removing temp files

niekwit · Jul 5, 2024 · 680e672 · 680e672
1 parent b3a33ad
commit 680e672
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/workflow/rules/damid.smk b/workflow/rules/damid.smk
@@ -16,7 +16,7 @@ if config["plasmid_fasta"] == "none":
             ),
         output:
             bf=expand("results/bedgraph/{{dir}}/{bg_sample}-vs-Dam-norm.gatc.bedgraph", bg_sample=BG_SAMPLES),
-            bam=expand("results/bam/{{dir}}/{sample}.bam", sample=SAMPLES),
+            bam=temp(expand("results/bam/{{dir}}/{sample}.bam", sample=SAMPLES)),
         params:
             idxdir=lambda wildcards, input: input["idx"][0][:-6],
             paired=paired_end,
@@ -87,7 +87,7 @@ else:
                 ),
             output:
                 bf=expand("results/bedgraph/{{dir}}/{bg_sample}-vs-Dam-norm.gatc.bedgraph", bg_sample=BG_SAMPLES),
-                bam=expand("results/bam/{{dir}}/{sample}.bam", sample=SAMPLES),
+                bam=temp(expand("results/bam/{{dir}}/{sample}.bam", sample=SAMPLES)),
             params:
                 idxdir=lambda wildcards, input: input["idx"][0][:-6],
                 paired=paired_end,
@@ -153,7 +153,7 @@ else:
                 ),
             output:
                 bf=expand("results/bedgraph/{{dir}}/{bg_sample}-vs-Dam.norm.gatc.bedgraph", bg_sample=BG_SAMPLES),
-                bam=expand("results/bam/{{dir}}/{sample}.bam", sample=SAMPLES),
+                bam=temp(expand("results/bam/{{dir}}/{sample}.bam", sample=SAMPLES)),
             params:
                 idxdir=lambda wildcards, input: input["idx"][0][:-6],
                 paired=paired_end,

diff --git a/workflow/scripts/damidseq_pipeline.py b/workflow/scripts/damidseq_pipeline.py
@@ -151,6 +151,11 @@ def allfastq(directory):
             new_name = bam.replace("-ext300", "")
             os.rename(bam, new_name)
 
+    # Remove all trimmed fastq files
+    shell(
+        "rm results/trimmed/{directory}/*.fastq.gz"
+        )
+
     # Destroy temporary directory
     print(f"Cleaning up temporary directory {temp_dir.name}")
     temp_dir.cleanup()