Merge pull request #50 from metagenlab/gzip

Compress reads in simulators rule

Author: farchaab

mess/workflow/envs/conda/pigz.yml

@@ -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

mess/workflow/envs/containers.yml

@@ -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:

mess/workflow/rules/processing/reads.smk

@@ -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:

mess/workflow/rules/simulate/long_reads.smk

@@ -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:
@@ -86,5 +86,6 @@ rule art_illumina:
         -f {params.cov} -na {params.args} \\
         -o {params.prefix} \\
         &> {log}
+        gzip {params.prefix}*.fq
         {params.cmd}
         """