Commit d008ab65 authored by peguerin's avatar peguerin
Browse files

run

parent 927c5aa3
...@@ -3,8 +3,6 @@ __license__ = "MIT" ...@@ -3,8 +3,6 @@ __license__ = "MIT"
configfile: "../config.yaml" configfile: "../config.yaml"
RUNS, = glob_wildcards('raw/{run}_R1.fastq.gz')
SAMPLES, = glob_wildcards('01-raw/{sample}.fasta') SAMPLES, = glob_wildcards('01-raw/{sample}.fasta')
rule all: rule all:
...@@ -13,7 +11,7 @@ rule all: ...@@ -13,7 +11,7 @@ rule all:
expand('02-filtered/{sample}.l.u.fasta',sample=SAMPLES), expand('02-filtered/{sample}.l.u.fasta',sample=SAMPLES),
expand('02-filtered/{sample}.r.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('03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES),
expand('03-cleaned/{run}_{sa}.c.r.l.u.fasta',run=RUNS), expand('03-cleaned/{run}_{sa}.c.r.l.u.fasta',run=config["fastqFiles"]),
expand('../99-log/05-dereplicate_samples/{sample}.log',sample=SAMPLES), expand('../99-log/05-dereplicate_samples/{sample}.log',sample=SAMPLES),
expand('../99-log/06-goodlength_samples/{sample}.log',sample=SAMPLES), expand('../99-log/06-goodlength_samples/{sample}.log',sample=SAMPLES),
expand('../99-log/07-clean_pcrerr/{sample}.log',sample=SAMPLES), expand('../99-log/07-clean_pcrerr/{sample}.log',sample=SAMPLES),
......
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