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Compress reads in simulators rule #50

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Merged
farchaab merged 2 commits into from
Jun 26, 2025
Merged

Compress reads in simulators rule #50

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1bc2682
gzip fastqs in simulator rule
farchaab Jun 25, 2025
13c994b
remove pigz conda env and container
farchaab Jun 25, 2025
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5 changes: 0 additions & 5 deletions mess/workflow/envs/conda/pigz.yml
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1 change: 0 additions & 1 deletion mess/workflow/envs/containers.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ art: docker://quay.io/biocontainers/art:2016.06.05--heacdb12_11
assembly_finder: docker://ghcr.io/metagenlab/assembly_finder:v0.8.0
bioconvert: docker://quay.io/biocontainers/bioconvert:1.1.1--pyhdfd78af_0
curl: docker://quay.io/biocontainers/curl:7.80.0
pigz: docker://quay.io/biocontainers/pigz:2.8
pbccs: docker://quay.io/biocontainers/pbccs:6.4.0--h9ee0642_0
pbsim3: docker://quay.io/biocontainers/pbsim3:3.0.4--h4ac6f70_0
seqkit: docker://quay.io/biocontainers/seqkit:2.8.2--h9ee0642_0
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20 changes: 0 additions & 20 deletions mess/workflow/rules/processing/reads.smk
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Expand Up @@ -340,26 +340,6 @@ rule get_cami_profile:
"""


rule compress_contig_fastqs:
input:
fastq,
output:
fastq_gz,
resources:
mem_mb=config.resources.sml.mem,
mem=str(config.resources.sml.mem) + "MB",
time=config.resources.sml.time,
threads: config.resources.sml.cpu
conda:
os.path.join(dir.conda, "pigz.yml")
container:
containers.pigz
shell:
"""
pigz -p {threads} {input}
"""


sample_fastq_out = []
if SKIP_SHUFFLE:
if PAIRED:
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4 changes: 2 additions & 2 deletions mess/workflow/rules/simulate/long_reads.smk
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Expand Up @@ -12,8 +12,8 @@ if PASSES > 1:
pbsim3_out = temp(prefix + ".sam")
rename = f"mv {prefix}_0001.sam {prefix}.sam"
else:
pbsim3_out = temp(prefix + ".fq")
rename = f"mv {prefix}_0001.fastq {prefix}.fq"
pbsim3_out = temp(prefix + ".fq.gz")
rename = f"gzip -c {prefix}_0001.fastq > {prefix}.fq.gz"


rule pbsim3:
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5 changes: 3 additions & 2 deletions mess/workflow/rules/simulate/short_reads.smk
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Expand Up @@ -37,8 +37,8 @@ if ERRFREE:


fastq_out = [
temp(fq_prefix + "1.fq"),
temp(fq_prefix + "2.fq"),
temp(fq_prefix + "1.fq.gz"),
temp(fq_prefix + "2.fq.gz"),
]

if not PAIRED:
Expand Down Expand Up @@ -86,5 +86,6 @@ rule art_illumina:
-f {params.cov} -na {params.args} \\
-o {params.prefix} \\
&> {log}
gzip {params.prefix}*.fq
{params.cmd}
"""