Commit 1e5eade5 authored by peguerin's avatar peguerin

format snakemake

parent fc3761a6
......@@ -2,14 +2,14 @@ __author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
configfile: "config.yaml"
RUNS, = glob_wildcards('raw/{run}_R1.fastq.gz')
BARCODES, = glob_wildcards('barcodes/{barcode}.dat')
RUNS, = glob_wildcards('{folder}/{run}_R1.fastq.gz', folder=config["fastqFolderPath"])
BARCODES, = glob_wildcards('{folder}/{barcode}.dat', folder=config["fastqFolderPath"])
DICBARCODES={}
i=0
for bc in BARCODES:
DICBARCODES[RUNS[i]]="barcodes/"+bc+".dat"
i=i+1
#print(DICBARCODES)
print(DICBARCODES)
rule all:
input:
expand('assembled/{run}/{run}.fastq', run=RUNS),
......
container:
/media/superdisk/utils/conteneurs/obitools.simg
fastqFolderPath:
/media/superdisk/edna/donnees/test/tiny_rhone_miseq/
illuminapairedend:
s_min : 40
good_length_samples:
......
configfile: "config.yaml"
RUNS, = glob_wildcards('raw/{run}_R1.fastq.gz')
BARCODES, = glob_wildcards('barcodes/{barcode}.dat')
DICBARCODES={}
i=0
for bc in BARCODES:
DICBARCODES[RUNS[i]]="barcodes/"+bc+".dat"
i=i+1
#print(DICBARCODES)
rule all:
input:
expand('assembled/{run}/{run}.fastq', run=RUNS),
expand('assembled/{run}/{run}.ali.fastq', run=RUNS),
expand('assembled/{run}/{run}.ali.assigned.fastq', run=RUNS),
expand('assembled/{run}/{run}.unidentified.fastq', run=RUNS),
expand('log/remove_unaligned/{run}.log',run=RUNS),
expand('log/illuminapairedend/{run}.log',run=RUNS),
expand('log/assign_sequences/{run}.log',run=RUNS),
expand('log/split_sequences/{run}.log',run=RUNS)
__author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
### Paired end alignment then keep reads with quality > 40
rule illuminapairedend:
......
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