Build branch main with version main (a13b57d)

Build pipeline: viash-hub.biobox.main-t7scl Source commit: a13b57d04a Source message: Add bases2fastq (#167)
2024-11-26 14:40:26 +00:00
parent 6b56570131
commit 38a478d5ae
331 changed files with 8597 additions and 880 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,8 @@

 * `sgedemux`: demultiplexing sequencing data generated on Singular Genomics' sequencing instruments (PR #166).

+* `bases2fasta`: demultiplexing sequencing data generated by Element Biosciences instruments (PR #167).
+
 ## BUG FIXES

 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
--- a/src/bases2fastq/config.vsh.yaml
+++ b/src/bases2fastq/config.vsh.yaml
@@ -0,0 +1,200 @@
+name: bases2fastq
+description: |
+  Bases2Fastq demultiplexes sequencing data generated by Element Biosciences instruments and converts base calls into FASTQ files.
+keywords: ["demultiplex", "fastq", "demux", "Element Biosciences"]
+links:
+  documentation: https://docs.elembio.io/docs/bases2fastq/introduction/
+license: Proprietairy
+requirements:
+  commands: [bases2fastq]
+authors:
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Input
+    arguments:
+      - name: "--analysis_directory"
+        type: file
+        description: Location of analysis directory
+        required: true
+        example: "input/"
+      - name: --run_manifest
+        alternatives: [-r]
+        type: file
+        description: Location of run manifest to use instead of default RunManifest.csv found in analysis directory
+        required: false
+
+  - name: Output
+    arguments:
+      - name: "--output_directory"
+        alternatives: ["-o"]
+        type: file
+        direction: output
+        required: true
+        description: Location to save output fastqs
+        example: fastq_dir
+      - name: "--report"
+        type: file
+        required: false
+        direction: output
+        description: Output location for the HTML report
+      - name: "--logs"
+        type: file
+        direction: output
+        required: false
+        description: Directory containing log files
+        example: logs_dir
+  - name: Arguments
+    arguments:
+      - name: --chemistry_version
+        type: string
+        required: false
+        description: Run parameters override, chemistry version.
+      - name: "--demux_only"
+        alternatives: [-d]
+        type: boolean_true
+        description: |
+          Generate demux files and indexing stats without generating FASTQ
+      - name: "--detect_adapters"
+        type: boolean_true
+        description: |
+          Detect adapters sequences, overriding any sequences present in run manifest.
+      - name: "--error_on_missing"
+        type: boolean_true
+        description: |
+          Terminate execution for a missing file (by default, missing files are
+          skipped and execution continues). Also set by --strict.
+      - name: "--exclude_tile"
+        alternatives: [-e]
+        multiple: true
+        type: string
+        description: |
+          Regex matching tile names to exclude. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
+      - name: "--filter_mask"
+        type: string
+        description: |
+          Run parameters override, custom pass filter mask.
+      - name: "--flowcell_id"
+        type: string
+        description: |
+          Run parameters override, flowcell ID.
+      - name: "--force_index_orientation"
+        type: boolean_true
+        description: |
+          Do not attempt to find orientation for I1/I2 reads (reverse complement).
+          Use orientation given in run manifest.
+      - name: "--group_fastq"
+        type: boolean_true
+        description: |
+           Group all FASTQ/stats/metrics for a project are in the project folder.
+      - name: "--i1_cycles"
+        type: integer
+        min: 1
+        description: |
+          Run parameters override, I1 cycles.
+      - name: "--i2_cycles"
+        type: integer
+        min: 1
+        description: |
+          Run parameters override, I2 cycles
+      - name: "--include_tile"
+        alternatives: [-i]
+        type: string
+        multiple: true
+        description: |
+          Regex matching tile names to include. This flag
+          can be specified multiple times. (e.g. L1.*C0[23]S.)
+      - name: "--kit_configuration"
+        type: string
+        description: |
+          Run parameters override, kit configuration.
+      - name: "--legacy_fastq"
+        type: boolean_true
+        description: |
+          Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)
+      - name: "--log_level"
+        type: string
+        alternatives: [-l]
+        choices: ["DEBUG", "INFO", "WARNING", "ERROR"]
+        description: |
+          Severity level for logging.
+        example: INFO
+      - name: "--no_error_on_invalid"
+        type: boolean_true
+        description: |
+          Skip invalid files and continue execution. Overridden by --strict options
+      - name:  "--no_projects"
+        type: boolean_true
+        description: |
+          Disable project directories
+      - name: "--num_unassigned"
+        type: integer
+        min: 0
+        max: 1000
+        example: 30
+        description: |
+          Max Number of unassigned sequences to report.
+      - name: "--preparation_workflow"
+        type: string
+        description: |
+          Run parameters override, preparation workflow. 
+      - name: --qc_only
+        type: boolean_true
+        description: |
+          Quickly generate run stats for single tile without generating FASTQ.
+          Use --include_tile/--exclude_tile to define custom tile set.
+      - name: --r1_cycles
+        type: integer
+        min: 1
+        description: |
+          Run parameters override, R1 cycles.
+      - name: --r2_cycles
+        type: integer
+        min: 1
+        description: |
+          Run parameters override, R2 cycles.
+      - name: "--split_lanes"
+        type: boolean_true
+        description: |
+          Split FASTQ files by lane.
+      - name: --strict
+        type: boolean_true
+        description: |
+          In strict mode any invalid or missing input file will terminate execution 
+          (overrides no_error_on_invalid and sets --error_on_missing)
+  
+        # --help, -h                      Display this usage statement              
+        # --input-remote, NAME            Rclone remote name for remote ANALYSIS_DIRECTORY
+        # --num-threads, -p NUMBER        Number of threads (default 1)
+        # --output-remote, NAME           Rclone remote name for remote OUTPUT_DIRECTORY
+        # --settings SELECTION            Run manifest settings override. This option may be specified multiple times.
+        # --version, -v                   Display bases2fastq version
+        # --skip-qc-report SELECTION      Do not generate HTML QC report.
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+- type: docker
+  image: elembio/bases2fastq:2.1.0
+  setup:
+    - type: apt
+      packages:
+        - procps
+        - tree
+    - type: docker
+      run: |
+        echo "bases2fastq: $(bases2fastq --version | cut -d' ' -f3)" > /var/software_versions.txt
+  test_setup:
+    - type: apt
+      packages: curl
+
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/bases2fastq/help.txt
+++ b/src/bases2fastq/help.txt
@@ -0,0 +1,40 @@
+
+Usage: bases2fastq [OPTIONS] ANALYSIS_DIRECTORY OUTPUT_DIRECTORY
+
+positional arguments:
+        ANALYSIS_DIRECTORY              Location of analysis directory
+        OUTPUT_DIRECTORY                Location to save output
+
+optional arguments:
+        --chemistry-version VERSION     Run parameters override, chemistry version.
+        --demux-only, -d                Generate demux files and indexing stats without generating FASTQ
+        --detect-adapters               Detect adapters sequences, overriding any sequences present in run manifest.
+        --error-on-missing              Terminate execution for a missing file (by default, missing files are skipped and execution continues). Also set by --strict.
+        --exclude-tile, -e SELECTION    Regex matching tile names to exclude. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
+        --filter-mask MASK              Run parameters override, custom pass filter mask.
+        --flowcell-id FLOWCELL_ID       Run parameters override, flowcell ID.
+        --force-index-orientation       Do not attempt to find orientation for I1/I2 reads (reverse complement). Use orientation given in run manifest.
+        --group-fastq                   Group all FASTQ/stats/metrics for a project are in the project folder (default false)
+        --help, -h                      Display this usage statement
+        --i1-cycles NUM_CYCLES          Run parameters override, I1 cycles.
+        --i2-cycles NUM_CYCLES          Run parameters override, I2 cycles.
+        --include-tile, -i SELECTION    Regex matching tile names to include. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
+        --input-remote, NAME            Rclone remote name for remote ANALYSIS_DIRECTORY
+        --kit-configuration KIT_CONFIG  Run parameters override, kit configuration.
+        --legacy-fastq                  Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)
+        --log-level, -l LEVEL           Severity level for logging. i.e. DEBUG, INFO, WARNING, ERROR (default INFO)
+        --no-error-on-invalid           Skip invalid files and continue execution (by default, execution is terminated for an invalid file). Overridden by --strict options.
+        --no-projects                   Disable project directories (default false)
+        --num-threads, -p NUMBER        Number of threads (default 1)
+        --num-unassigned NUMBER         Max Number of unassigned sequences to report. Must be <= 1000 (default 30)
+        --output-remote, NAME           Rclone remote name for remote OUTPUT_DIRECTORY
+        --preparation-workflow WORKFLOW Run parameters override, preparation workflow.
+        --qc-only                       Quickly generate run stats for single tile without generating FASTQ. Use --include-tile/--exclude-tile to define custom tile set.
+        --r1-cycles NUM_CYCLES          Run parameters override, R1 cycles.
+        --r2-cycles NUM_CYCLES          Run parameters override, R2 cycles.
+        --run-manifest, -r PATH         Location of run manifest to use instead of default RunManifest.csv found in analysis directory
+        --settings SELECTION            Run manifest settings override. This option may be specified multiple times.
+        --skip-qc-report SELECTION      Do not generate HTML QC report.
+        --split-lanes                   Split FASTQ files by lane
+        --strict, -s                    In strict mode any invalid or missing input file will terminate execution (overrides no-error-on-invalid and sets --error-on-missing)
+        --version, -v                   Display bases2fastq version
--- a/src/bases2fastq/script.sh
+++ b/src/bases2fastq/script.sh
@@ -0,0 +1,111 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=(
+    par_demux_only
+    par_detect_adapters
+    par_error_on_missing
+    par_group_fastq
+    par_legacy_fastq
+    par_no_error_on_invalid
+    par_no_projects
+    par_qc_only
+    par_split_lanes
+    par_skip_qc_report
+    par_strict
+    par_force_index_orientation
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# NOTE: --preparation-workflow is bugged in bases2fastq
+args=(
+    ${par_demux_only:+--demux-only}
+    ${par_detect_adapters:+--detect-adapters}
+    ${par_error_on_missing:+--error-on-missing}
+    ${par_group_fastq:+--group-fastq}
+    ${par_legacy_fastq:+--legacy-fastq}
+    ${par_no_error_on_invalid:+--no-error-on-invalid}
+    ${par_no_projects:+--no-projects}
+    ${par_split_lanes:+--split-lanes}
+    ${par_strict:+--strict}
+    ${par_force_index_orientation:+--force-index-orientation}
+    ${par_chemistry_version:+--chemistry-version "$par_chemistry_version"}
+    ${par_filter_mask:+--filter-mask "$par_filter_mask"}
+    ${par_flowcell_id:+--flowcell-id "$par_flowcell_id"}
+    ${par_i1_cycles:+--i1-cycles "$par_i1_cycles"}
+    ${par_i2_cycles:+--i2-cycles "$par_i2_cycles"}
+    ${par_r1_cycles:+--r1-cycles "$par_r1_cycles"}
+    ${par_r2_cycles:+--r2-cycles "$par_r2_cycles"}
+    ${par_kit_configuration:+--kit-configuration "$par_kit_configuration"}
+    ${par_log_level:+--log-level "$par_log_level"}
+    ${par_num_unassigned:+--num-unassigned "$par_num_unassigned"}
+    ${par_preparation_workflow:+--preparation-workflow "$par_preparation_workflow"}
+    ${meta_cpus:+--num-threads "$meta_cpus"}
+    ${par_run_manifest:+--run-manifest "$par_run_manifest"}
+)
+
+# Create arrays for inputs that contain multiple arguments
+IFS=";" read -ra exclude_tile <<< "$par_exclude_tile"
+IFS=";" read -ra include_tile <<< "$par_include_tile"
+
+if [ -z "$par_report" ]; then
+    args+=( --skip-qc-report )
+fi
+
+for arg_value in "${exclude_tile[@]}"; do
+    args+=( "--exclude-tile" "$arg_value" )
+done
+
+for arg_value in "${include_tile[@]}"; do
+    args+=( "--include-tile" "$arg_value" )
+done
+
+echo "> Creating temporary directory."
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
+echo "> Created $TMPDIR"
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
+args+=( "$par_analysis_directory" "$TMPDIR")
+echo "> Running bases2fastq with arguments: ${args[@]}"
+bases2fastq ${args[@]}
+echo "> Done running sgdemux"
+
+echo "> Output folder:"
+tree "$TMPDIR"
+
+echo "> Moving FASTQ files into final output directory"
+mkdir -p "$par_output_directory/"
+mv "$TMPDIR"/Samples/* --target-directory="$par_output_directory"
+
+if [ ! -z "$par_report" ]; then
+  echo "> Moving HTML report to the output ($par_report)"
+  mv "$TMPDIR"/*.html "$par_report"
+else
+  echo " > Leaving reports alone"
+fi
+
+# Logs is everything else
+if [ ! -z "$par_logs" ]; then
+  mkdir -p "$par_logs"
+  echo "> Moving logs to their own location ($par_logs)"
+  mv "$TMPDIR/"* "$par_logs/"
+else
+  echo "> Not moving logs"
+fi
+
+
+
--- a/src/bases2fastq/test.sh
+++ b/src/bases2fastq/test.sh
@@ -0,0 +1,200 @@
+#!/bin/bash
+
+set -eou pipefail
+
+# Helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+
+assert_file_not_exists() {
+  [ ! -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+
+assert_directory_exists() {
+  [ -d "$1" ] || { echo "Directory '$1' does not exist" && exit 1; }
+}
+
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+
+# Example output
+# Note that the format of the fastq file names and organization into subfolders
+# can differ based on the arguments provided to bases2fastq
+
+# |-- 20230404-Bases2Fastq-Sim_QC.html
+# |-- IndexAssignment.csv
+# |-- Metrics.csv
+# |-- RunManifest.csv
+# |-- RunManifest.json
+# |-- RunParameters.json
+# |-- RunStats.json
+# |-- Samples
+# |   |-- DefaultProject
+# |   |   |-- DefaultProject_IndexAssignment.csv
+# |   |   |-- DefaultProject_Metrics.csv
+# |   |   |-- DefaultProject_QC.html
+# |   |   |-- DefaultProject_RunStats.json
+# |   |   |-- sample_0
+# |   |   |   |-- sample_0_L1_R1.fastq.gz
+# |   |   |   |-- sample_0_L1_R2.fastq.gz
+# |   |   |   |-- sample_0_L2_R1.fastq.gz
+# |   |   |   |-- sample_0_L2_R2.fastq.gz
+# |   |   |   `-- sample_0_stats.json
+# |   |   |-- sample_1
+# |   |   |   |-- sample_1_L1_R1.fastq.gz
+# |   |   |   |-- sample_1_L1_R2.fastq.gz
+# |   |   |   |-- sample_1_L2_R1.fastq.gz
+# |   |   |   |-- sample_1_L2_R2.fastq.gz
+# |   |   |   `-- sample_1_stats.json
+# |   |   |-- sample_2
+# |   |   |   |-- sample_2_L1_R1.fastq.gz
+# |   |   |   |-- sample_2_L1_R2.fastq.gz
+# |   |   |   |-- sample_2_L2_R1.fastq.gz
+# |   |   |   |-- sample_2_L2_R2.fastq.gz
+# |   |   |   `-- sample_2_stats.json
+# |   |   |-- sample_3
+# |   |   |   |-- sample_3_L1_R1.fastq.gz
+# |   |   |   |-- sample_3_L1_R2.fastq.gz
+# |   |   |   |-- sample_3_L2_R1.fastq.gz
+# |   |   |   |-- sample_3_L2_R2.fastq.gz
+# |   |   |   `-- sample_3_stats.json
+# |   |   `-- sample_4
+# |   |       |-- sample_4_L1_R1.fastq.gz
+# |   |       |-- sample_4_L1_R2.fastq.gz
+# |   |       |-- sample_4_L2_R1.fastq.gz
+# |   |       |-- sample_4_L2_R2.fastq.gz
+# |   |       `-- sample_4_stats.json
+# |   `-- Unassigned
+# |       |-- Unassigned_L1_R1.fastq.gz
+# |       |-- Unassigned_L1_R2.fastq.gz
+# |       |-- Unassigned_L2_R1.fastq.gz
+# |       `-- Unassigned_L2_R2.fastq.gz
+# |-- UnassignedSequences.csv
+# `-- info
+#     |-- Bases2Fastq.log
+#     `-- RunManifestErrors.json
+
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Unpack test input files
+TAR_DIR="$TMPDIR/tar"
+mkdir -p "$TAR_DIR"
+curl http://element-public-data.s3.amazonaws.com/bases2fastq-share/bases2fastq-v2/20230404-bases2fastq-sim-151-151-9-9.tar.gz \
+-o "$TAR_DIR/20230404-bases2fastq-sim-151-151-9-9.tar.gz"
+
+BCL_DIR="$TMPDIR/bcl"
+mkdir "$BCL_DIR"
+tar -xvf "$TAR_DIR/20230404-bases2fastq-sim-151-151-9-9.tar.gz" -C "$BCL_DIR"
+
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
+expected_out_dir="$TMPDIR/test1/out"
+expected_report="$TMPDIR/report.html"
+expected_logs="$TMPDIR/logs"
+"$meta_executable" \
+    --analysis_directory "$BCL_DIR/20230404-bases2fastq-sim-151-151-9-9" \
+    --output_directory "$expected_out_dir" \
+    --logs "$expected_logs" \
+    --report "$expected_report" \
+    --include_tile "L1R02C01S1;L2R21C01S1;L1R02C01S2;L2R21C01S2;L1R03C01S2;L2R20C01S2" \
+    --exclude_tile "L1R04C01S1" \
+    --chemistry_version 2 \
+    --i1_cycles 10 \
+    --i2_cycles 10 \
+    --r1_cycles 152 \
+    --r2_cycles 152 \
+    --kit_configuration "300Cycles" \
+    --detect_adapters \
+    --error_on_missing \
+    --flowcell_id foo \
+    --force_index_orientation \
+    --group_fastq \
+    --legacy_fastq \
+    --log_level DEBUG \
+    --no_projects \
+    --num_unassigned 30 \
+    --strict \
+    --run_manifest "$BCL_DIR/20230404-bases2fastq-sim-151-151-9-9/RunManifest.csv"
+
+assert_directory_exists "$expected_out_dir"
+assert_directory_exists "$expected_logs"
+assert_file_exists "$expected_report"
+assert_file_not_empty "$expected_report"
+
+expected_samples=(
+  Undetermined_S0
+  sample_0_S1
+  sample_1_S2
+  sample_2_S3
+  sample_3_S4
+  sample_4_S5
+)
+
+for sample in "${expected_samples[@]}"; do
+  for lane in "L001" "L002"; do 
+    for orientation in "R1" "R2"; do
+      assert_file_exists "$expected_out_dir/${sample}_${lane}_${orientation}_001.fastq.gz"
+    done
+  done
+done
+popd > /dev/null
+
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
+expected_out_dir="$TMPDIR/test3/out"
+"$meta_executable" \
+    --analysis_directory "$BCL_DIR/20230404-bases2fastq-sim-151-151-9-9" \
+    --output_directory "$expected_out_dir"
+
+expected_samples=(
+  sample_0
+  sample_1
+  sample_2
+  sample_3
+  sample_4
+)
+tree "$expected_out_dir"
+
+for sample in "${expected_samples[@]}"; do
+    for orientation in "R1" "R2"; do
+      assert_file_exists "$expected_out_dir/DefaultProject/${sample}/${sample}_${orientation}.fastq.gz"
+  done
+done
+assert_file_exists "$expected_out_dir/Unassigned/Unassigned_R1.fastq.gz"
+assert_file_exists "$expected_out_dir/Unassigned/Unassigned_R2.fastq.gz"
+popd > /dev/null
+
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
+expected_out_dir="$TMPDIR/test4/out"
+"$meta_executable" \
+    --analysis_directory "$BCL_DIR/20230404-bases2fastq-sim-151-151-9-9" \
+    --output_directory "$expected_out_dir" \
+    --split_lanes
+
+expected_samples=(
+  "Unassigned/Unassigned"
+  DefaultProject/sample_0/sample_0
+  DefaultProject/sample_1/sample_1
+  DefaultProject/sample_2/sample_2
+  DefaultProject/sample_3/sample_3
+  DefaultProject/sample_4/sample_4
+)
+tree "$expected_out_dir"
+
+for sample in "${expected_samples[@]}"; do
+  for lane in "L1" "L2"; do 
+    for orientation in "R1" "R2"; do
+      assert_file_exists "$expected_out_dir/${sample}_${lane}_${orientation}.fastq.gz"
+    done
+  done
+done
+popd > /dev/null
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,9 +235,9 @@ build_info:
  output: "target/executable/agat/agat_convert_bed2gff"
  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -515,9 +515,9 @@ 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="2024-11-14T13:16:47Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:12Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,9 +225,9 @@ build_info:
  output: "target/executable/agat/agat_convert_embl2gff"
  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -505,9 +505,9 @@ 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="2024-11-14T13:16:49Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:14Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -230,9 +230,9 @@ build_info:
  output: "target/executable/agat/agat_convert_genscan2gff"
  executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
+++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
@@ -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_genscan2gff"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:50Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:14Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml
@@ -186,9 +186,9 @@ build_info:
  output: "target/executable/agat/agat_convert_mfannot2gff"
  executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff
+++ b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff
@@ -480,9 +480,9 @@ 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_mfannot2gff"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:02Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,9 +228,9 @@ 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"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -519,9 +519,9 @@ 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="2024-11-14T13:16:47Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:12Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,9 +188,9 @@ 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"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -484,9 +484,9 @@ 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="2024-11-14T13:16:48Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:13Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,9 +195,9 @@ 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"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -493,9 +493,9 @@ 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="2024-11-14T13:16:46Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
@@ -186,9 +186,9 @@ build_info:
  output: "target/executable/agat/agat_sp_add_introns"
  executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
+++ b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
@@ -479,9 +479,9 @@ 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_sp_add_introns"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:48Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:12Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
@@ -236,9 +236,9 @@ build_info:
  output: "target/executable/agat/agat_sp_filter_feature_from_kill_list"
  executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
+++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
@@ -517,9 +517,9 @@ 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_sp_filter_feature_from_kill_list"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:49Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:14Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
@@ -184,9 +184,9 @@ build_info:
  output: "target/executable/agat/agat_sp_merge_annotations"
  executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
+++ b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
@@ -482,9 +482,9 @@ 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_sp_merge_annotations"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:49Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:13Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
@@ -231,9 +231,9 @@ build_info:
  output: "target/executable/agat/agat_sp_statistics"
  executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics
+++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics
@@ -507,9 +507,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:48Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:13Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml
+++ b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml
@@ -227,9 +227,9 @@ build_info:
  output: "target/executable/agat/agat_sq_stat_basic"
  executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic
+++ b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic
@@ -507,9 +507,9 @@ 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_sq_stat_basic"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:02Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,9 +706,9 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -754,9 +754,9 @@ 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="2024-11-14T13:16:51Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:15Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bases2fastq/.config.vsh.yaml
+++ b/target/executable/bases2fastq/.config.vsh.yaml
@@ -0,0 +1,421 @@
+name: "bases2fastq"
+version: "main"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--analysis_directory"
+    description: "Location of analysis directory"
+    info: null
+    example:
+    - "input"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--run_manifest"
+    alternatives:
+    - "-r"
+    description: "Location of run manifest to use instead of default RunManifest.csv\
+      \ found in analysis directory"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_directory"
+    alternatives:
+    - "-o"
+    description: "Location to save output fastqs"
+    info: null
+    example:
+    - "fastq_dir"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--report"
+    description: "Output location for the HTML report"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--logs"
+    description: "Directory containing log files"
+    info: null
+    example:
+    - "logs_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--chemistry_version"
+    description: "Run parameters override, chemistry version."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--demux_only"
+    alternatives:
+    - "-d"
+    description: "Generate demux files and indexing stats without generating FASTQ\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--detect_adapters"
+    description: "Detect adapters sequences, overriding any sequences present in run\
+      \ manifest.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--error_on_missing"
+    description: "Terminate execution for a missing file (by default, missing files\
+      \ are\nskipped and execution continues). Also set by --strict.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--exclude_tile"
+    alternatives:
+    - "-e"
+    description: "Regex matching tile names to exclude. This flag can be specified\
+      \ multiple times. (e.g. L1.*C0[23]S.)\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--filter_mask"
+    description: "Run parameters override, custom pass filter mask.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--flowcell_id"
+    description: "Run parameters override, flowcell ID.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force_index_orientation"
+    description: "Do not attempt to find orientation for I1/I2 reads (reverse complement).\n\
+      Use orientation given in run manifest.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--group_fastq"
+    description: "Group all FASTQ/stats/metrics for a project are in the project folder.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--i1_cycles"
+    description: "Run parameters override, I1 cycles.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--i2_cycles"
+    description: "Run parameters override, I2 cycles\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--include_tile"
+    alternatives:
+    - "-i"
+    description: "Regex matching tile names to include. This flag\ncan be specified\
+      \ multiple times. (e.g. L1.*C0[23]S.)\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--kit_configuration"
+    description: "Run parameters override, kit configuration.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--legacy_fastq"
+    description: "Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--log_level"
+    alternatives:
+    - "-l"
+    description: "Severity level for logging.\n"
+    info: null
+    example:
+    - "INFO"
+    required: false
+    choices:
+    - "DEBUG"
+    - "INFO"
+    - "WARNING"
+    - "ERROR"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_error_on_invalid"
+    description: "Skip invalid files and continue execution. Overridden by --strict\
+      \ options\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_projects"
+    description: "Disable project directories\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--num_unassigned"
+    description: "Max Number of unassigned sequences to report.\n"
+    info: null
+    example:
+    - 30
+    required: false
+    min: 0
+    max: 1000
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--preparation_workflow"
+    description: "Run parameters override, preparation workflow. \n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--qc_only"
+    description: "Quickly generate run stats for single tile without generating FASTQ.\n\
+      Use --include_tile/--exclude_tile to define custom tile set.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--r1_cycles"
+    description: "Run parameters override, R1 cycles.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--r2_cycles"
+    description: "Run parameters override, R2 cycles.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--split_lanes"
+    description: "Split FASTQ files by lane.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--strict"
+    description: "In strict mode any invalid or missing input file will terminate\
+      \ execution \n(overrides no_error_on_invalid and sets --error_on_missing)\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences\
+  \ instruments and converts base calls into FASTQ files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "demultiplex"
+- "fastq"
+- "demux"
+- "Element Biosciences"
+license: "Proprietairy"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+  documentation: "https://docs.elembio.io/docs/bases2fastq/introduction/"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "elembio/bases2fastq:2.1.0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "tree"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bases2fastq: $(bases2fastq --version | cut -d' ' -f3)\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "curl"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bases2fastq/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bases2fastq"
+  executable: "target/executable/bases2fastq/bases2fastq"
+  viash_version: "0.9.0"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/bases2fastq/bases2fastq
+++ b/target/executable/bases2fastq/bases2fastq
--- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
@@ -368,9 +368,9 @@ build_info:
  output: "target/executable/bbmap/bbmap_bbsplit"
  executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
@@ -600,9 +600,9 @@ cp -r bbmap/* /usr/local/bin
 RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:51Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:15Z"
 LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -469,9 +469,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_annotate"
  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:00Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
@@ -335,9 +335,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_concat"
  executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_concat/bcftools_concat
+++ b/target/executable/bcftools/bcftools_concat/bcftools_concat
@@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_norm"
  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
@@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:00Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,9 +185,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -458,9 +458,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_stats"
  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,9 +418,9 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -599,9 +599,9 @@ 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="2024-11-14T13:16:57Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:21Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -274,9 +274,9 @@ 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"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- 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
@@ -554,9 +554,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /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="2024-11-14T13:17:01Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -1115,9 +1115,9 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
@@ -954,9 +954,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /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_sequence_analysis"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:01Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
@@ -235,9 +235,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bamtobed"
  executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
+++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
@@ -522,9 +522,9 @@ 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_bamtobed"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:58Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:21Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,9 +187,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bamtofastq"
  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -483,9 +483,9 @@ 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="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,9 +176,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -480,9 +480,9 @@ 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_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:00Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,9 +214,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bedtobam"
  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -496,9 +496,9 @@ 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="2024-11-14T13:17:01Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -337,9 +337,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -591,9 +591,9 @@ 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_genomecov"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:01Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,9 +232,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -526,9 +526,9 @@ 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="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,9 +273,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -552,9 +552,9 @@ 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_groupby"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:58Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,9 +410,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -633,9 +633,9 @@ 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="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,9 +210,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -500,9 +500,9 @@ 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_links"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:00Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,9 +279,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -558,9 +558,9 @@ 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_merge"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:01Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_sort"
  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -509,9 +509,9 @@ 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="2024-11-14T13:16:59Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,9 +158,9 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -475,9 +475,9 @@ 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="2024-11-14T13:16:57Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:21Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,9 +145,9 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -465,9 +465,9 @@ 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="2024-11-14T13:16:57Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:20Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -423,9 +423,9 @@ build_info:
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -632,9 +632,9 @@ 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="2024-11-14T13:16:57Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:20Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml
+++ b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml
@@ -195,9 +195,9 @@ build_info:
  output: "target/executable/cellranger/cellranger_mkref"
  executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/cellranger/cellranger_mkref/cellranger_mkref
+++ b/target/executable/cellranger/cellranger_mkref/cellranger_mkref
@@ -481,9 +481,9 @@ RUN apt-get update && \

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:57Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:21Z"
 LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,9 +740,9 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -831,9 +831,9 @@ 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="2024-11-14T13:16:52Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:16Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,9 +317,9 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -589,9 +589,9 @@ 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="2024-11-14T13:16:48Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:13Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1028,9 +1028,9 @@ 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="2024-11-14T13:17:02Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -340,9 +340,9 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -601,9 +601,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-11-14T13:17:03Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:26Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -754,9 +754,9 @@ 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="2024-11-14T13:16:46Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:11Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -190,9 +190,9 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -493,9 +493,9 @@ mv target/release/fq /usr/local/bin/ && \
 cd / && rm -rf /fq

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:55Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:19Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -807,9 +807,9 @@ 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="2024-11-14T13:16:50Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:14Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -218,9 +218,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -506,9 +506,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:49Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:14Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -246,9 +246,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -522,9 +522,9 @@ mv kallisto/kallisto /usr/local/bin/
 RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-11-14T13:16:49Z"
+LABEL org.opencontainers.image.created="2024-11-26T14:03:14Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="065297be5fb2d88020fc50e042bb3f49c9254ae9"
+LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,9 +507,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/Show More
+++ b/Show More