Commit 60295aef authored by peguerin's avatar peguerin
Browse files

demultiplexing reformat

parent 08114143
...@@ -2,18 +2,18 @@ __author__ = "Pierre-Edouard Guerin" ...@@ -2,18 +2,18 @@ __author__ = "Pierre-Edouard Guerin"
__license__ = "MIT" __license__ = "MIT"
SAMPLES, = glob_wildcards('02-demultiplex/02-01-raw/{sample}.fasta') SAMPLES, = glob_wildcards('01-raw/{sample}.fasta')
rule all: rule all:
input: input:
expand('02-demultiplex/02-02-filtered/{sample}.uniq.fasta',sample=SAMPLES), expand('02-filtered/{sample}.uniq.fasta',sample=SAMPLES),
expand('02-demultiplex/02-02-filtered/{sample}.l.u.fasta',sample=SAMPLES), expand('02-filtered/{sample}.l.u.fasta',sample=SAMPLES),
expand('02-demultiplex/02-02-filtered/{sample}.r.l.u.fasta',sample=SAMPLES), expand('02-filtered/{sample}.r.l.u.fasta',sample=SAMPLES),
expand('02-demultiplex/02-03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES), expand('03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES),
expand('log/dereplicate_samples/{sample}.log',sample=SAMPLES), expand('../99-log/dereplicate_samples/{sample}.log',sample=SAMPLES),
expand('log/goodlength_samples/{sample}.log',sample=SAMPLES), expand('../99-log/goodlength_samples/{sample}.log',sample=SAMPLES),
expand('log/clean_pcrerr/{sample}.log',sample=SAMPLES), expand('../99-log/clean_pcrerr/{sample}.log',sample=SAMPLES),
expand('log/rm_internal_samples/{sample}.log',sample=SAMPLES) expand('../99-log/rm_internal_samples/{sample}.log',sample=SAMPLES)
include: "00-rules/filtered.smk" include: "../00-rules/filtered.smk"
...@@ -28,6 +28,9 @@ mkdir -p 01-assembly 02-demultiplex/02-01-raw 02-demultiplex/02-02-filtered 02-d ...@@ -28,6 +28,9 @@ mkdir -p 01-assembly 02-demultiplex/02-01-raw 02-demultiplex/02-02-filtered 02-d
cd 01-assembly cd 01-assembly
snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120 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 ## clean
......
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