From b9a961d987bb51e8b0175d5842fd24c43c48cc47 Mon Sep 17 00:00:00 2001 From: emmarousseau Date: Mon, 1 Jul 2024 17:13:35 +0100 Subject: [PATCH] Update src/samtools/samtools_fastq/script.sh Co-authored-by: Robrecht Cannoodt --- src/samtools/samtools_fastq/script.sh | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/samtools/samtools_fastq/script.sh b/src/samtools/samtools_fastq/script.sh index 40949856..0cad9cfe 100644 --- a/src/samtools/samtools_fastq/script.sh +++ b/src/samtools/samtools_fastq/script.sh @@ -11,7 +11,14 @@ set -e [[ "$par_copy_tags" == "false" ]] && unset par_copy_tags [[ "$par_casava" == "false" ]] && unset par_casava -samtools "$par_command" \ +if [[ "$meta_name" == "samtools_fasta" ]]; then + subcommand=fasta +elif [[ "$meta_name" == "samtools_fastq" ]]; then + subcommand=fastq +else + echo "Unrecognized component name" && exit 1 +fi +samtools "$subcommand" \ ${par_no_suffix:+-n} \ ${par_suffix:+-N} \ ${par_use_oq:+-O} \