From 6385c6c14d616ec7a489f088ea29396b3022085c Mon Sep 17 00:00:00 2001 From: Katherine Eaton Date: Sat, 12 Jun 2021 15:17:54 -0400 Subject: [PATCH] restrict multiqc to qualimap and snippy modules --- workflow/rules/qc.smk | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk index 1504575e..fda54400 100644 --- a/workflow/rules/qc.smk +++ b/workflow/rules/qc.smk @@ -40,14 +40,15 @@ rule multiqc: for path in identify_paths(outdir="qualimap", reads_origin=wildcards.reads_origin)]), snippy_pairwise_dir = lambda wildcards: remove_duplicates([os.path.dirname(path) + "/" for path in identify_paths(outdir="snippy_pairwise", reads_origin=wildcards.reads_origin)]), + snippy_multi_txt = results_dir + "/snippy_multi/{reads_origin}/snippy-multi.txt", wildcard_constraints: reads_origin="(assembly|sra|local|all)", output: results_dir + "/multiqc/{reads_origin}/multiqc_report.html", - results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_snippy_variants_1.pdf", - results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_qualimap_gc_content_1.pdf", - results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_qualimap_genome_fraction_1.pdf", - results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_qualimap_coverage_histogram_1.pdf", + #results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_snippy_variants_1.pdf", + #results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_qualimap_gc_content_1.pdf", + #results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_qualimap_genome_fraction_1.pdf", + #results_dir + "/multiqc/{reads_origin}/multiqc_plots/pdf/mqc_qualimap_coverage_histogram_1.pdf", dir = directory(results_dir + "/multiqc/{reads_origin}/"), log = results_dir + "/multiqc/{reads_origin}/multiqc.log", resources: @@ -63,8 +64,11 @@ rule multiqc: --export \ --outdir {output.dir} \ --force \ + --module qualimap \ + --module snippy \ {input.qualimap_dir} \ - {input.snippy_pairwise_dir} 2> {output.log}; + {input.snippy_pairwise_dir} \ + {input.snippy_multi_txt} 2> {output.log}; """ # -----------------------------------------------------------------------------#