Commit 899c5609 authored by peguerin's avatar peguerin
Browse files

debug cat

parent 60170f9e
......@@ -4,9 +4,6 @@ rule cat_samples:
'03-cleaned/{run}/{sample}.c.r.l.u.fasta'
params:
dir='03-cleaned/{run}/'
output:
'../03-filtered/{run}.fasta'
log:
'../99-log/09-cat_samples/{run}/{sample}.log'
merged='../03-filtered/{run}.fasta'
shell:
'''ls {input} > {log}; cat {params.dir}*.c.r.l.u.fasta > {output}'''
\ No newline at end of file
'''ls {input} > {log}; cat {params.dir}*.c.r.l.u.fasta > {params.merged}'''
\ No newline at end of file
......@@ -15,8 +15,7 @@ rule all:
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),
expand('../99-log/09-cat_samples/{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"
include: "../00-rules/cat_samples.smk"
......
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