Commit 927c5aa3 authored by peguerin's avatar peguerin
Browse files

cat

parent 8ba20e15
...@@ -3,6 +3,7 @@ __license__ = "MIT" ...@@ -3,6 +3,7 @@ __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')
...@@ -11,7 +12,8 @@ rule all: ...@@ -11,7 +12,8 @@ rule all:
expand('02-filtered/{sample}.uniq.fasta',sample=SAMPLES), expand('02-filtered/{sample}.uniq.fasta',sample=SAMPLES),
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('../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),
...@@ -19,3 +21,12 @@ rule all: ...@@ -19,3 +21,12 @@ rule all:
include: "../00-rules/filtered.smk" include: "../00-rules/filtered.smk"
### Concatenate sequences from each sample of the same run
rule cat_samples:
input:
'03-cleaned/{run}_{sa}.c.r.l.u.fasta'
output:
'03-filtered/{run}_run.fasta'
shell:
'''cat {input} > {output}'''
\ No newline at end of file
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