added cleanup rule, remove temp taxdump

metagenlab · Apr 26, 2024 · 8412730 · 8412730
1 parent e730b14
commit 8412730
Showing 1 changed file with 31 additions and 9 deletions.
diff --git a/mess/workflow/rules/processing/reads.smk b/mess/workflow/rules/processing/reads.smk
@@ -239,9 +239,9 @@ if BAM:
 
     rule download_taxdump:
         output:
-            temp(os.path.join(TAXONKIT, "taxdump.tar.gz")),
+            os.path.join(TAXONKIT, "taxdump.tar.gz"),
         log:
-            os.path.join(dir.out.logs, "curl", "taxdump.log"),
+            os.path.join(dir.out.logs, "curl.log"),
         resources:
             mem_mb=config.resources.sml.mem,
             mem=str(config.resources.sml.mem) + "MB",
@@ -265,13 +265,11 @@ if BAM:
         params:
             dir=TAXONKIT,
         log:
-            os.path.join(dir.out.logs, "tar", "taxdump.log"),
+            os.path.join(dir.out.logs, "taxdump.log"),
         resources:
             mem_mb=config.resources.sml.mem,
             mem=str(config.resources.sml.mem) + "MB",
             time=config.resources.sml.time,
-        log:
-            os.path.join(dir.out.logs, "wget", "taxdump.log"),
         conda:
             os.path.join(dir.env, "utils.yml")
         shell:
@@ -482,30 +480,54 @@ if not SKIP_SHUFFLE:
             os.path.join(dir.out.fastq, "{sample}_R{p}.fq.gz")
             if PAIRED
             else os.path.join(dir.out.fastq, "{sample}.fq.gz"),
-        conda:
-            os.path.join(dir.env, "seqkit.yml")
         benchmark:
             os.path.join(
                 dir.out.bench, "seqkit", "anonymize", "{sample}_R{p}.txt"
             ) if PAIRED else os.path.join(
                 dir.out.bench, "seqkit", "anonymize", "{sample}.txt"
             )
-        params:
-            seqkit_replace,
         log:
             os.path.join(dir.out.logs, "seqkit", "replace", "{sample}_R{p}.log")
             if PAIRED
             else os.path.join(dir.out.logs, "seqkit", "replace", "{sample}.log"),
             os.path.join(dir.out.logs, "anonymized_reads", "{sample}_R{p}.tsv")
             if PAIRED
             else os.path.join(dir.out.logs, "anonymized_reads", "{sample}.tsv"),
+        params:
+            seqkit_replace,
         resources:
             mem_mb=config.resources.sml.mem,
             mem=str(config.resources.sml.mem) + "MB",
             time=config.resources.norm.time,
+        conda:
+            os.path.join(dir.env, "seqkit.yml")
         shell:
             """
             seqkit seq {input} | seqkit replace \\
             -p .+ -r "{params}" -o {output} 2> {log[0]}
             paste -d '\t' <(seqkit seq -n {output}) <(seqkit seq -n {input}) > {log[1]} 
             """
+
+
+rule cleanup_files:
+    input:
+        list_reads,
+        os.path.join(dir.out.base, "replicates.tsv"),
+        os.path.join(dir.out.base, "samples.tsv"),
+        os.path.join(dir.out.processing, "split"),
+    output:
+        temp(os.path.join(dir.out.base, "cleanup.done")),
+    resources:
+        mem_mb=config.resources.sml.mem,
+        mem=str(config.resources.sml.mem) + "MB",
+        time=config.resources.norm.time,
+    params:
+        proc=dir.out.processing,
+        base=dir.out.base,
+    conda:
+        os.path.join(dir.env, "utils.yml")
+    shell:
+        """
+        rm -rf {params[0]}
+        touch {output}
+        """