Remove FastQ files when no longer needed

CHANGELOG.rst

@@ -27,6 +27,10 @@ Changes
     replaced by a MultiQC report)
 * Replace FastQC with Sequali
 
+Bugfixes
+========
+* Fix a bug where the trimmed FastQ files are not removed when no longer needed
+
 Updates
 =======
 * Update Cutadapt to 4.6

Snakefile

@@ -41,15 +41,12 @@ module qc_seq:
 use rule * from qc_seq as qc_seq_*
 
 
-# Make the trimmed, merged FastQ files temporary
-use rule merge_fastqs_r1 from qc_seq as qc_seq_merge_fastqs_r1 with:
+# Make the final trimmed, merged FastQ files from the qc_seq module temporary
+use rule cutadapt from qc_seq as qc_seq_cutadapt with:
     output:
-        merged=temp("{sample}/qc-seq/{sample}-R1.fq.gz"),
-
-
-use rule merge_fastqs_r2 from qc_seq as qc_seq_merge_fastqs_r2 with:
-    output:
-        merged=temp("{sample}/qc-seq/{sample}-R2.fq.gz"),
+        fq1=temp("{sample}/qc-seq/{sample}-R1.fq.gz"),
+        fq2=temp("{sample}/qc-seq/{sample}-R2.fq.gz"),
+        json="{sample}/qc-seq/{sample}.cutadapt.json",
 
 
 module itd:

test/test_hamlet.yml

@@ -110,9 +110,9 @@
     # Test log files
     - path: "log/create_summary.SRR8615409.txt"
     # FastQ files should be cleaned up when they are no longer needed
-    - path: SRR8615409/SRR8615409-R1.fq.gz
+    - path: SRR8615409/qc-seq/SRR8615409-R1.fq.gz
       should_exist: false
-    - path: SRR8615409/SRR8615409-R2.fq.gz
+    - path: SRR8615409/qc-seq/SRR8615409-R2.fq.gz
       should_exist: false
     # Test the fusions results
     # We should detect both a BCR::ABL1 and FLT3::FLT3 in the raw fusion results