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edna
snakemake_only_obitools
Commits
2f34c59f
Commit
2f34c59f
authored
Nov 18, 2019
by
peguerin
Browse files
cat
parent
2e411efe
Changes
3
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00-rules/cat_samples.smk
0 → 100644
View file @
2f34c59f
### Concatenate sequences from each sample of the same run
rule cat_samples:
input:
'03-cleaned/{run}/{sample}.c.r.l.u.fasta'
params:
dir='03-cleaned/{run}/'
output:
'../03-filtered/{run}.fasta'
shell:
'''cat {params.dir}*.c.r.l.u.fasta > {output}'''
\ No newline at end of file
00-rules/demultiplex.smk
View file @
2f34c59f
...
...
@@ -21,10 +21,10 @@ rule split_sequences:
input:
'03-assign_sequences/{run}.ali.assigned.fastq'
params:
'../02-demultiplex/01-raw/{run}/'
dir=
'../02-demultiplex/01-raw/{run}/'
singularity:
config["container"]
log:
'../99-log/01-assembly/04-split_sequences/{run}.log'
shell:
'''mkdir -p {params}; obisplit -p "{params}" -t sample --fasta {input} 2> {log}'''
'''mkdir -p {params
.dir
}; obisplit -p "{params}" -t sample --fasta {input} 2> {log}'''
02-demultiplex/Snakefile
View file @
2f34c59f
...
...
@@ -12,11 +12,11 @@ rule all:
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',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"
include: "../00-rules/cat_samples.smk"
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