demultiplexing reformat

02-demultiplex/Snakefile

@@ -2,18 +2,18 @@ __author__ = "Pierre-Edouard Guerin"
 __license__ = "MIT"
 
 
-SAMPLES, = glob_wildcards('02-demultiplex/02-01-raw/{sample}.fasta')
+SAMPLES, = glob_wildcards('01-raw/{sample}.fasta')
 
 rule all:
     input:
-        expand('02-demultiplex/02-02-filtered/{sample}.uniq.fasta',sample=SAMPLES),
-        expand('02-demultiplex/02-02-filtered/{sample}.l.u.fasta',sample=SAMPLES),
-        expand('02-demultiplex/02-02-filtered/{sample}.r.l.u.fasta',sample=SAMPLES),
-        expand('02-demultiplex/02-03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES),        
-        expand('log/dereplicate_samples/{sample}.log',sample=SAMPLES),
-        expand('log/goodlength_samples/{sample}.log',sample=SAMPLES),
-        expand('log/clean_pcrerr/{sample}.log',sample=SAMPLES),
-        expand('log/rm_internal_samples/{sample}.log',sample=SAMPLES)
+        expand('02-filtered/{sample}.uniq.fasta',sample=SAMPLES),
+        expand('02-filtered/{sample}.l.u.fasta',sample=SAMPLES),
+        expand('02-filtered/{sample}.r.l.u.fasta',sample=SAMPLES),
+        expand('03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES),        
+        expand('../99-log/dereplicate_samples/{sample}.log',sample=SAMPLES),
+        expand('../99-log/goodlength_samples/{sample}.log',sample=SAMPLES),
+        expand('../99-log/clean_pcrerr/{sample}.log',sample=SAMPLES),
+        expand('../99-log/rm_internal_samples/{sample}.log',sample=SAMPLES)
 
-include: "00-rules/filtered.smk"
+include: "../00-rules/filtered.smk"
 

main.sh

@@ -28,6 +28,9 @@ mkdir -p 01-assembly 02-demultiplex/02-01-raw 02-demultiplex/02-02-filtered 02-d
 
 cd 01-assembly
 snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+cd ..
+cd 02-demultiplex
+snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
 
 
 ## clean