
     resources:
         mem_mb=4100
     wrapper:

RNA_Seq_Cecere/RNA-seq.snakefile

@@ -567,7 +567,7 @@ rule map_on_genome:
     resources:
         io=5
     threads:
-        4
+        8
     #shell:
     #    mapping_command(aligner)
     wrapper:
@@ -620,7 +620,7 @@ rule remap_on_genome:
     resources:
         io=5
     threads:
-        4
+        8
     #shell:
     #    mapping_command(aligner)
     wrapper:

Ribo-seq/Ribo-seq.snakefile

@@ -755,7 +755,7 @@ rule map_on_genome:
         log = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_{read_type}.log"),
         err = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_{read_type}.err")
     threads:
-        4
+        8
     wrapper:
         f"file://{wrappers_dir}/map_on_genome"
 
@@ -787,7 +787,7 @@ rule sam2indexedbam:
         log = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
         err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
     threads:
-        4
+        8
     resources:
         mem_mb=4100
     wrapper:

small_RNA-seq/small_RNA-seq.snakefile

@@ -1014,7 +1014,7 @@ rule map_on_genome:
         log = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_%s.log" % size_selected),
         err = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_%s.err" % size_selected)
     threads:
-        4
+        8
     resources:
         mem_mb=700
     wrapper:
@@ -1067,7 +1067,7 @@ rule remap_on_genome:
         log = OPJ(log_dir, "remap_on_genome", "{lib}_{rep}_{read_type}.log"),
         err = OPJ(log_dir, "remap_on_genome", "{lib}_{rep}_{read_type}.err")
     threads:
-        4
+        8
     resources:
         mem_mb=700
     wrapper:
@@ -1102,7 +1102,7 @@ rule sam2indexedbam:
         log = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
         err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
     threads:
-        4
+        8
     resources:
         mem_mb=4100
     wrapper: