Commit 2f34c59f authored by peguerin's avatar peguerin
Browse files

cat

parent 2e411efe
### 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
......@@ -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}'''
......@@ -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"
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment