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Commit 2e411efe authored by peguerin's avatar peguerin
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parent 780f0026
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02-demultiplex/Snakefile
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......@@ -5,21 +5,18 @@ configfile: "../config.yaml"
(RUNS,SAMPLES) = glob_wildcards('01-raw/{run}/{sample}.fasta')
print(SAMPLES)
print("-------------")
print(RUNS)
rule all:
input:
expand('02-filtered/{run}/{sample}.uniq.fasta',run=RUNS, sample=SAMPLES),
expand('02-filtered/{run}/{sample}.l.u.fasta',run=RUNS, sample=SAMPLES),
expand('02-filtered/{run}/{sample}.r.l.u.fasta',run=RUNS, sample=SAMPLES),
expand('03-cleaned/{run}/{sample}.c.r.l.u.fasta',run=RUNS, sample=SAMPLES),
expand('02-filtered/{run}/{sample}.uniq.fasta', zip, run=RUNS, sample=SAMPLES),
expand('02-filtered/{run}/{sample}.l.u.fasta',zip, run=RUNS, sample=SAMPLES),
expand('02-filtered/{run}/{sample}.r.l.u.fasta',zip, run=RUNS, sample=SAMPLES),
expand('03-cleaned/{run}/{sample}.c.r.l.u.fasta',zip, run=RUNS, sample=SAMPLES),
expand('../03-filtered/{run}.fasta',run=config["fastqFiles"]),
expand('../99-log/05-dereplicate_samples/{run}/{sample}.log',run=RUNS, sample=SAMPLES),
expand('../99-log/06-goodlength_samples/{run}/{sample}.log',run=RUNS, sample=SAMPLES),
expand('../99-log/07-clean_pcrerr/{run}/{sample}.log',run=RUNS, sample=SAMPLES),
expand('../99-log/08-rm_internal_samples/{run}/{sample}.log',run=RUNS, sample=SAMPLES)
expand('../99-log/05-dereplicate_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
expand('../99-log/06-goodlength_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
expand('../99-log/07-clean_pcrerr/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
expand('../99-log/08-rm_internal_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES)
include: "../00-rules/filter_samples.smk"
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