condition chunk or not

02_assembly/Snakefile

@@ -64,19 +64,30 @@ listChunks = [*range(1,(config['illuminapairedend']['nb_chunk']+1))]
 ###############################################################################
 # RULES
 ###############################################################################
-rule all:
-    input:
-        expand("{folder}{run}_R1.fastq.gz", run=uniqRuns,folder=config["fichiers"]["folder_fastq"]),
-        expand('../results/02_assembly/01_illuminapairedend/{run}_{chunk}.fastq', run=uniqRuns, chunk=listChunks),
-        expand('../results/02_assembly/01_illuminapairedend/{run}.fastq', run=uniqRuns),
-        expand('../results/02_assembly/02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
-        expand('../logs/02_assembly/02_remove_unaligned/{run}.log',run=uniqRuns),
-        expand('../logs/02_assembly/01_illuminapairedend/{run}_{chunk}.log',run=uniqRuns, chunk=listChunks)
 
-ruleorder: split_fastq > illuminapairedend > merge_chunks > remove_unaligned
+## scatters fastq
+if config['illuminapairedend']['nb_chunk'] != 0:
+    rule all:
+        input:
+            expand("{folder}{run}_R1.fastq.gz", run=uniqRuns,folder=config["fichiers"]["folder_fastq"]),
+            expand('../results/02_assembly/01_illuminapairedend/{run}_{chunk}.fastq', run=uniqRuns, chunk=listChunks),
+            expand('../results/02_assembly/01_illuminapairedend/{run}.fastq', run=uniqRuns),
+            expand('../results/02_assembly/02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
+            expand('../logs/02_assembly/02_remove_unaligned/{run}.log',run=uniqRuns),
+            expand('../logs/02_assembly/01_illuminapairedend/{run}_{chunk}.log',run=uniqRuns, chunk=listChunks)
+    ruleorder: split_fastq > illuminapairedend > merge_chunks > remove_unaligned
+    include: "rules/split_fastq.smk"
+    include: "rules/chunk_illuminapairedend.smk"
+    include: "rules/remove_unaligned.smk"
+## keep original fastq files
+else:
+    rule all:
+        input:
+            expand("{folder}{run}_R1.fastq.gz", run=uniqRuns,folder=config["fichiers"]["folder_fastq"]),
+            expand('../results/02_assembly/01_illuminapairedend/{run}.fastq', run=uniqRuns),
+            expand('../results/02_assembly/02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
+            expand('../logs/02_assembly/02_remove_unaligned/{run}.log',run=uniqRuns),
+            expand('../logs/02_assembly/01_illuminapairedend/{run}.log',run=uniqRuns)
+    include: "rules/illuminapairedend.smk"
+    include: "rules/remove_unaligned.smk"
 
-#include: "rules/illuminapairedend.smk"
-#include: "rules/remove_unaligned.smk"
-include: "rules/split_fastq.smk"
-include: "rules/chunk_illuminapairedend.smk"
-include: "rules/remove_unaligned.smk"