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edna
snakemake_only_obitools
Commits
899c5609
Commit
899c5609
authored
Nov 18, 2019
by
peguerin
Browse files
debug cat
parent
60170f9e
Changes
2
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00-rules/cat_samples.smk
View file @
899c5609
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@@ -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
02-demultiplex/Snakefile
View file @
899c5609
...
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@@ -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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