From ae7480b354be1985190a188e37fd4de01bac13be Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@gustaveroussy.fr>
Date: Tue, 16 Jul 2024 15:32:11 +0200
Subject: [PATCH] Compress fastpq

---
 CHANGELOG.md             | 6 ++++++
 workflow/rules/fastp.smk | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1501b6c..0c345c7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# 4.1.0
+
+## Features:
+
+* Fastp output compressed
+
 # 4.0.0
 
 ## Features:
diff --git a/workflow/rules/fastp.smk b/workflow/rules/fastp.smk
index 0a08a9d..dd2cf84 100644
--- a/workflow/rules/fastp.smk
+++ b/workflow/rules/fastp.smk
@@ -19,7 +19,7 @@ rule fair_bowtie2_mapping_fastp_trimming_pair_ended:
     output:
         trimmed=temp(
             expand(
-                "tmp/fair_bowtie2_mapping_fastp_trimming_pair_ended/{sample}.{stream}.fastq",
+                "tmp/fair_bowtie2_mapping_fastp_trimming_pair_ended/{sample}.{stream}.fastq.gz",
                 stream=stream_tuple,
                 allow_missing=True,
             )
@@ -64,7 +64,7 @@ use rule fair_bowtie2_mapping_fastp_trimming_pair_ended as fair_bowtie2_mapping_
         ],
     output:
         trimmed=temp(
-            "tmp/fair_bowtie2_mapping_fastp_trimming_single_ended/{sample}.fastq"
+            "tmp/fair_bowtie2_mapping_fastp_trimming_single_ended/{sample}.fastq.gz"
         ),
         html=report(
             "results/QC/report_se/{sample}.html",