Commit 5a608107 authored by peguerin's avatar peguerin
Browse files

cat again

parent d008ab65
......@@ -11,7 +11,7 @@ rule all:
expand('02-filtered/{sample}.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/{run}_{sa}.c.r.l.u.fasta',run=config["fastqFiles"]),
expand('../03-filtered/{run}.fasta',run=config["fastqFiles"]),
expand('../99-log/05-dereplicate_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),
......@@ -22,9 +22,9 @@ 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'
params:
'03-cleaned/{run}*.c.r.l.u.fasta'
output:
'03-filtered/{run}_run.fasta'
'../03-filtered/{run}.fasta'
shell:
'''cat {input} > {output}'''
\ No newline at end of file
'''cat {params} > {output}'''
\ No newline at end of file
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