Build branch main with version main (b3fcd52)

Build pipeline: viash-hub.biobox.main-8bbc7

Source commit: b3fcd52f20

Source message: Fix multiple components (#162)

* output index when only_build_index is true

* fix threads option

* fix argument type and add log

* fix output handling

* fix output arguments and update docker image

* fix log2stderr argument and remove discard reads option

* remove echo

* update bbsplit build index test

* add workdir

* apply suggestions from code review

* accept more than two reference files

* update changelog

* update changelog

* remove indentation

* minor fixes

* fix descriptions

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml

@@ -46,15 +46,12 @@ argument_groups:
     description: "If set, only builds the index. Otherwise, mapping is performed."
     info: null
     direction: "input"
-  - type: "string"
+  - type: "file"
     name: "--build"
-    description: "Designate index to use. Corresponds to the number specified when\
-      \ building the index.\nIf building the index, this will be the build's id. If\
-      \ multiple references are indexed\nin the same directory, each needs a unique\
-      \ build ID. Default: 1.\n"
+    description: "Index to be used for mapping. \n"
     info: null
-    example:
-    - "1"
+    must_exist: true
+    create_parent: true
     required: false
     direction: "input"
     multiple: false
@@ -168,6 +165,18 @@ argument_groups:
     direction: "input"
 - name: "Output"
   arguments:
+  - type: "file"
+    name: "--index"
+    description: "Location to write the index.\n"
+    info: null
+    example:
+    - "BBSplit_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
   - type: "file"
     name: "--fastq_1"
     description: "Output file for read 1.\n"
@@ -353,15 +362,15 @@ engines:
 - type: "native"
   id: "native"
 build_info:
-  config: "src/bbmap_bbsplit/config.vsh.yaml"
+  config: "src/bbmap/bbmap_bbsplit/config.vsh.yaml"
   runner: "executable"
   engine: "docker|native"
   output: "target/executable/bbmap/bbmap_bbsplit"
   executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
   viash_version: "0.9.0"
-  git_commit: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
   name: "biobox"
   version: "main"