Commit 1e5eade5 authored by peguerin's avatar peguerin
Browse files

format snakemake

parent fc3761a6

Snakefile

+3 −3
Original line number Diff line number Diff line
@@ -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),

config.yaml

+2 −0
Original line number Diff line number Diff line 
container:

  /media/superdisk/utils/conteneurs/obitools.simg

fastqFolderPath:

  /media/superdisk/edna/donnees/test/tiny_rhone_miseq/

illuminapairedend:

  s_min : 40

good_length_samples:

rules/step1.smk

+3 −19
Original line number Diff line number Diff line 
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: