Compress fastpq

tdayris · Jul 16, 2024 · ae7480b · ae7480b
1 parent b89611b
commit ae7480b
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git 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
@@ -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",