Commit c28064aa authored by peguerin's avatar peguerin

add barcode

parent 1e5eade5
......@@ -2,16 +2,12 @@ __author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
configfile: "config.yaml"
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)
rule all:
input:
expand("{folder}/{fastqf}_R1.fastq.gz", fastqf=config["fastqFiles"],folder=config["fastqFolderPath"]),
expand("{folder}/{barcode}.dat", barcode=config["barcodeFiles"],folder=config["fastqFolderPath"]),
expand('assembled/{run}/{run}.fastq', run=RUNS),
expand('assembled/{run}/{run}.ali.fastq', run=RUNS),
expand('assembled/{run}/{run}.ali.assigned.fastq', run=RUNS),
......
......@@ -2,6 +2,30 @@ container:
/media/superdisk/utils/conteneurs/obitools.simg
fastqFolderPath:
/media/superdisk/edna/donnees/test/tiny_rhone_miseq/
fastqFiles:
- 161124_SND393_A_L005_GWM-849
- 161124_SND393_A_L005_GWM-850
- 161124_SND393_A_L005_GWM-851
- 161124_SND393_A_L005_GWM-852
- 161124_SND393_A_L005_GWM-853
- 161124_SND393_A_L005_GWM-854
- 161124_SND393_A_L005_GWM-855
- 161124_SND393_A_L005_GWM-856
- 161124_SND393_A_L005_GWM-857
- 161124_SND393_A_L005_GWM-858
- 161124_SND393_A_L005_GWM-859
barcodeFiles:
- MB1016K_Teleo
- MB1016L_Teleo
- MB1016M_Teleo
- MB1016N_Teleo
- MB1016O_Teleo
- MB1016P_Teleo
- MB1016Q_Teleo
- MB1016R_Teleo
- MB1016S_Teleo
- MB1016T_Teleo
- MB1016U_Teleo
illuminapairedend:
s_min : 40
good_length_samples:
......
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