From 892af7ae300274ef4d802bc7980adbb6943104c7 Mon Sep 17 00:00:00 2001 From: Redmar van den Berg Date: Thu, 6 Jun 2024 11:02:08 +0200 Subject: [PATCH] Remove FastQ files when no longer needed --- CHANGELOG.rst | 4 ++++ Snakefile | 13 +++++-------- test/test_hamlet.yml | 4 ++-- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c263366..93bc1d6 100644 --- a/CHANGELOG.rst +++ b/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 diff --git a/Snakefile b/Snakefile index e152faf..ded6b66 100644 --- a/Snakefile +++ b/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: diff --git a/test/test_hamlet.yml b/test/test_hamlet.yml index 307a69a..85290c0 100644 --- a/test/test_hamlet.yml +++ b/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