From 061d78af8307d5ae80b2ff38344e537f655950ba Mon Sep 17 00:00:00 2001
From: Max <visze@users.noreply.github.com>
Date: Tue, 26 Nov 2024 09:17:26 +0100
Subject: [PATCH] make similar for count qc

---
 workflow/rules/qc_report.smk | 40 ++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/workflow/rules/qc_report.smk b/workflow/rules/qc_report.smk
index ac8aa35..8221a7b 100644
--- a/workflow/rules/qc_report.smk
+++ b/workflow/rules/qc_report.smk
@@ -110,25 +110,25 @@ rule qc_report_count:
             cp {input.quarto_script} {output.quarto_file};
             cd `dirname {output.quarto_file}`;
             quarto render `basename {output.quarto_file}` --output `basename {output.count_file}` \
-            -P assignment:{wildcards.assignment} \
-            -P project:{wildcards.project} \
-            -P dna_over_rna_plot:{input.dna_over_rna} \
-            -P dna_over_rna_thresh_plot:{input.dna_over_rna_thresh} \
-            -P dna_oligo_coor_min_thre_plot:{input.dna_oligo_coor_min_thre_plot} \
-            -P rna_oligo_coor_min_thre_plot:{input.rna_oligo_coor_min_thre_plot} \
-            -P dna_oligo_coor_plot:{input.dna_oligo_coor_plot} \
-            -P rna_oligo_coor_plot:{input.rna_oligo_coor_plot} \
-            -P ratio_oligo_coor_plot:{input.ratio_oligo_coor_plot} \
-            -P ratio_oligo_min_thre_plot:{input.ratio_oligo_min_thre_plot} \
-            -P statistics_all_merged:{input.statistics_all_merged} \
-            -P counts_per_oligo_dna:{input.counts_per_oligo_dna} \
-            -P counts_per_oligo_rna:{input.counts_per_oligo_rna} \
-            -P statistics_all_single:{input.statistics_all_single} \
-            -P activity_all:{input.activity_all} \
-            -P activity_thresh:{input.activity_thresh} \
-            -P statistics_all_oligo_cor_all:{input.statistics_all_oligo_cor_all} \
-            -P statistics_all_oligo_cor_thresh:{input.statistics_all_oligo_cor_thresh} \
-            -P thresh:{params.thresh} \
-            -P workdir:{params.workdir}
+            -P "assignment:{wildcards.assignment}" \
+            -P "project:{wildcards.project}" \
+            -P "dna_over_rna_plot:{input.dna_over_rna}" \
+            -P "dna_over_rna_thresh_plot:{input.dna_over_rna_thresh}" \
+            -P "dna_oligo_coor_min_thre_plot:{input.dna_oligo_coor_min_thre_plot}" \
+            -P "rna_oligo_coor_min_thre_plot:{input.rna_oligo_coor_min_thre_plot}" \
+            -P "dna_oligo_coor_plot:{input.dna_oligo_coor_plot}" \
+            -P "rna_oligo_coor_plot:{input.rna_oligo_coor_plot}" \
+            -P "ratio_oligo_coor_plot:{input.ratio_oligo_coor_plot}" \
+            -P "ratio_oligo_min_thre_plot:{input.ratio_oligo_min_thre_plot}" \
+            -P "statistics_all_merged:{input.statistics_all_merged}" \
+            -P "counts_per_oligo_dna:{input.counts_per_oligo_dna}" \
+            -P "counts_per_oligo_rna:{input.counts_per_oligo_rna}" \
+            -P "statistics_all_single:{input.statistics_all_single}" \
+            -P "activity_all:{input.activity_all}" \
+            -P "activity_thresh:{input.activity_thresh}" \
+            -P "statistics_all_oligo_cor_all:{input.statistics_all_oligo_cor_all}" \
+            -P "statistics_all_oligo_cor_thresh:{input.statistics_all_oligo_cor_thresh}" \
+            -P "thresh:{params.thresh}" \
+            -P "workdir:{params.workdir}"
         ) &> {log}
         """