.gitattributes

+*.smk linguist-language=Python
+Snakefile linguist-language=Python
\ No newline at end of file

Snakefile

+__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"
\ No newline at end of file