Commit c28064aa authored by peguerin's avatar peguerin
Browse files

add barcode

parent 1e5eade5

Snakefile

+4 −8
Original line number Diff line number Diff line
@@ -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),

config.yaml

+24 −0
Original line number Diff line number Diff line
@@ -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: