From 6b011dd14821385c282e030c6d993d2116aed23f Mon Sep 17 00:00:00 2001
From: WackerO <43847497+WackerO@users.noreply.github.com>
Date: Wed, 20 Jul 2022 12:42:40 +0200
Subject: [PATCH] SVDB MERGE samtools version (#1913)

* Started (again) to work on bgzipping SVDB_MERGE output

* Updated test yml

* SVDB_MERGE now bgzips output

* Fixed singularity, renamed tests in test.yml

* Added samtools version

Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
---
 modules/svdb/merge/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf
index 365718af..05fb2b17 100644
--- a/modules/svdb/merge/main.nf
+++ b/modules/svdb/merge/main.nf
@@ -41,6 +41,7 @@ process SVDB_MERGE {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 
@@ -52,6 +53,7 @@ process SVDB_MERGE {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }