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Fix downsample #222

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merged 3 commits into from
Sep 16, 2019
Merged

Fix downsample #222

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f4e8cbd
edited file names for downsample fastqs
tiagofilipe12 Oct 9, 2018
6561cb5
stringified depth for file name
tiagofilipe12 Oct 9, 2018
de8eb94
Merge branch 'dev' into fix_downsample
cimendes Sep 16, 2019
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5 changes: 3 additions & 2 deletions flowcraft/generator/templates/downsample_fastq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,8 @@ process downsample_fastq_{{ pid }} {
{% include "post.txt" ignore missing %}

tag { "${sample_id}" }
publishDir "results/downsample_fastq_{{ pid }}/", pattern: "*_ss.*"

publishDir "results/downsample_fastq_{{ pid }}/", pattern: "*_ss_*.*"

input:
set sample_id, file(fastq_pair) from {{ input_channel }}
Expand All @@ -27,7 +28,7 @@ process downsample_fastq_{{ pid }} {
val clear from checkpointClear_{{ pid }}

output:
set sample_id, file('*_ss.*') into {{ output_channel }}
set sample_id, file('*_ss_*.*') into {{ output_channel }}
{% with task_name="downsample_fastq" %}
{%- include "compiler_channels.txt" ignore missing -%}
{% endwith %}
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10 changes: 6 additions & 4 deletions flowcraft/templates/downsample_fastq.py
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Expand Up @@ -134,15 +134,17 @@ def main(sample_id, fastq_pair, genome_size, depth, clear, seed):
# print ("Writing R1.fq.gz")
ps = subprocess.Popen(('seqtk', 'sample', parsed_seed, p1, str(ratio)),
stdout=subprocess.PIPE)
with open('{}_ss.fq.gz'.format(bn1), 'w') as outfile:
with open('{}_ss_{}.fq.gz'.format(bn1, str(target_depth)), 'w') as \
outfile:
subprocess.Popen(('gzip', '--fast', '-c'),
stdin=ps.stdout, stdout=outfile )
ps.wait()

# print ("Writing R2.fq.gz")
ps = subprocess.Popen(('seqtk', 'sample', parsed_seed, p2, str(ratio)),
stdout=subprocess.PIPE)
with open('{}_ss.fq.gz'.format(bn2), 'w') as outfile:
with open('{}_ss_{}.fq.gz'.format(bn2, str(target_depth)), 'w') as \
outfile:
subprocess.Popen(('gzip', '--fast', '-c'),
stdin=ps.stdout, stdout=outfile)
ps.wait()
Expand All @@ -157,8 +159,8 @@ def main(sample_id, fastq_pair, genome_size, depth, clear, seed):
os.remove(rp)

else:
shutil.copy(p1, "{}._ss.fq.gz".format(bn1))
shutil.copy(p2, "{}._ss.fq.gz".format(bn2))
os.symlink(p1, "{}_ss_{}.fq.gz".format(bn1, str(target_depth)))
os.symlink(p2, "{}_ss_{}.fq.gz".format(bn2, str(target_depth)))

# Record the original estimated coverage
with open(".report.json", "w") as fh:
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