From c23e2230f5e9887d3894df86984633eeb94062f8 Mon Sep 17 00:00:00 2001 From: ASLeonard Date: Wed, 10 Apr 2024 08:27:00 +0200 Subject: [PATCH] only fail if non-installed programs are required --- partition-before-pggb | 4 ++++ pggb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/partition-before-pggb b/partition-before-pggb index 30dd1a7..36e4b86 100755 --- a/partition-before-pggb +++ b/partition-before-pggb @@ -276,11 +276,15 @@ check_tool_availability "seqwish" "seqwish" check_tool_availability "smoothxg" "smoothxg" check_tool_availability "odgi" "odgi" check_tool_availability "gfaffix" "gfaffix" +if [ "$vcf_spec" != "false" ]; then check_tool_availability "vg" "vg" check_tool_availability "vcfbub" "vcfbub" check_tool_availability "vcfwave" "vcfwave" check_tool_availability "bcftools" "bcftools" +fi +if [[ $multiqc == true ]]; then check_tool_availability "MultiQC" "multiqc" +fi # If there are missing tools, report them and exit if [ ${#missing_tools[@]} -ne 0 ]; then diff --git a/pggb b/pggb index 9765353..ad3b772 100755 --- a/pggb +++ b/pggb @@ -276,11 +276,15 @@ check_tool_availability "seqwish" "seqwish" check_tool_availability "smoothxg" "smoothxg" check_tool_availability "odgi" "odgi" check_tool_availability "gfaffix" "gfaffix" +if [ "$vcf_spec" != "false" ]; then check_tool_availability "vg" "vg" check_tool_availability "vcfbub" "vcfbub" check_tool_availability "vcfwave" "vcfwave" check_tool_availability "bcftools" "bcftools" +fi +if [[ $multiqc == true ]]; then check_tool_availability "MultiQC" "multiqc" +fi # If there are missing tools, report them and exit if [ ${#missing_tools[@]} -ne 0 ]; then