From e820801c76774d7e5f2d7dbae1167335e488a116 Mon Sep 17 00:00:00 2001 From: alsmith Date: Thu, 21 Mar 2024 18:15:07 +0000 Subject: [PATCH] Fix logic in get_fastqc_files function --- seqnado/workflow/rules/qc.smk | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/seqnado/workflow/rules/qc.smk b/seqnado/workflow/rules/qc.smk index 6358bedc..ffa5140c 100644 --- a/seqnado/workflow/rules/qc.smk +++ b/seqnado/workflow/rules/qc.smk @@ -96,8 +96,9 @@ use rule samtools_stats as samtools_stats_filtered with: def get_fastqc_files(wildcards): - single_end_assays = [name for name in SAMPLE_NAMES if DESIGN.query(name).is_paired == True] - paired_end_assays = [name for name in SAMPLE_NAMES if DESIGN.query(name).is_paired == False] + single_end_assays = [name for name in SAMPLE_NAMES if DESIGN.query(name).is_paired == False] + paired_end_assays = [name for name in SAMPLE_NAMES if DESIGN.query(name).is_paired == True] + fastqc_raw_paired = expand( "seqnado_output/qc/fastqc_raw/{sample}_{read}_fastqc.html", @@ -123,7 +124,7 @@ def get_fastqc_files(wildcards): all_qc_files = [] for files in [fastqc_raw_paired, fastqc_trimmed_paired, fastqc_raw_single, fastqc_trimmed_single]: if files: - all_qc_files.extend(files) + all_qc_files.extend(*files) return all_qc_files