From 680e672a5bed865a34e9d6cbe847f75320c2d75d Mon Sep 17 00:00:00 2001
From: niekwit <41302859+niekwit@users.noreply.github.com>
Date: Fri, 5 Jul 2024 13:06:49 +0100
Subject: [PATCH] removing temp files

---
 workflow/rules/damid.smk              | 6 +++---
 workflow/scripts/damidseq_pipeline.py | 5 +++++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/workflow/rules/damid.smk b/workflow/rules/damid.smk
index 91bf2c3..ae5c5a3 100644
--- 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
index 5c5811b..8ba384c 100644
--- 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()