diff --git a/src/qualimap/qualimap_rnaseq/config.vsh.yaml b/src/qualimap/qualimap_rnaseq/config.vsh.yaml
index 35e8c6ff..ffc807ab 100644
--- a/src/qualimap/qualimap_rnaseq/config.vsh.yaml
+++ b/src/qualimap/qualimap_rnaseq/config.vsh.yaml
@@ -97,7 +97,7 @@ engines:
     setup:   
       - type: docker
         run: |
-          echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')
+          echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt
 runners: 
   - type: executable
   - type: nextflow
diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
index 1902895f..2deff57f 100644
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,7 +235,7 @@ build_info:
   output: "target/executable/agat/agat_convert_bed2gff"
   executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
index 7de36b7f..e3a735b7 100755
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -514,9 +514,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:57Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:53Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
index 151039f6..dfc2c69a 100644
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
   output: "target/executable/agat/agat_convert_embl2gff"
   executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
index 8816dd20..cef0465a 100755
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -504,9 +504,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:57Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:53Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index 798fc3b4..639f3f23 100644
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gff2gtf"
   executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
index 17c42535..e0df15ff 100755
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -518,9 +518,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:58Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:53Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index 3ca74b75..948e0c62 100644
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gff2tsv"
   executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
index d33a63a2..d350ff37 100755
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -483,9 +483,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:57Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:52Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index 85174ce6..ee0987d1 100644
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,7 +195,7 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gxf2gxf"
   executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
index f4c4179b..95e6b56a 100755
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -492,9 +492,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:56Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:52Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml
index d480984c..7b682146 100644
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,7 +706,7 @@ build_info:
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba
index 2a37ebf9..078326a5 100755
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -753,9 +753,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:59Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:54Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml
index 1190e893..99d41307 100644
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,7 +418,7 @@ build_info:
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert
index ae15aa0c..0d2cc0a5 100755
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -598,9 +598,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:58Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index 3930ee93..fcc6dce9 100644
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -270,7 +270,7 @@ build_info:
   output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
index 9d3abcaf..595d1b26 100755
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -548,9 +548,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-08-21T07:01:01Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:57Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index 1eee8649..f9f1f30f 100644
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bamtofastq"
   executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
index b1207775..c0c75752 100755
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -482,9 +482,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:47Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
index 4d20fca3..5ba82883 100644
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bedtobam"
   executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
index 3706e934..5c6c06e4 100755
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -495,9 +495,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:48Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
index 2bc7b389..964358b4 100644
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
index 5a8625d7..359f8e58 100755
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -525,9 +525,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:47Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
index a8efae55..2a99c2dd 100644
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,7 +410,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_intersect"
   executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
index 030ffe0c..20cd8746 100755
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -632,9 +632,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:47Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
index 768db3d4..596e9338 100644
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_sort"
   executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort
index c0a6f3e1..b6965303 100755
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -508,9 +508,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:48Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
index e6cb3450..a89a493d 100644
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
   output: "target/executable/busco/busco_download_datasets"
   executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets
index c1a242bf..e238f5eb 100755
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -474,9 +474,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:55Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:51Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
index d009328d..a1cbffdb 100644
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,7 +145,7 @@ build_info:
   output: "target/executable/busco/busco_list_datasets"
   executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets
index 482d02f4..6ddc9278 100755
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -464,9 +464,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:56Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:51Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml
index c2fcd66c..38def265 100644
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -423,7 +423,7 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run
index 819827a9..ec80317b 100755
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -631,9 +631,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:56Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:52Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml
index 856c83f7..6655d901 100644
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,7 +740,7 @@ build_info:
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt
index 4793903a..e8500c6c 100755
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -830,9 +830,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-08-21T07:01:00Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:56Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml
index 30fb22da..612e4740 100644
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,7 +317,7 @@ build_info:
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/falco/falco b/target/executable/falco/falco
index 21866b3f..a1481f77 100755
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -588,9 +588,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-08-21T07:01:01Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:56Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml
index b1277bf7..9080aee7 100644
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,7 +1083,7 @@ build_info:
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp
index f4c1dbd5..ac1e17d6 100755
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1027,9 +1027,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:58Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:53Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml
index ee3d3d39..d3860160 100644
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,7 +645,7 @@ build_info:
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts
index bfb22b6d..6bce49e8 100755
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -753,9 +753,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:54Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:49Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml
index bab2933c..b7eb47f1 100644
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,7 +685,7 @@ build_info:
   output: "target/executable/gffread"
   executable: "target/executable/gffread/gffread"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread
index acb36c40..4570b419 100755
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -806,9 +806,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:46Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
index 5a48e737..06fa7ccc 100644
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,7 +507,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_call"
   executable: "target/executable/lofreq/lofreq_call/lofreq_call"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call
index 25d387c3..87187df4 100755
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -655,9 +655,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:53Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
index ae4650c3..dc26b392 100644
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
index dd103e44..1566ab18 100755
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -500,9 +500,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:53Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml
index 42cdb1e6..3f8446ae 100644
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,7 +456,7 @@ build_info:
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc
index bc018937..46a94342 100755
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -636,9 +636,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-08-21T07:01:00Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml
index eca540df..c184bf70 100644
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,7 +398,7 @@ build_info:
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/pear/pear b/target/executable/pear/pear
index e935c57d..27051834 100755
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -596,9 +596,9 @@ echo "pear: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:48Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:44Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
index c205e499..ea532b61 100644
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -252,7 +252,7 @@ engines:
   setup:
   - type: "docker"
     run:
-    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')\n"
+    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
   entrypoint: []
   cmd: null
 - type: "native"
@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/qualimap/qualimap_rnaseq"
   executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
index 0383d823..486f1715 100755
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -522,13 +522,13 @@ function ViashDockerfile {
     cat << 'VIASHDOCKER'
 FROM quay.io/biocontainers/qualimap:2.3--hdfd78af_0
 ENTRYPOINT []
-RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')
+RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:52Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:48Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml
index ad7a50f9..6e2249be 100644
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +277,7 @@ build_info:
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index
index 98beb8f9..49643dd3 100755
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -545,9 +545,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:59Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:55Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml
index 392db5f7..83c2aeb3 100644
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,7 +1173,7 @@ build_info:
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant
index e2e2d3a0..a6c0f20e 100755
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1167,9 +1167,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:59Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:55Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml
index 65a47b1f..34b06b1e 100644
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate
index 6fa838d3..be27cf19 100755
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -518,9 +518,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:51Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:46Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
index 043597d3..4b3bedcb 100644
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,7 +243,7 @@ build_info:
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx
index 5e2db129..25267a46 100755
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -511,9 +511,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:50Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:46Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
index cfa6d480..1e01678a 100644
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fasta"
   executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta
index ec7567de..8d54410b 100755
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
@@ -624,9 +624,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:51Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:47Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
index 206c1215..94751304 100644
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq
index e9ca7f26..d9c80df6 100755
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:50Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:45Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
index 79b1a078..b9b9bec2 100644
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat
index 9575aa54..447bdc17 100755
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -473,9 +473,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:50Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:45Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
index 7ecd2a05..19ad185e 100644
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats
index 63b3828d..d607a173 100755
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -477,9 +477,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:49Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:44Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml
index 3b9f0223..7d9f7c1d 100644
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index
index 0f9cfd3c..86cd5356 100755
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -484,9 +484,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:49Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:44Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml
index b6977ec8..2e326440 100644
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -332,7 +332,7 @@ build_info:
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort
index b5318209..afca18d2 100755
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -555,9 +555,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:51Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:47Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml
index cf2c0c31..dc6c8734 100644
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats
index 5aaa5912..5038847f 100755
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -574,9 +574,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:52Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:47Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml
index d5b7454e..18025587 100644
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -665,7 +665,7 @@ build_info:
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view
index 6c41658a..d0547b59 100755
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -824,9 +824,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:49Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:45Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
index 7cd94c97..dc95e735 100644
--- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/seqtk/seqtk_sample"
   executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample
index 62625cae..9cbf3e5f 100755
--- a/target/executable/seqtk/seqtk_sample/seqtk_sample
+++ b/target/executable/seqtk/seqtk_sample/seqtk_sample
@@ -480,9 +480,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-08-21T07:01:02Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:57Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
index fbb142e7..370ae9e5 100644
--- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,7 +196,7 @@ build_info:
   output: "target/executable/seqtk/seqtk_subseq"
   executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
index 31f14049..9b2f8fa5 100755
--- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq
+++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
@@ -490,9 +490,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-08-21T07:01:01Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:57Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml
index 1682696e..cfffc7b1 100644
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2663,7 +2663,7 @@ build_info:
   output: "target/executable/star/star_align_reads"
   executable: "target/executable/star/star_align_reads/star_align_reads"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads
index ce95ead7..4235edf7 100755
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1919,9 +1919,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:55Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:50Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml
index c3c6e902..6134a601 100644
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -333,7 +333,7 @@ build_info:
   output: "target/executable/star/star_genome_generate"
   executable: "target/executable/star/star_genome_generate/star_genome_generate"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate
index ddc58a1b..628997d2 100755
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -576,9 +576,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:54Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:50Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
index b187d9c4..d483e9f8 100644
--- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,7 +611,7 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_dedup"
   executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
index 6fdcf490..644ee581 100755
--- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
+++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
@@ -769,9 +769,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:53Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:48Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
index 002b4103..2ab52ff2 100644
--- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,7 +449,7 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_extract"
   executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
index 360cd4bf..ca40ad5f 100755
--- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
+++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
@@ -636,9 +636,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
-LABEL org.opencontainers.image.created="2024-08-21T07:00:52Z"
+LABEL org.opencontainers.image.created="2024-08-21T07:17:48Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+LABEL org.opencontainers.image.revision="1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
 LABEL org.opencontainers.image.version="qualimap"
 
 VIASHDOCKER
diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
index 9f6d207e..4e1a9153 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,7 +235,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_bed2gff"
   executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf
index dbf1d52c..d9daf012 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf
@@ -3066,7 +3066,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_bed2gff",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
index 172b7977..a8d5440f 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_embl2gff"
   executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf
index d8a0b66f..064453c6 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf
@@ -3059,7 +3059,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_embl2gff",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index 3a393136..4365051a 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2gtf"
   executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
index 0a4484c3..06dd1a98 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
@@ -3042,7 +3042,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index ffaa82df..52a045d6 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2tsv"
   executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
index 92e07291..c677ecf6 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
@@ -3020,7 +3020,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index 76f64f38..0b7bf6f8 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,7 +195,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gxf2gxf"
   executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
index b65d81d7..48641599 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
@@ -3020,7 +3020,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json
deleted file mode 100644
index 79b232fd..00000000
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json
+++ /dev/null
@@ -1,119 +0,0 @@
-{
-"$schema": "http://json-schema.org/draft-07/schema",
-"title": "agat_convert_sp_gxf2gxf",
-"description": "This script fixes and/or standardizes any GTF/GFF file into full sorted\nGTF/GFF file. It AGAT parser removes duplicate features, fixes\nduplicated IDs, adds missing ID and/or Parent attributes, deflates\nfactorized attributes (attributes with several parents are duplicated\nwith uniq ID), add missing features when possible (e.g. add exon if only\nCDS described, add UTR if CDS and exon described), fix feature locations\n(e.g. check exon is embedded in the parent features mRNA, gene), etc...\n\nAll AGAT\u0027s scripts with the _sp_ prefix use the AGAT parser, before to\nperform any supplementary task. So, it is not necessary to run this\nscript prior the use of any other _sp_ script.\n",
-"type": "object",
-"definitions": {
-
-    
-    
-    "inputs" : {
-    "title": "Inputs",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "gxf": {
-                "type":
-                "string",
-                "description": "Type: `file`, required, example: `input.gff`. String - Input GTF/GFF file",
-                "help_text": "Type: `file`, required, example: `input.gff`. String - Input GTF/GFF file. Compressed file with .gz extension is accepted.\n"
-            
-            }
-    
-
-}
-},
-    
-    
-    "outputs" : {
-    "title": "Outputs",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "output": {
-                "type":
-                "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. String - Output GFF file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. String - Output GFF file. If no output file is specified, the output will be written to STDOUT.\n"
-            ,
-                "default": "$id.$key.output.gff"
-            }
-    
-
-}
-},
-    
-    
-    "arguments" : {
-    "title": "Arguments",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "config": {
-                "type":
-                "string",
-                "description": "Type: `file`, example: `custom_agat_config.yaml`. String - Input agat config file",
-                "help_text": "Type: `file`, example: `custom_agat_config.yaml`. String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n"
-            
-            }
-    
-
-}
-},
-    
-    
-    "nextflow input-output arguments" : {
-    "title": "Nextflow input-output arguments",
-    "type": "object",
-    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
-    "properties": {
-    
-        
-                "publish_dir": {
-                "type":
-                "string",
-                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
-                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
-            
-            }
-    
-
-        ,
-                "param_list": {
-                "type":
-                "string",
-                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
-                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
-                "hidden": true
-            
-            }
-    
-
-}
-}
-},
-"allOf": [
-
-    {
-    "$ref": "#/definitions/inputs"
-    },
-
-    {
-    "$ref": "#/definitions/outputs"
-    },
-
-    {
-    "$ref": "#/definitions/arguments"
-    },
-
-    {
-    "$ref": "#/definitions/nextflow input-output arguments"
-    }
-]
-}
diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml
index 53bf7152..20ffbffa 100644
--- a/target/nextflow/arriba/.config.vsh.yaml
+++ b/target/nextflow/arriba/.config.vsh.yaml
@@ -706,7 +706,7 @@ build_info:
   output: "target/nextflow/arriba"
   executable: "target/nextflow/arriba/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf
index 17f7854c..56b11ff6 100644
--- a/target/nextflow/arriba/main.nf
+++ b/target/nextflow/arriba/main.nf
@@ -3566,7 +3566,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/arriba",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml
index 05c3a5bc..0c479061 100644
--- a/target/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/nextflow/bcl_convert/.config.vsh.yaml
@@ -418,7 +418,7 @@ build_info:
   output: "target/nextflow/bcl_convert"
   executable: "target/nextflow/bcl_convert/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf
index 216ba5ed..6b9e9d17 100644
--- a/target/nextflow/bcl_convert/main.nf
+++ b/target/nextflow/bcl_convert/main.nf
@@ -3303,7 +3303,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcl_convert",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index bf772f6e..c0ced1f2 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -270,7 +270,7 @@ build_info:
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
index 0dcf2f37..91180856 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
@@ -3116,7 +3116,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index 0960986c..859ffbe2 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bamtofastq"
   executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
index 05cec1e0..45ad35d2 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
@@ -3024,7 +3024,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bamtofastq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
index e199a7f4..2b6bb780 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bedtobam"
   executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
index 7e6a2864..23b23413 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf
+++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
@@ -3057,7 +3057,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bedtobam",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
index 7a11efed..5b4ff80c 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_getfasta"
   executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf
index f36fcb88..e2bb1721 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/main.nf
+++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf
@@ -3060,7 +3060,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_getfasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
index adeb5d3a..2c519de3 100644
--- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,7 +410,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_intersect"
   executable: "target/nextflow/bedtools/bedtools_intersect/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf
index 97854d68..f6dd943f 100644
--- a/target/nextflow/bedtools/bedtools_intersect/main.nf
+++ b/target/nextflow/bedtools/bedtools_intersect/main.nf
@@ -3256,7 +3256,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_intersect",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json b/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json
deleted file mode 100644
index 9ef264fa..00000000
--- a/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json
+++ /dev/null
@@ -1,400 +0,0 @@
-{
-"$schema": "http://json-schema.org/draft-07/schema",
-"title": "bedtools_intersect",
-"description": "bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n",
-"type": "object",
-"definitions": {
-
-    
-    
-    "inputs" : {
-    "title": "Inputs",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "input_a": {
-                "type":
-                "string",
-                "description": "Type: `file`, required, example: `input_a.bed`. The input file (BED/GFF/VCF/BAM) to be used as the -a file",
-                "help_text": "Type: `file`, required, example: `input_a.bed`. The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
-            
-            }
-    
-
-        ,
-                "input_b": {
-                "type":
-                "string",
-                "description": "Type: List of `file`, required, example: `input_b.bed`, multiple_sep: `\":\"`. The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)",
-                "help_text": "Type: List of `file`, required, example: `input_b.bed`, multiple_sep: `\":\"`. The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
-            
-            }
-    
-
-}
-},
-    
-    
-    "outputs" : {
-    "title": "Outputs",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "output": {
-                "type":
-                "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n"
-            ,
-                "default": "$id.$key.output.bed"
-            }
-    
-
-}
-},
-    
-    
-    "options" : {
-    "title": "Options",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "write_a": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Write the original A entry for each overlap",
-                "help_text": "Type: `boolean_true`, default: `false`. Write the original A entry for each overlap."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "write_b": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Write the original B entry for each overlap",
-                "help_text": "Type: `boolean_true`, default: `false`. Write the original B entry for each overlap. \nUseful for knowing _what_ A overlaps. Restricted by -f and -r.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "left_outer_join": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Perform a \"left outer join\"",
-                "help_text": "Type: `boolean_true`, default: `false`. Perform a \"left outer join\". That is, for each feature in A report each overlap with B. \nIf no overlaps are found, report a NULL feature for B.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "write_overlap": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features",
-                "help_text": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r. \n  Only A features with overlap are reported.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "write_overlap_plus": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features",
-                "help_text": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r. \n  However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "report_A_if_no_overlap": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Write the original A entry _if_ no overlap is found",
-                "help_text": "Type: `boolean_true`, default: `false`. Write the original A entry _if_ no overlap is found. \n- In other words, just report the fact \u003e=1 hit was found.\n- Overlaps restricted by -f and -r. \n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "number_of_overlaps_A": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. For each entry in A, report the number of overlaps with B",
-                "help_text": "Type: `boolean_true`, default: `false`. For each entry in A, report the number of overlaps with B.\n- Reports 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f and -r.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "report_no_overlaps_A": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Only report those entries in A that have _no overlaps_ with B",
-                "help_text": "Type: `boolean_true`, default: `false`. Only report those entries in A that have _no overlaps_ with B.\n- Similar to \"grep -v\" (an homage).\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "uncompressed_bam": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output",
-                "help_text": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output. Default writes compressed BAM."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "same_strand": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Require same strandedness",
-                "help_text": "Type: `boolean_true`, default: `false`. Require same strandedness.  That is, only report hits in B.\nthat overlap A on the _same_ strand.\n- By default, overlaps are reported without respect to strand.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "opposite_strand": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Require different strandedness",
-                "help_text": "Type: `boolean_true`, default: `false`. Require different strandedness.  That is, only report hits in B\nthat overlap A on the _opposite_ strand.\n- By default, overlaps are reported without respect to strand.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "min_overlap_A": {
-                "type":
-                "number",
-                "description": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of A",
-                "help_text": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of A.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
-            
-            }
-    
-
-        ,
-                "min_overlap_B": {
-                "type":
-                "number",
-                "description": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of B",
-                "help_text": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
-            
-            }
-    
-
-        ,
-                "reciprocal_overlap": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Require that the fraction overlap be reciprocal for A AND B",
-                "help_text": "Type: `boolean_true`, default: `false`. Require that the fraction overlap be reciprocal for A AND B.\n- In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap 90% of A and A _also_ overlaps 90% of B.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "either_overlap": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Require that the minimum fraction be satisfied for A OR B",
-                "help_text": "Type: `boolean_true`, default: `false`. Require that the minimum fraction be satisfied for A OR B.\n- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would have to be satisfied.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "split": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals",
-                "help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "genome": {
-                "type":
-                "string",
-                "description": "Type: `file`, example: `genome.txt`. Provide a genome file to enforce consistent chromosome \nsort order across input files",
-                "help_text": "Type: `file`, example: `genome.txt`. Provide a genome file to enforce consistent chromosome \nsort order across input files. Only applies when used \nwith -sorted option.\n"
-            
-            }
-    
-
-        ,
-                "nonamecheck": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. For sorted data, don\u0027t throw an error if the file \nhas different naming conventions for the same chromosome \n(e",
-                "help_text": "Type: `boolean_true`, default: `false`. For sorted data, don\u0027t throw an error if the file \nhas different naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\").\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "sorted": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input",
-                "help_text": "Type: `boolean_true`, default: `false`. Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "names": {
-                "type":
-                "string",
-                "description": "Type: `string`. When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record",
-                "help_text": "Type: `string`. When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record.\n"
-            
-            }
-    
-
-        ,
-                "filenames": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. When using multiple databases, show each complete filename instead of a fileId when also printing the DB record",
-                "help_text": "Type: `boolean_true`, default: `false`. When using multiple databases, show each complete filename instead of a fileId when also printing the DB record."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "sortout": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. When using multiple databases, sort the output DB hits for each record",
-                "help_text": "Type: `boolean_true`, default: `false`. When using multiple databases, sort the output DB hits for each record."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "bed": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED",
-                "help_text": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "header": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results",
-                "help_text": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results."
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "no_buffer_output": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Disable buffered output",
-                "help_text": "Type: `boolean_true`, default: `false`. Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files \nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n"
-            ,
-                "default": "False"
-            }
-    
-
-        ,
-                "io_buffer_size": {
-                "type":
-                "integer",
-                "description": "Type: `integer`. Specify amount of memory to use for input buffer",
-                "help_text": "Type: `integer`. Specify amount of memory to use for input buffer.\nTakes an integer argument. Optional suffixes K/M/G supported.\nNote: currently has no effect with compressed files.       \n"
-            
-            }
-    
-
-}
-},
-    
-    
-    "nextflow input-output arguments" : {
-    "title": "Nextflow input-output arguments",
-    "type": "object",
-    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
-    "properties": {
-    
-        
-                "publish_dir": {
-                "type":
-                "string",
-                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
-                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
-            
-            }
-    
-
-        ,
-                "param_list": {
-                "type":
-                "string",
-                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
-                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
-                "hidden": true
-            
-            }
-    
-
-}
-}
-},
-"allOf": [
-
-    {
-    "$ref": "#/definitions/inputs"
-    },
-
-    {
-    "$ref": "#/definitions/outputs"
-    },
-
-    {
-    "$ref": "#/definitions/options"
-    },
-
-    {
-    "$ref": "#/definitions/nextflow input-output arguments"
-    }
-]
-}
diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
index 29a88ee8..fa5240b2 100644
--- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_sort"
   executable: "target/nextflow/bedtools/bedtools_sort/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf
index 0914d594..0784f175 100644
--- a/target/nextflow/bedtools/bedtools_sort/main.nf
+++ b/target/nextflow/bedtools/bedtools_sort/main.nf
@@ -3066,7 +3066,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_sort",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
index 9cb32945..7db161c2 100644
--- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
   output: "target/nextflow/busco/busco_download_datasets"
   executable: "target/nextflow/busco/busco_download_datasets/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf
index 1407b5c6..9b163f9a 100644
--- a/target/nextflow/busco/busco_download_datasets/main.nf
+++ b/target/nextflow/busco/busco_download_datasets/main.nf
@@ -2985,7 +2985,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_download_datasets",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
index 907af319..9a85e1cc 100644
--- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,7 +145,7 @@ build_info:
   output: "target/nextflow/busco/busco_list_datasets"
   executable: "target/nextflow/busco/busco_list_datasets/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf
index d407efa6..0e1147ae 100644
--- a/target/nextflow/busco/busco_list_datasets/main.nf
+++ b/target/nextflow/busco/busco_list_datasets/main.nf
@@ -2971,7 +2971,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_list_datasets",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json
deleted file mode 100644
index c2f65754..00000000
--- a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json
+++ /dev/null
@@ -1,71 +0,0 @@
-{
-"$schema": "http://json-schema.org/draft-07/schema",
-"title": "busco_list_datasets",
-"description": "Lists the available busco datasets",
-"type": "object",
-"definitions": {
-
-    
-    
-    "outputs" : {
-    "title": "Outputs",
-    "type": "object",
-    "description": "No description",
-    "properties": {
-    
-        
-                "output": {
-                "type":
-                "string",
-                "description": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n",
-                "help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n"
-            ,
-                "default": "$id.$key.output.txt"
-            }
-    
-
-}
-},
-    
-    
-    "nextflow input-output arguments" : {
-    "title": "Nextflow input-output arguments",
-    "type": "object",
-    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
-    "properties": {
-    
-        
-                "publish_dir": {
-                "type":
-                "string",
-                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
-                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
-            
-            }
-    
-
-        ,
-                "param_list": {
-                "type":
-                "string",
-                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
-                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
-                "hidden": true
-            
-            }
-    
-
-}
-}
-},
-"allOf": [
-
-    {
-    "$ref": "#/definitions/outputs"
-    },
-
-    {
-    "$ref": "#/definitions/nextflow input-output arguments"
-    }
-]
-}
diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml
index 7af42796..ed6ed16a 100644
--- a/target/nextflow/busco/busco_run/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_run/.config.vsh.yaml
@@ -423,7 +423,7 @@ build_info:
   output: "target/nextflow/busco/busco_run"
   executable: "target/nextflow/busco/busco_run/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf
index 0680494a..1530313c 100644
--- a/target/nextflow/busco/busco_run/main.nf
+++ b/target/nextflow/busco/busco_run/main.nf
@@ -3283,7 +3283,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_run",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_run/nextflow_schema.json b/target/nextflow/busco/busco_run/nextflow_schema.json
new file mode 100644
index 00000000..64390d89
--- /dev/null
+++ b/target/nextflow/busco/busco_run/nextflow_schema.json
@@ -0,0 +1,471 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "busco_run",
+"description": "Assessment of genome assembly and annotation completeness with single copy orthologs",
+"type": "object",
+"definitions": {
+
+    
+    
+    "inputs" : {
+    "title": "Inputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format",
+                "help_text": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.\n"
+            
+            }
+    
+
+        ,
+                "mode": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run",
+                "help_text": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run. There are three valid modes:\n  - geno or genome, for genome assemblies (DNA)\n  - tran or transcriptome, for transcriptome assemblies (DNA)\n  - prot or proteins, for annotated gene sets (protein)\n",
+                "enum": ["genome", "geno", "transcriptome", "tran", "proteins", "prot"]
+            
+            
+            }
+    
+
+        ,
+                "lineage_dataset": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed",
+                "help_text": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. \nThe full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\" flag can be set to automatically find the optimal lineage path.\nBUSCO will automatically download the requested dataset if it is not already present in the download folder. \nYou can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using the busco/busco_download_dataset component.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "outputs" : {
+    "title": "Outputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "short_summary_json": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format",
+                "help_text": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format.\n"
+            ,
+                "default": "$id.$key.short_summary_json.json"
+            }
+    
+
+        ,
+                "short_summary_txt": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format",
+                "help_text": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format.\n"
+            ,
+                "default": "$id.$key.short_summary_txt.txt"
+            }
+    
+
+        ,
+                "full_table": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format",
+                "help_text": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format.\n"
+            ,
+                "default": "$id.$key.full_table.tsv"
+            }
+    
+
+        ,
+                "missing_busco_list": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format",
+                "help_text": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format.\n"
+            ,
+                "default": "$id.$key.missing_busco_list.tsv"
+            }
+    
+
+        ,
+                "output_dir": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir/`. The full output directory, if so desired",
+                "help_text": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir/`. The full output directory, if so desired.\n"
+            ,
+                "default": "$id.$key.output_dir.output_dir"
+            }
+    
+
+}
+},
+    
+    
+    "resource and run settings" : {
+    "title": "Resource and Run Settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "force": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Force rewriting of existing files",
+                "help_text": "Type: `boolean_true`, default: `false`. Force rewriting of existing files. Must be used when output files with the provided name already exist.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "quiet": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "restart": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed",
+                "help_text": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "tar": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space",
+                "help_text": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "lineage dataset settings" : {
+    "title": "Lineage Dataset Settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "auto_lineage": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed",
+                "help_text": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "auto_lineage_euk": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path",
+                "help_text": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "auto_lineage_prok": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path",
+                "help_text": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "datasets_version": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n",
+                "help_text": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "augustus settings" : {
+    "title": "Augustus Settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "augustus": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs",
+                "help_text": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "augustus_parameters": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github",
+                "help_text": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\nParameters should be contained within a single string, without whitespace and seperated by commas.\n"
+            
+            }
+    
+
+        ,
+                "augustus_species": {
+                "type":
+                "string",
+                "description": "Type: `string`. Specify the augustus species\n",
+                "help_text": "Type: `string`. Specify the augustus species\n"
+            
+            }
+    
+
+        ,
+                "long": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode",
+                "help_text": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "bbtools settings" : {
+    "title": "BBTools Settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "contig_break": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis",
+                "help_text": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis.\n"
+            
+            }
+    
+
+        ,
+                "limit": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO",
+                "help_text": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO.\nThis option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline.\n"
+            
+            }
+    
+
+        ,
+                "scaffold_composition": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition",
+                "help_text": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "blast settings" : {
+    "title": "BLAST Settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "e_value": {
+                "type":
+                "number",
+                "description": "Type: `double`. E-value cutoff for BLAST searches",
+                "help_text": "Type: `double`. E-value cutoff for BLAST searches.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "protein gene prediction settings" : {
+    "title": "Protein Gene Prediction settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "miniprot": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor",
+                "help_text": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "metaeuk settings" : {
+    "title": "MetaEuk Settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "metaeuk": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor",
+                "help_text": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "metaeuk_parameters": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github",
+                "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n"
+            
+            }
+    
+
+        ,
+                "metaeuk_rerun_parameters": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github",
+                "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/inputs"
+    },
+
+    {
+    "$ref": "#/definitions/outputs"
+    },
+
+    {
+    "$ref": "#/definitions/resource and run settings"
+    },
+
+    {
+    "$ref": "#/definitions/lineage dataset settings"
+    },
+
+    {
+    "$ref": "#/definitions/augustus settings"
+    },
+
+    {
+    "$ref": "#/definitions/bbtools settings"
+    },
+
+    {
+    "$ref": "#/definitions/blast settings"
+    },
+
+    {
+    "$ref": "#/definitions/protein gene prediction settings"
+    },
+
+    {
+    "$ref": "#/definitions/metaeuk settings"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}
diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml
index 7e526f2d..c67cec13 100644
--- a/target/nextflow/cutadapt/.config.vsh.yaml
+++ b/target/nextflow/cutadapt/.config.vsh.yaml
@@ -740,7 +740,7 @@ build_info:
   output: "target/nextflow/cutadapt"
   executable: "target/nextflow/cutadapt/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf
index e037c66e..02ae623e 100644
--- a/target/nextflow/cutadapt/main.nf
+++ b/target/nextflow/cutadapt/main.nf
@@ -3593,7 +3593,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/cutadapt",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml
index 249d747c..92f68331 100644
--- a/target/nextflow/falco/.config.vsh.yaml
+++ b/target/nextflow/falco/.config.vsh.yaml
@@ -317,7 +317,7 @@ build_info:
   output: "target/nextflow/falco"
   executable: "target/nextflow/falco/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf
index 7a41eb91..310e7c54 100644
--- a/target/nextflow/falco/main.nf
+++ b/target/nextflow/falco/main.nf
@@ -3144,7 +3144,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/falco",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml
index a6343f34..797c9686 100644
--- a/target/nextflow/fastp/.config.vsh.yaml
+++ b/target/nextflow/fastp/.config.vsh.yaml
@@ -1083,7 +1083,7 @@ build_info:
   output: "target/nextflow/fastp"
   executable: "target/nextflow/fastp/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf
index 213b89d8..47396518 100644
--- a/target/nextflow/fastp/main.nf
+++ b/target/nextflow/fastp/main.nf
@@ -3997,7 +3997,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/fastp",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml
index b6b8aff1..6e0df048 100644
--- a/target/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/nextflow/featurecounts/.config.vsh.yaml
@@ -645,7 +645,7 @@ build_info:
   output: "target/nextflow/featurecounts"
   executable: "target/nextflow/featurecounts/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf
index fa4ea6b8..798c0be8 100644
--- a/target/nextflow/featurecounts/main.nf
+++ b/target/nextflow/featurecounts/main.nf
@@ -3523,7 +3523,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/featurecounts",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml
index 6ec65249..11e24355 100644
--- a/target/nextflow/gffread/.config.vsh.yaml
+++ b/target/nextflow/gffread/.config.vsh.yaml
@@ -685,7 +685,7 @@ build_info:
   output: "target/nextflow/gffread"
   executable: "target/nextflow/gffread/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf
index b2b9c0f2..a0ed7e34 100644
--- a/target/nextflow/gffread/main.nf
+++ b/target/nextflow/gffread/main.nf
@@ -3580,7 +3580,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/gffread",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
index 07d76b28..4c2ffe52 100644
--- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,7 +507,7 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_call"
   executable: "target/nextflow/lofreq/lofreq_call/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf
index 476a775d..ce37d4f6 100644
--- a/target/nextflow/lofreq/lofreq_call/main.nf
+++ b/target/nextflow/lofreq/lofreq_call/main.nf
@@ -3388,7 +3388,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_call",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
index afdc6819..d7a624dd 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_indelqual"
   executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf
index 22fae3cc..f06a3418 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/main.nf
+++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf
@@ -3051,7 +3051,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_indelqual",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json
similarity index 61%
rename from target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json
rename to target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json
index 59912ee3..fc09ea50 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json
+++ b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json
@@ -1,7 +1,7 @@
 {
 "$schema": "http://json-schema.org/draft-07/schema",
-"title": "bedtools_bamtofastq",
-"description": "Conversion tool for extracting FASTQ records from sequence alignments in BAM format.\n",
+"title": "lofreq_indelqual",
+"description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\u0027s BQSR (\u003e=2) If that\u0027s not possible, use this subcommand.\nThe command has two modes: \u0027uniform\u0027 and \u0027dindel\u0027:\n- \u0027uniform\u0027 will assign a given value uniformly, whereas\n- \u0027dindel\u0027 will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n",
 "type": "object",
 "definitions": {
 
@@ -17,8 +17,18 @@
                 "input": {
                 "type":
                 "string",
-                "description": "Type: `file`, required. Input BAM file to be converted to FASTQ",
-                "help_text": "Type: `file`, required. Input BAM file to be converted to FASTQ."
+                "description": "Type: `file`, required, example: `normal.bam`. Input BAM file",
+                "help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n"
+            
+            }
+    
+
+        ,
+                "ref": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel)",
+                "help_text": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel).\n"
             
             }
     
@@ -34,24 +44,13 @@
     "properties": {
     
         
-                "fastq": {
+                "out": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.fastq.fastq`. Output FASTQ file",
-                "help_text": "Type: `file`, required, default: `$id.$key.fastq.fastq`. Output FASTQ file."
+                "description": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file",
+                "help_text": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file.\n"
             ,
-                "default": "$id.$key.fastq.fastq"
-            }
-    
-
-        ,
-                "fastq2": {
-                "type":
-                "string",
-                "description": "Type: `file`, default: `$id.$key.fastq2.fastq2`. FASTQ for second end",
-                "help_text": "Type: `file`, default: `$id.$key.fastq2.fastq2`. FASTQ for second end. Used if BAM contains paired-end data.\nBAM should be sorted by query name is creating paired FASTQ.\n"
-            ,
-                "default": "$id.$key.fastq2.fastq2"
+                "default": "$id.$key.out.bam"
             }
     
 
@@ -59,18 +58,39 @@
 },
     
     
-    "options" : {
-    "title": "Options",
+    "arguments" : {
+    "title": "Arguments",
     "type": "object",
     "description": "No description",
     "properties": {
     
         
-                "tags": {
+                "uniform": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases",
+                "help_text": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel).\n"
+            
+            }
+    
+
+        ,
+                "dindel": {
                 "type":
                 "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Create FASTQ based on the mate info in the BAM R2 and Q2 tags",
-                "help_text": "Type: `boolean_true`, default: `false`. Create FASTQ based on the mate info in the BAM R2 and Q2 tags.\n"
+                "description": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref)",
+                "help_text": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref).\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "verbose": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Be verbose",
+                "help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n"
             ,
                 "default": "False"
             }
@@ -121,7 +141,7 @@
     },
 
     {
-    "$ref": "#/definitions/options"
+    "$ref": "#/definitions/arguments"
     },
 
     {
diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml
index 982b9e76..474c7697 100644
--- a/target/nextflow/multiqc/.config.vsh.yaml
+++ b/target/nextflow/multiqc/.config.vsh.yaml
@@ -456,7 +456,7 @@ build_info:
   output: "target/nextflow/multiqc"
   executable: "target/nextflow/multiqc/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf
index 3014c2c6..0c067868 100644
--- a/target/nextflow/multiqc/main.nf
+++ b/target/nextflow/multiqc/main.nf
@@ -3340,7 +3340,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/multiqc",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml
index ca6e4455..4aa05474 100644
--- a/target/nextflow/pear/.config.vsh.yaml
+++ b/target/nextflow/pear/.config.vsh.yaml
@@ -398,7 +398,7 @@ build_info:
   output: "target/nextflow/pear"
   executable: "target/nextflow/pear/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf
index 3c47d2bd..6368a29e 100644
--- a/target/nextflow/pear/main.nf
+++ b/target/nextflow/pear/main.nf
@@ -3233,7 +3233,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/pear",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
index bff4c40c..f51fba6d 100644
--- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -252,7 +252,7 @@ engines:
   setup:
   - type: "docker"
     run:
-    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')\n"
+    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
   entrypoint: []
   cmd: null
 - type: "native"
@@ -264,7 +264,7 @@ build_info:
   output: "target/nextflow/qualimap/qualimap_rnaseq"
   executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
index fd132076..03ff0946 100644
--- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf
+++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
@@ -3087,7 +3087,7 @@ meta = [
         {
           "type" : "docker",
           "run" : [
-            "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//')\n"
+            "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
           ]
         }
       ]
@@ -3103,7 +3103,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/qualimap/qualimap_rnaseq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
index 1b451807..003b8e80 100644
--- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +277,7 @@ build_info:
   output: "target/nextflow/salmon/salmon_index"
   executable: "target/nextflow/salmon/salmon_index/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf
index 11164449..9228cc03 100644
--- a/target/nextflow/salmon/salmon_index/main.nf
+++ b/target/nextflow/salmon/salmon_index/main.nf
@@ -3103,7 +3103,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_index",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
index 38979ae3..06ff2174 100644
--- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,7 +1173,7 @@ build_info:
   output: "target/nextflow/salmon/salmon_quant"
   executable: "target/nextflow/salmon/salmon_quant/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf
index 7d0de287..e8885e61 100644
--- a/target/nextflow/salmon/salmon_quant/main.nf
+++ b/target/nextflow/salmon/salmon_quant/main.nf
@@ -3938,7 +3938,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_quant",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
index e0563f7d..06a2139e 100644
--- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_collate"
   executable: "target/nextflow/samtools/samtools_collate/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf
index 827fadae..18961b50 100644
--- a/target/nextflow/samtools/samtools_collate/main.nf
+++ b/target/nextflow/samtools/samtools_collate/main.nf
@@ -3114,7 +3114,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_collate",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
index e4b0062d..4b338259 100644
--- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,7 +243,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_faidx"
   executable: "target/nextflow/samtools/samtools_faidx/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf
index 61b1e2a3..fb903b0d 100644
--- a/target/nextflow/samtools/samtools_faidx/main.nf
+++ b/target/nextflow/samtools/samtools_faidx/main.nf
@@ -3086,7 +3086,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_faidx",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
index 28bc252a..32d5d5ae 100644
--- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_fasta"
   executable: "target/nextflow/samtools/samtools_fasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf
index 9a92aae7..b861be08 100644
--- a/target/nextflow/samtools/samtools_fasta/main.nf
+++ b/target/nextflow/samtools/samtools_fasta/main.nf
@@ -3278,7 +3278,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
index e68b3220..0afe62e2 100644
--- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_fastq"
   executable: "target/nextflow/samtools/samtools_fastq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf
index b1e85156..b403a236 100644
--- a/target/nextflow/samtools/samtools_fastq/main.nf
+++ b/target/nextflow/samtools/samtools_fastq/main.nf
@@ -3278,7 +3278,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fastq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
index b4d17f34..baf68bf6 100644
--- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_flagstat"
   executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf
index c332943d..2347d944 100644
--- a/target/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/nextflow/samtools/samtools_flagstat/main.nf
@@ -3002,7 +3002,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_flagstat",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
index 90ea03bb..aa0a80bd 100644
--- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_idxstats"
   executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf
index 6b828d53..9d11e782 100644
--- a/target/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/nextflow/samtools/samtools_idxstats/main.nf
@@ -3014,7 +3014,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_idxstats",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
index 0c67a6b0..2c95e58c 100644
--- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_index"
   executable: "target/nextflow/samtools/samtools_index/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf
index abc08324..85b31467 100644
--- a/target/nextflow/samtools/samtools_index/main.nf
+++ b/target/nextflow/samtools/samtools_index/main.nf
@@ -3027,7 +3027,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_index",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
index 8a7b8834..cc2142db 100644
--- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -332,7 +332,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_sort"
   executable: "target/nextflow/samtools/samtools_sort/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf
index 991bbc26..2f296785 100644
--- a/target/nextflow/samtools/samtools_sort/main.nf
+++ b/target/nextflow/samtools/samtools_sort/main.nf
@@ -3199,7 +3199,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_sort",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
index 1ee0c9c3..c2c4c397 100644
--- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_stats"
   executable: "target/nextflow/samtools/samtools_stats/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf
index 83749a85..4a8a3fd6 100644
--- a/target/nextflow/samtools/samtools_stats/main.nf
+++ b/target/nextflow/samtools/samtools_stats/main.nf
@@ -3269,7 +3269,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_stats",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
index 6fd652fb..6195ac00 100644
--- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
@@ -665,7 +665,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_view"
   executable: "target/nextflow/samtools/samtools_view/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf
index 52ef1e75..5de598e4 100644
--- a/target/nextflow/samtools/samtools_view/main.nf
+++ b/target/nextflow/samtools/samtools_view/main.nf
@@ -3450,7 +3450,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_view",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
index d8eb835a..c4d0cb21 100644
--- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/nextflow/seqtk/seqtk_sample"
   executable: "target/nextflow/seqtk/seqtk_sample/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf
index 7f8dd131..c43e8ef5 100644
--- a/target/nextflow/seqtk/seqtk_sample/main.nf
+++ b/target/nextflow/seqtk/seqtk_sample/main.nf
@@ -3004,7 +3004,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_sample",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
index 10afff7b..20d2bd91 100644
--- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,7 +196,7 @@ build_info:
   output: "target/nextflow/seqtk/seqtk_subseq"
   executable: "target/nextflow/seqtk/seqtk_subseq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf
index 30176bf6..1ff2a3c7 100644
--- a/target/nextflow/seqtk/seqtk_subseq/main.nf
+++ b/target/nextflow/seqtk/seqtk_subseq/main.nf
@@ -3034,7 +3034,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_subseq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml
index 77f86191..3f8a5719 100644
--- a/target/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2663,7 +2663,7 @@ build_info:
   output: "target/nextflow/star/star_align_reads"
   executable: "target/nextflow/star/star_align_reads/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf
index 1886f2bc..9614f148 100644
--- a/target/nextflow/star/star_align_reads/main.nf
+++ b/target/nextflow/star/star_align_reads/main.nf
@@ -5917,7 +5917,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_align_reads",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
index 4324d0d1..8cb0d12b 100644
--- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -333,7 +333,7 @@ build_info:
   output: "target/nextflow/star/star_genome_generate"
   executable: "target/nextflow/star/star_genome_generate/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf
index 2b364228..03a5d2cf 100644
--- a/target/nextflow/star/star_genome_generate/main.nf
+++ b/target/nextflow/star/star_genome_generate/main.nf
@@ -3169,7 +3169,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_genome_generate",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
index 90ac782a..6897b283 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,7 +611,7 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_dedup"
   executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
index f0d33bd6..4f9457ff 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
@@ -3461,7 +3461,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_dedup",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
index 2cd0f1f7..7d1e8b81 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,7 +449,7 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_extract"
   executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "c407a88b173a2a25054ac2ee7e2abdd639d7efc4"
+  git_commit: "1b0257c8bd57bdf0b9a8e993437f54750c79dce2"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf
index 38413b45..86ee1627 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf
@@ -3290,7 +3290,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_extract",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "c407a88b173a2a25054ac2ee7e2abdd639d7efc4",
+    "git_commit" : "1b0257c8bd57bdf0b9a8e993437f54750c79dce2",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {