diff --git a/CHANGELOG.md b/CHANGELOG.md
index e3b16036..b5c403af 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,14 @@
-# biobox unreleased
+# biobox x.x.x
+
+## BUG FIXES
+
+* `pear`: fix component not exiting with the correct exitcode when PEAR fails.
+
+* `cutadapt`: fix `--par_quality_cutoff_r2` argument.
+
+* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
+
+# biobox 0.1.0
 
 ## BREAKING CHANGES
 
@@ -6,7 +16,6 @@
   Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
   splitting up certain file paths.
 
-* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
 
 ## NEW FEATURES
 
diff --git a/src/cutadapt/script.sh b/src/cutadapt/script.sh
index a1ea69f1..20c92724 100644
--- a/src/cutadapt/script.sh
+++ b/src/cutadapt/script.sh
@@ -127,7 +127,7 @@ mod_args=$(echo \
   ${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \
   ${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \
   ${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \
-  ${par_quality_cutoff_r2:+--quality-cutoff_r2 "${par_quality_cutoff_r2}"} \
+  ${par_quality_cutoff_r2:+-Q "${par_quality_cutoff_r2}"} \
   ${par_quality_base:+--quality-base "${par_quality_base}"} \
   ${par_poly_a:+--poly-a} \
   ${par_length:+--length "${par_length}"} \
diff --git a/src/pear/script.sh b/src/pear/script.sh
index f7d6a28f..9eff147b 100644
--- a/src/pear/script.sh
+++ b/src/pear/script.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 ## VIASH END
 
diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml
index db1f28d8..a0c06ce4 100644
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -688,7 +688,7 @@ build_info:
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 49d4bd61..b7a877ec 100755
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -749,9 +749,9 @@ ENTRYPOINT []
 RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:57Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:43Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml
index 52e99e41..f628c26a 100644
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -386,7 +386,7 @@ build_info:
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 e8ad7482..aa00f34c 100755
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -593,9 +593,9 @@ rm /tmp/bcl-convert.rpm
 RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:56Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
index 3b76c9b4..9ba22e7f 100644
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -217,7 +217,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 2348437f..3830f9a8 100755
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -521,9 +521,9 @@ RUN apt-get update && \
 RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:56Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
index 7c238116..9576a67f 100644
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -144,7 +144,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 01008e70..202b406d 100755
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -470,9 +470,9 @@ ENTRYPOINT []
 RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:51Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:36Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
index ab22b28c..6dc36699 100644
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -131,7 +131,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 f353e78c..8de5acf6 100755
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -460,9 +460,9 @@ ENTRYPOINT []
 RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:51Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:36Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml
index f70b247a..d85f39b7 100644
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -404,7 +404,7 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 1a37a623..4df2d4bd 100755
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -623,9 +623,9 @@ ENTRYPOINT []
 RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:52Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:37Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml
index 88c72f16..19b35df0 100644
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -727,7 +727,7 @@ build_info:
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 764f4bbc..e605865f 100755
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -826,9 +826,9 @@ RUN pip install --upgrade pip && \
 RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:48Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:34Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
@@ -2585,7 +2585,7 @@ mod_args=\$(echo \\
   \${par_cut_r2:+--cut_r2 "\${par_cut_r2}"} \\
   \${par_nextseq_trim:+--nextseq-trim "\${par_nextseq_trim}"} \\
   \${par_quality_cutoff:+--quality-cutoff "\${par_quality_cutoff}"} \\
-  \${par_quality_cutoff_r2:+--quality-cutoff_r2 "\${par_quality_cutoff_r2}"} \\
+  \${par_quality_cutoff_r2:+-Q "\${par_quality_cutoff_r2}"} \\
   \${par_quality_base:+--quality-base "\${par_quality_base}"} \\
   \${par_poly_a:+--poly-a} \\
   \${par_length:+--length "\${par_length}"} \\
diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml
index 058d3d51..02e0f5e8 100644
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -304,7 +304,7 @@ build_info:
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 3f4cbdd2..c219d350 100755
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -584,9 +584,9 @@ make install
 RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:48Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:33Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml
index 59af4997..33f75412 100644
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1065,7 +1065,7 @@ build_info:
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 f23ec939..0e0c2f06 100755
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1023,9 +1023,9 @@ ENTRYPOINT []
 RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:49Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:34Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml
index 683d566a..371efc12 100644
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -631,7 +631,7 @@ build_info:
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 8a510a11..fe37b70d 100755
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -749,9 +749,9 @@ ENTRYPOINT []
 RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:58Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:43Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml
index 4bb2edfc..d2b7fe75 100644
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -671,7 +671,7 @@ build_info:
   output: "target/executable/gffread"
   executable: "target/executable/gffread/gffread"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 056269d3..340a827a 100755
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -802,9 +802,9 @@ ENTRYPOINT []
 RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:49Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:34Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
index 9d3f1f58..9285b64f 100644
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -489,7 +489,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_call"
   executable: "target/executable/lofreq/lofreq_call/lofreq_call"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 aa5816fd..8081de18 100755
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -651,9 +651,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
 echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:52Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:37Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
index 8603857b..643bb6c8 100644
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -197,7 +197,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 3f8214f1..8610f271 100755
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -496,9 +496,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
 echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:52Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:37Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml
index 415cef3a..1bb74ee3 100644
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -438,7 +438,7 @@ build_info:
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 91f2d2e8..ae6007f6 100755
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -632,9 +632,9 @@ ENTRYPOINT []
 RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:47Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml
index ae2ffb0b..f736d3a9 100644
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -380,7 +380,7 @@ build_info:
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 11b80d88..990eac7c 100755
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -592,9 +592,9 @@ RUN version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \
 echo "pear: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:56Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:41Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
@@ -1504,6 +1504,8 @@ trap interrupt INT SIGINT
 cat > "\$tempscript" << 'VIASHMAIN'
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_FORWARD_FASTQ+x} ]; then echo "${VIASH_PAR_FORWARD_FASTQ}" | sed "s#'#'\"'\"'#g;s#.*#par_forward_fastq='&'#" ; else echo "# par_forward_fastq="; fi )
diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml
index 6d955d40..ceb89591 100644
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -263,7 +263,7 @@ build_info:
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 b5d13151..0ae6fe21 100755
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -541,9 +541,9 @@ ENTRYPOINT []
 RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:57Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:42Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml
index d608a7d1..f638d7a6 100644
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1159,7 +1159,7 @@ build_info:
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 acc1c713..c3ce9f1d 100755
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1163,9 +1163,9 @@ ENTRYPOINT []
 RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:57Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:42Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml
index b6daf069..2142ba05 100644
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -250,7 +250,7 @@ build_info:
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 8130da13..aeb4b38f 100755
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -514,9 +514,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:54Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
index 3a27d991..7a140a97 100644
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -229,7 +229,7 @@ build_info:
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 90ea5bba..706bf942 100755
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -507,9 +507,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:55Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
index 3bdb498b..6ef36d6f 100644
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -417,7 +417,7 @@ build_info:
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 943b7dfa..b7b82907 100755
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -620,9 +620,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:53Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
index 03f8878b..36f59dad 100644
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -159,7 +159,7 @@ build_info:
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 5b9ed339..486cbce0 100755
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -469,9 +469,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:55Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
index 8cae5c45..4e5f4525 100644
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -169,7 +169,7 @@ build_info:
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 7cbebe0b..20882952 100755
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -473,9 +473,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:54Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml
index 52507e55..369264d1 100644
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -175,7 +175,7 @@ build_info:
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 52b1f7cb..95db8c3e 100755
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -480,9 +480,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:53Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml
index 1ea1aef6..c564ccc0 100644
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -318,7 +318,7 @@ build_info:
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 39a34ace..3fc2b35d 100755
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -551,9 +551,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:55Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml
index dfc28d17..3739308e 100644
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -380,7 +380,7 @@ build_info:
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 bf34b5a7..0980f3b9 100755
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -568,9 +568,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:54Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml
index 86f5bcf7..64ef5c8d 100644
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -651,7 +651,7 @@ build_info:
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 7cd7172c..97541c29 100755
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -820,9 +820,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:53Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml
index 348a2e92..aa233ced 100644
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2108,7 +2108,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 ba8350e4..c41eff3c 100755
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1665,9 +1665,9 @@ RUN apt-get update && \
 RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:50Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:35Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml
index aa988696..628baa98 100644
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -319,7 +319,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 44d06698..bd9d800e 100755
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -572,9 +572,9 @@ RUN apt-get update && \
 RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-07-01T09:28:50Z"
+LABEL org.opencontainers.image.created="2024-07-01T14:59:35Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
+LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
 LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
 
 VIASHDOCKER
diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml
index 0f7f0867..af87a3d4 100644
--- a/target/nextflow/arriba/.config.vsh.yaml
+++ b/target/nextflow/arriba/.config.vsh.yaml
@@ -688,7 +688,7 @@ build_info:
   output: "target/nextflow/arriba"
   executable: "target/nextflow/arriba/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 cb0dc00b..3e7fd875 100644
--- a/target/nextflow/arriba/main.nf
+++ b/target/nextflow/arriba/main.nf
@@ -3534,7 +3534,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/arriba",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 6fb0d532..346f8509 100644
--- a/target/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/nextflow/bcl_convert/.config.vsh.yaml
@@ -386,7 +386,7 @@ build_info:
   output: "target/nextflow/bcl_convert"
   executable: "target/nextflow/bcl_convert/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 79c81a70..aab201dc 100644
--- a/target/nextflow/bcl_convert/main.nf
+++ b/target/nextflow/bcl_convert/main.nf
@@ -3249,7 +3249,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcl_convert",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 cf4a2fac..9f43c3b4 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -217,7 +217,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_getfasta"
   executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 df499079..b6aa179b 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/main.nf
+++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf
@@ -3033,7 +3033,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_getfasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 bdf13439..cda6a765 100644
--- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
@@ -144,7 +144,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 b474654c..461d6ce5 100644
--- a/target/nextflow/busco/busco_download_datasets/main.nf
+++ b/target/nextflow/busco/busco_download_datasets/main.nf
@@ -2959,7 +2959,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_download_datasets",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 e05a2b58..c291579d 100644
--- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
@@ -131,7 +131,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 07803eb2..8eded2d4 100644
--- a/target/nextflow/busco/busco_list_datasets/main.nf
+++ b/target/nextflow/busco/busco_list_datasets/main.nf
@@ -2945,7 +2945,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_list_datasets",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml
index e6540a64..11798900 100644
--- a/target/nextflow/busco/busco_run/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_run/.config.vsh.yaml
@@ -404,7 +404,7 @@ build_info:
   output: "target/nextflow/busco/busco_run"
   executable: "target/nextflow/busco/busco_run/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 ee46e020..c56325c1 100644
--- a/target/nextflow/busco/busco_run/main.nf
+++ b/target/nextflow/busco/busco_run/main.nf
@@ -3251,7 +3251,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_run",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml
index e639b99c..a5a48ecc 100644
--- a/target/nextflow/cutadapt/.config.vsh.yaml
+++ b/target/nextflow/cutadapt/.config.vsh.yaml
@@ -727,7 +727,7 @@ build_info:
   output: "target/nextflow/cutadapt"
   executable: "target/nextflow/cutadapt/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 be1845b2..a9ad8c63 100644
--- a/target/nextflow/cutadapt/main.nf
+++ b/target/nextflow/cutadapt/main.nf
@@ -3568,7 +3568,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/cutadapt",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
@@ -3805,7 +3805,7 @@ mod_args=\\$(echo \\\\
   \\${par_cut_r2:+--cut_r2 "\\${par_cut_r2}"} \\\\
   \\${par_nextseq_trim:+--nextseq-trim "\\${par_nextseq_trim}"} \\\\
   \\${par_quality_cutoff:+--quality-cutoff "\\${par_quality_cutoff}"} \\\\
-  \\${par_quality_cutoff_r2:+--quality-cutoff_r2 "\\${par_quality_cutoff_r2}"} \\\\
+  \\${par_quality_cutoff_r2:+-Q "\\${par_quality_cutoff_r2}"} \\\\
   \\${par_quality_base:+--quality-base "\\${par_quality_base}"} \\\\
   \\${par_poly_a:+--poly-a} \\\\
   \\${par_length:+--length "\\${par_length}"} \\\\
diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml
index 3ac27f4f..72a1dbf9 100644
--- a/target/nextflow/falco/.config.vsh.yaml
+++ b/target/nextflow/falco/.config.vsh.yaml
@@ -304,7 +304,7 @@ build_info:
   output: "target/nextflow/falco"
   executable: "target/nextflow/falco/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 f13442d7..ca9e9083 100644
--- a/target/nextflow/falco/main.nf
+++ b/target/nextflow/falco/main.nf
@@ -3119,7 +3119,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/falco",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 59122324..c4b9ec22 100644
--- a/target/nextflow/fastp/.config.vsh.yaml
+++ b/target/nextflow/fastp/.config.vsh.yaml
@@ -1065,7 +1065,7 @@ build_info:
   output: "target/nextflow/fastp"
   executable: "target/nextflow/fastp/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 3a5e6056..257260da 100644
--- a/target/nextflow/fastp/main.nf
+++ b/target/nextflow/fastp/main.nf
@@ -3965,7 +3965,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/fastp",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 cb0047de..bcff0d02 100644
--- a/target/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/nextflow/featurecounts/.config.vsh.yaml
@@ -631,7 +631,7 @@ build_info:
   output: "target/nextflow/featurecounts"
   executable: "target/nextflow/featurecounts/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 9844692c..51519325 100644
--- a/target/nextflow/featurecounts/main.nf
+++ b/target/nextflow/featurecounts/main.nf
@@ -3497,7 +3497,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/featurecounts",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 5f4ac0c9..f393c439 100644
--- a/target/nextflow/gffread/.config.vsh.yaml
+++ b/target/nextflow/gffread/.config.vsh.yaml
@@ -671,7 +671,7 @@ build_info:
   output: "target/nextflow/gffread"
   executable: "target/nextflow/gffread/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 5a55f0c5..ddb6c163 100644
--- a/target/nextflow/gffread/main.nf
+++ b/target/nextflow/gffread/main.nf
@@ -3554,7 +3554,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/gffread",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 4aef735b..c4bcda7b 100644
--- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
@@ -489,7 +489,7 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_call"
   executable: "target/nextflow/lofreq/lofreq_call/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 b03c8927..9312fc0e 100644
--- a/target/nextflow/lofreq/lofreq_call/main.nf
+++ b/target/nextflow/lofreq/lofreq_call/main.nf
@@ -3356,7 +3356,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_call",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 20fef47c..b625eeb0 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -197,7 +197,7 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_indelqual"
   executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 68272dd8..50af84f1 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/main.nf
+++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf
@@ -3019,7 +3019,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_indelqual",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml
index a6124ea4..15640fbd 100644
--- a/target/nextflow/multiqc/.config.vsh.yaml
+++ b/target/nextflow/multiqc/.config.vsh.yaml
@@ -438,7 +438,7 @@ build_info:
   output: "target/nextflow/multiqc"
   executable: "target/nextflow/multiqc/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 b640f71b..17153dc2 100644
--- a/target/nextflow/multiqc/main.nf
+++ b/target/nextflow/multiqc/main.nf
@@ -3310,7 +3310,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/multiqc",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 2d23d62f..fc6cfa7e 100644
--- a/target/nextflow/pear/.config.vsh.yaml
+++ b/target/nextflow/pear/.config.vsh.yaml
@@ -380,7 +380,7 @@ build_info:
   output: "target/nextflow/pear"
   executable: "target/nextflow/pear/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 78f944be..8473d09c 100644
--- a/target/nextflow/pear/main.nf
+++ b/target/nextflow/pear/main.nf
@@ -3201,7 +3201,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/pear",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
@@ -3243,6 +3243,8 @@ tempscript=".viash_script.sh"
 cat > "$tempscript" << VIASHMAIN
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_FORWARD_FASTQ+x} ]; then echo "${VIASH_PAR_FORWARD_FASTQ}" | sed "s#'#'\\"'\\"'#g;s#.*#par_forward_fastq='&'#" ; else echo "# par_forward_fastq="; fi )
diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
index baf1bbc7..c516dbc6 100644
--- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -263,7 +263,7 @@ build_info:
   output: "target/nextflow/salmon/salmon_index"
   executable: "target/nextflow/salmon/salmon_index/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 35f73b85..6ed600c2 100644
--- a/target/nextflow/salmon/salmon_index/main.nf
+++ b/target/nextflow/salmon/salmon_index/main.nf
@@ -3077,7 +3077,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_index",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 11d517a4..c3cc27cf 100644
--- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1159,7 +1159,7 @@ build_info:
   output: "target/nextflow/salmon/salmon_quant"
   executable: "target/nextflow/salmon/salmon_quant/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 d41f9346..9ad2c672 100644
--- a/target/nextflow/salmon/salmon_quant/main.nf
+++ b/target/nextflow/salmon/salmon_quant/main.nf
@@ -3912,7 +3912,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_quant",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 0af5fd56..02c171be 100644
--- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
@@ -250,7 +250,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_collate"
   executable: "target/nextflow/samtools/samtools_collate/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 3082ff32..bfd6ef44 100644
--- a/target/nextflow/samtools/samtools_collate/main.nf
+++ b/target/nextflow/samtools/samtools_collate/main.nf
@@ -3088,7 +3088,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_collate",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 b8656865..93b9a6b8 100644
--- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
@@ -229,7 +229,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_faidx"
   executable: "target/nextflow/samtools/samtools_faidx/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 13ceba63..76ddec94 100644
--- a/target/nextflow/samtools/samtools_faidx/main.nf
+++ b/target/nextflow/samtools/samtools_faidx/main.nf
@@ -3060,7 +3060,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_faidx",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 17b1b013..26d12ac4 100644
--- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
@@ -417,7 +417,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_fastq"
   executable: "target/nextflow/samtools/samtools_fastq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 2d5ba879..122e2a03 100644
--- a/target/nextflow/samtools/samtools_fastq/main.nf
+++ b/target/nextflow/samtools/samtools_fastq/main.nf
@@ -3252,7 +3252,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fastq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 3437f55f..12a98c95 100644
--- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -159,7 +159,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_flagstat"
   executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 bd548781..7105414e 100644
--- a/target/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/nextflow/samtools/samtools_flagstat/main.nf
@@ -2976,7 +2976,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_flagstat",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 549c54b4..ec14b011 100644
--- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -169,7 +169,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_idxstats"
   executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 fc0ca424..f385eb6b 100644
--- a/target/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/nextflow/samtools/samtools_idxstats/main.nf
@@ -2988,7 +2988,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_idxstats",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 77c54c12..7e66c38b 100644
--- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -175,7 +175,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_index"
   executable: "target/nextflow/samtools/samtools_index/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 30b107d8..b643394e 100644
--- a/target/nextflow/samtools/samtools_index/main.nf
+++ b/target/nextflow/samtools/samtools_index/main.nf
@@ -3001,7 +3001,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_index",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 1793ccb6..3858120e 100644
--- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -318,7 +318,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_sort"
   executable: "target/nextflow/samtools/samtools_sort/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 06d6c28d..68e8d2b5 100644
--- a/target/nextflow/samtools/samtools_sort/main.nf
+++ b/target/nextflow/samtools/samtools_sort/main.nf
@@ -3173,7 +3173,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_sort",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 4c00ba7a..9e38cf68 100644
--- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -380,7 +380,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_stats"
   executable: "target/nextflow/samtools/samtools_stats/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 20ad25f8..7f80b397 100644
--- a/target/nextflow/samtools/samtools_stats/main.nf
+++ b/target/nextflow/samtools/samtools_stats/main.nf
@@ -3238,7 +3238,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_stats",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 96eb3d74..c5f8bc78 100644
--- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
@@ -651,7 +651,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_view"
   executable: "target/nextflow/samtools/samtools_view/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 e6a1a0e8..921e2ad3 100644
--- a/target/nextflow/samtools/samtools_view/main.nf
+++ b/target/nextflow/samtools/samtools_view/main.nf
@@ -3424,7 +3424,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_view",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 042fb3a4..1ce9826d 100644
--- a/target/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2108,7 +2108,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 8daff48d..e734fe97 100644
--- a/target/nextflow/star/star_align_reads/main.nf
+++ b/target/nextflow/star/star_align_reads/main.nf
@@ -5023,7 +5023,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_align_reads",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "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 64aa49b9..c033beef 100644
--- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -319,7 +319,7 @@ 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: "d95b3721d5e175d323b41232c045364d60d38d1d"
+  git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
   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 83c6b8dc..f1f25140 100644
--- a/target/nextflow/star/star_genome_generate/main.nf
+++ b/target/nextflow/star/star_genome_generate/main.nf
@@ -3143,7 +3143,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_genome_generate",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
+    "git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {