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This is an archived project. Repository and other project resources are read-only.
Commits on Source (2)
format snakemake
· cafc4216
peguerin
authored
Sep 25, 2019
cafc4216
add gitattributes
· a3f55938
peguerin
authored
Sep 25, 2019
a3f55938
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.gitattributes
0 → 100644
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a3f55938
*.smk linguist-language=Python
Snakefile linguist-language=Python
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Snakefile
0 → 100644
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a3f55938
__author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
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)
include: "rules/step1.smk"
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script
s/step1.s
f
→
rule
s/step1.s
mk
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a3f55938
File moved
script
s/step2.sf
→
rule
s/step2.sf
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a3f55938
File moved
script
s/step3.sf
→
rule
s/step3.sf
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File moved
script
s/step4.sf
→
rule
s/step4.sf
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a3f55938
File moved