Commit 23ebc881 authored by peguerin's avatar peguerin
Browse files

condition chunk or not

parent 3648e68a
...@@ -64,19 +64,30 @@ listChunks = [*range(1,(config['illuminapairedend']['nb_chunk']+1))] ...@@ -64,19 +64,30 @@ listChunks = [*range(1,(config['illuminapairedend']['nb_chunk']+1))]
############################################################################### ###############################################################################
# RULES # 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"
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