debug step 1 4

00-rules/demultiplex.smk

@@ -21,7 +21,7 @@ rule split_sequences:
     input:
         '03-assign_sequences/{run}.ali.assigned.fastq'
     params:
-        '02-demultiplex/01-raw/{run}_sample_'
+        '../02-demultiplex/01-raw/{run}_sample_'
     singularity:
         config["container"]
     log:

main.sh

@@ -30,3 +30,6 @@ cd 01-assembly
 snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
 
 
+## clean
+snakemake -s Snakefile --delete-all-output --dry-run
+snakemake -s Snakefile --delete-all-output