Build branch main with version main (b3fcd52)

Build pipeline: viash-hub.biobox.main-8bbc7 Source commit: b3fcd52f20 Source message: Fix multiple components (#162) * output index when only_build_index is true * fix threads option * fix argument type and add log * fix output handling * fix output arguments and update docker image * fix log2stderr argument and remove discard reads option * remove echo * update bbsplit build index test * add workdir * apply suggestions from code review * accept more than two reference files * update changelog * update changelog * remove indentation * minor fixes * fix descriptions --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
2024-11-08 09:40:57 +00:00
parent c71aa10adc
commit b77e39f22a
331 changed files with 1302 additions and 1206 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,18 @@

 * `cutadapt`: Fix the the non-functional `action` parameter (PR #161).

+* `bbmap_bbsplit`: Change argument type of `build` to `file` and add output argument `index` (PR #162).
+
+* `kallisto/kallisto_index`: Fix command script to use `--threads` option (PR #162).
+
+* `kallisto/kallisto_quant`: Change type of argument `output_dir` to `file` and add output argument `log` (PR #162).
+
+* `rsem/rsem_calculate_expression`: Fix output handling (PR #162).
+
+* `sortmerna`: Change type pf argument `aligned` to `file`; update docker image; accept more than two reference files (PR #162).
+
+* `umi_tools/umi_tools_extract`: Remove `umi_discard_reads` option and change `log2stderr` to input argument (PR #162).
+
 ## MINOR CHANGES

 * `agat_convert_bed2gff`: change type of argument `inflate_off` from `boolean_false` to `boolean_true` (PR #160).
@@ -38,6 +50,8 @@

 * Upgrade to Viash 0.9.0.

+* `bbmap_bbsplit`: Move to namespace `bbmap` (PR #162).
+
 # biobox 0.2.0

 ## BREAKING CHANGES
--- a/src/bbmap/bbmap_bbsplit/config.vsh.yaml
+++ b/src/bbmap/bbmap_bbsplit/config.vsh.yaml
@@ -30,12 +30,9 @@ argument_groups:
    type: boolean_true
    description: If set, only builds the index. Otherwise, mapping is performed.
  - name: "--build"
-    type: string
+    type: file
    description: |
-      Designate index to use. Corresponds to the number specified when building the index.
-      If building the index, this will be the build's id. If multiple references are indexed
-      in the same directory, each needs a unique build ID. Default: 1.
-    example: "1"
+      Index to be used for mapping. 
  - name: "--qin"
    type: string
    description: |
@@ -95,6 +92,12 @@ argument_groups:

 - name: "Output"
  arguments:
+  - name: "--index"
+    type: file
+    description: |
+      Location to write the index.
+    direction: output
+    example: BBSplit_index
  - name: "--fastq_1"
    type: file
    description: |
--- a/src/bbmap/bbmap_bbsplit/help.txt
+++ b/src/bbmap/bbmap_bbsplit/help.txt
--- a/src/bbmap/bbmap_bbsplit/script.sh
+++ b/src/bbmap/bbmap_bbsplit/script.sh
@@ -30,17 +30,17 @@ if [ ! -d "$par_build" ]; then
 fi

 if $par_only_build_index; then
-    if [ ${#refs[@]} -gt 1 ]; then
+    if [ "${#refs[@]}" -gt 1 ]; then
        bbsplit.sh \
            --ref_primary="$primary_ref" \
            "${refs[@]}" \
-            path=$par_build
+            path=$par_index
    else
        echo "ERROR: Please specify at least two reference fasta files."
    fi
 else
    IFS=";" read -ra input <<< "$par_input"
-    tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
+    tmpdir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")
    index_files=''
    if [ -d "$par_build" ]; then
        index_files="path=$par_build"
@@ -51,7 +51,7 @@ else
    fi

    extra_args=""
-    if [ -n "$par_refstats" ]; then extra_args+=" --refstats $par_refstats"; fi
+    if [ -f "$par_refstats" ]; then extra_args+=" --refstats $par_refstats"; fi
    if [ -n "$par_ambiguous" ]; then extra_args+=" --ambiguous $par_ambiguous"; fi
    if [ -n "$par_ambiguous2" ]; then extra_args+=" --ambiguous2 $par_ambiguous2"; fi
    if [ -n "$par_minratio" ]; then extra_args+=" --minratio $par_minratio"; fi
--- a/src/bbmap/bbmap_bbsplit/test.sh
+++ b/src/bbmap/bbmap_bbsplit/test.sh
@@ -55,7 +55,7 @@ echo ">>> Building BBSplit index"
 "${meta_executable}" \
  --ref "genome.fasta;human.fa;sarscov2.fa" \
  --only_build_index \
-  --build "BBSplit_index" 
+  --index "BBSplit_index" 

 echo ">>> Check whether output exists"
 [ ! -d "BBSplit_index" ] && echo "BBSplit index does not exist!" && exit 1
--- a/src/kallisto/kallisto_index/Kallisto
+++ b/src/kallisto/kallisto_index/Kallisto
--- a/src/kallisto/kallisto_index/script.sh
+++ b/src/kallisto/kallisto_index/script.sh
@@ -28,7 +28,7 @@ kallisto index \
    ${par_min_size:+--min-size "${par_min_size}"} \
    ${par_ec_max_size:+--ec-max-size "${par_ec_max_size}"} \
    ${par_d_list:+--d-list "${par_d_list}"} \
-    ${meta_cpus:+--cpu "${meta_cpus}"} \
+    ${meta_cpus:+--threads "${meta_cpus}"} \
    ${par_tmp:+--tmp "${par_tmp}"} \
    "${par_input}"

--- a/src/kallisto/kallisto_quant/config.vsh.yaml
+++ b/src/kallisto/kallisto_quant/config.vsh.yaml
@@ -32,9 +32,15 @@ argument_groups:
  arguments:
  - name: "--output_dir"
    alternatives: ["-o"]
-    type: string
+    type: file
    description: Directory to write output to.
    required: true
+    direction: output
+  - name: "--log"
+    type: file
+    description: File containing log information from running kallisto quant
+    direction: output
+

 - name: "Options"
  arguments:
--- a/src/kallisto/kallisto_quant/script.sh
+++ b/src/kallisto/kallisto_quant/script.sh
@@ -41,6 +41,4 @@ kallisto quant \
    ${par_sd:+--sd "${par_sd}"} \
    ${par_seed:+--seed "${par_seed}"} \
    -o $par_output_dir \
-    ${input[*]}
-
-
+    ${input[*]} 2> >(tee -a $par_log >&2)
--- a/src/rsem/rsem_calculate_expression/script.sh
+++ b/src/rsem/rsem_calculate_expression/script.sh
@@ -5,13 +5,6 @@

 set -eo pipefail

-function clean_up {
-    rm -rf "$tmpdir"
-}
-trap clean_up EXIT
-
-tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
-
 if [ "$par_strandedness" == 'forward' ]; then
    strandedness='--strandedness forward'
 elif [ "$par_strandedness" == 'reverse' ]; then
@@ -22,14 +15,14 @@ fi

 IFS=";" read -ra input <<< $par_input

-INDEX=$(find -L $meta_resources_dir/$par_index -name "*.grp" | sed 's/\.grp$//')
+INDEX=$(find -L $par_index -name "*.grp" | sed 's/\.grp$//')

 unset_if_false=( par_paired par_quiet par_no_bam_output par_sampling_for_bam par_no_qualities 
                 par_alignments par_bowtie2 par_star par_hisat2_hca par_append_names 
                 par_single_cell_prior par_calc_pme par_calc_ci par_phred64_quals 
                 par_solexa_quals par_star_gzipped_read_file par_star_bzipped_read_file 
                 par_star_output_genome_bam par_estimate_rspd par_keep_intermediate_files 
-                 par_time par_run_pRSEM par_cap_stacked_chipseq_reads par_sort_bam_by_read_name )
+                 par_time par_run_pRSEM par_cap_stacked_chipseq_reads par_sort_bam_by_read_name par_sort_bam_by_coordinate )

 for par in ${unset_if_false[@]}; do
    test_val="${!par}"
@@ -60,12 +53,7 @@ rsem-calculate-expression \
    ${par_run_pRSEM:+--run-pRSEM} \
    ${par_cap_stacked_chipseq_reads:+--cap-stacked-chipseq-reads} \
    ${par_sort_bam_by_read_name:+--sort-bam-by-read-name} \
-    ${par_counts_gene:+--counts-gene "$par_counts_gene"} \
-    ${par_counts_transcripts:+--counts-transcripts "$par_counts_transcripts"} \
-    ${par_stat:+--stat "$par_stat"} \
-    ${par_bam_star:+--bam-star "$par_bam_star"} \
-    ${par_bam_genome:+--bam-genome "$par_bam_genome"} \
-    ${par_bam_transcript:+--bam-transcript "$par_bam_transcript"} \
+    ${par_sort_bam_by_coordinate:+--sort-bam-by-coordinate} \
    ${par_fai:+--fai "$par_fai"} \
    ${par_seed:+--seed "$par_seed"} \
    ${par_seed_length:+--seed-length "$par_seed_length"} \
@@ -101,3 +89,10 @@ rsem-calculate-expression \
    $INDEX \
    $par_id
   
+[[ -f "${par_id}.genes.results" ]] && mv "${par_id}.genes.results" $par_counts_gene
+[[ -f "${par_id}.isoforms.results" ]] && mv "${par_id}.isoforms.results" $par_counts_transcripts
+[[ -d "${par_id}.stat" ]] && mv "${par_id}.stat" $par_stat
+[[ -f "${par_id}.log" ]] && mv "${par_id}.log" $par_logs
+[[ -f "${par_id}.STAR.genome.bam" ]] && mv "${par_id}.STAR.genome.bam" $par_bam_star
+[[ -f "${par_id}.genome.bam" ]] && mv "${par_id}.genome.bam" $par_bam_genome
+[[ -f "${par_id}.transcript.bam" ]] && mv "${par_id}.transcript.bam" $par_bam_transcript
--- a/src/sortmerna/config.vsh.yaml
+++ b/src/sortmerna/config.vsh.yaml
@@ -42,15 +42,17 @@ argument_groups:
    description: Sortmerna log file.
  - name: "--output"
    alternatives: ["--aligned"]
-    type: string
+    type: file
    description: |
      Directory and file prefix for aligned output. The appropriate extension: 
      (fasta|fastq|blast|sam|etc) is automatically added.
      If 'dir' is not specified, the output is created in the WORKDIR/out/.
      If 'pfx' is not specified, the prefix 'aligned' is used.
+    direction: output
  - name: "--other"
-    type: string
-    description: Create Non-aligned reads output file with this path/prefix. Must be used with fastx. 
+    type: file
+    description: Create Non-aligned reads output file with this path/prefix. Must be used with fastx.
+    direction: output

 - name: "Options"
  arguments:
@@ -91,7 +93,7 @@ argument_groups:
    type: integer
    description: |
      search all alignments having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is
-      computed using seeds’ positions to expand hits into longer matches prior to Smith-Waterman alignment. Default: '2'.
+      computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. Default: '2'.
    example: 2
  - name: "--print_all_reads"
    type: boolean_true
@@ -152,7 +154,7 @@ argument_groups:
  - name: "--N"
    type: integer
    description: |
-      Smith-Waterman penalty for ambiguous letters (N’s) scored as --mismatch. Default: '-1'.\
+      Smith-Waterman penalty for ambiguous letters (N's) scored as --mismatch. Default: '-1'.
    example: -1
  - name: "--a"
    type: integer
@@ -207,7 +209,7 @@ argument_groups:
    - name: "--otu_map"
      type: boolean_true
      description: |
-        Output OTU map (input to QIIME’s make_otu_table.py).
+        Output OTU map (input to QIIME's make_otu_table.py).

 - name: "Advanced options"
  arguments:
@@ -226,7 +228,7 @@ argument_groups:
    description: |
      The number (or percentage if followed by %) of nucleotides to add to each edge of the alignment region on the
      reference sequence before performing Smith-Waterman alignment. Default: '4'.
-    example: 4
+    example: "4"
  - name: "--full_search"
    type: boolean_true
    description: |
@@ -263,8 +265,6 @@ argument_groups:
      Maximum number of positions to store for each unique L-mer. Set to 0 to store all positions. Default: '1000'
    example: 1000
  
-  
-
 resources:
  - type: bash_script
    path: script.sh
@@ -276,15 +276,12 @@ test_resources:
  
 engines:
 - type: docker
-  image: ubuntu:22.04
+  image: quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
  setup: 
    - type: docker
      run: |
-        apt-get update && \
-        apt-get install -y --no-install-recommends gzip cmake g++ wget && \
-        apt-get clean && \
-        wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/download/v4.3.6/sortmerna-4.3.6-Linux.sh && \
-        bash sortmerna-4.3.6-Linux.sh --skip-license
+        echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`
+
 runners: 
 - type: executable
- type: nextflow 
+- type: nextflow
--- a/src/sortmerna/script.sh
+++ b/src/sortmerna/script.sh
@@ -37,16 +37,11 @@ if [[ ! -z "$par_ribo_database_manifest" ]]; then

 elif [[ ! -z "$par_ref" ]]; then
    IFS=";" read -ra ref <<< "$par_ref"
-    # check if length is 2 and par_paired is set to true
-    if [[ "${#ref[@]}" -eq 2 && "$par_paired" == "true" ]]; then
-        refs="--ref ${ref[0]} --ref ${ref[1]}"
-    # check if length is 1 and par_paired is set to false
-    elif [[ "${#ref[@]}" -eq 1 && "$par_paired" == "false" ]]; then
-            refs="--ref $par_ref"      
-    else # if one reference provided but paired is set to true:
-        echo "Two reference fasta files are required for paired-end reads"
-            exit 1
-    fi
+    for i in "${ref[@]}"
+    do
+        refs+="-ref $i "
+    done
+
 else 
    echo "No reference fasta file(s) provided"
    exit 1
--- a/src/sortmerna/test.sh
+++ b/src/sortmerna/test.sh
@@ -31,7 +31,7 @@ rm -f rRNA_reads_fwd.fq.gz rRNA_reads_rev.fq.gz non_rRNA_reads_fwd.fq.gz non_rRN
 rm -rf kvdb/

 ################################################################################
-echo ">>> Testing for paired-end reads and --ref and --paired_out argumens"
+echo ">>> Testing for paired-end reads and --ref and --paired_out arguments"
 "$meta_executable" \
    --output "rRNA_reads" \
    --other "non_rRNA_reads" \
--- a/src/umi_tools/umi_tools_extract/config.vsh.yaml
+++ b/src/umi_tools/umi_tools_extract/config.vsh.yaml
@@ -128,12 +128,6 @@ argument_groups:
        Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying
        the reads with the same mapping position, but treat similar yet nonidentical UMIs differently. Default: `directional`
      example: "directional"
-    - name: --umi_discard_read
-      type: integer
-      choices: [0, 1, 2]
-      description: |
-        After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`
-      example: 0

  - name: Common Options
    arguments:
@@ -144,7 +138,6 @@ argument_groups:
    - name: --log2stderr
      type: boolean_true
      description: Send logging information to stderr.
-      direction: output
    - name: --verbose
      type: integer
      description: Log level. The higher, the more output.
--- a/src/umi_tools/umi_tools_extract/script.sh
+++ b/src/umi_tools/umi_tools_extract/script.sh
@@ -82,12 +82,3 @@ umi_tools extract \
    ${par_log2stderr:+--log2stderr} \
    ${par_verbose:+--verbose "$par_verbose"} \
    ${par_error:+--error "$par_error"}
-
-
-if [ "$par_umi_discard_read" == 1 ]; then
-    # discard read 1
-    rm "$par_read1_out"
-elif [ "$par_umi_discard_read" == 2 ]; then
-    # discard read 2 (-f to bypass file existence check)
-    rm -f "$par_read2_out"
-fi
--- 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:08Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:29Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:11Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:31Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:11Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:32Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:23Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:43Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:09Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:30Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:09Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:30Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:23Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:28Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:09Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:30Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:11Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:32Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:10Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:31Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:10Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:31Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:23Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:43Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:12Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:33Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
@@ -46,15 +46,12 @@ argument_groups:
    description: "If set, only builds the index. Otherwise, mapping is performed."
    info: null
    direction: "input"
-  - type: "string"
+  - type: "file"
    name: "--build"
-    description: "Designate index to use. Corresponds to the number specified when\
-      \ building the index.\nIf building the index, this will be the build's id. If\
-      \ multiple references are indexed\nin the same directory, each needs a unique\
-      \ build ID. Default: 1.\n"
+    description: "Index to be used for mapping. \n"
    info: null
-    example:
-    - "1"
+    must_exist: true
+    create_parent: true
    required: false
    direction: "input"
    multiple: false
@@ -168,6 +165,18 @@ argument_groups:
    direction: "input"
 - name: "Output"
  arguments:
+  - type: "file"
+    name: "--index"
+    description: "Location to write the index.\n"
+    info: null
+    example:
+    - "BBSplit_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
  - type: "file"
    name: "--fastq_1"
    description: "Output file for read 1.\n"
@@ -353,15 +362,15 @@ engines:
 - type: "native"
  id: "native"
 build_info:
-  config: "src/bbmap_bbsplit/config.vsh.yaml"
+  config: "src/bbmap/bbmap_bbsplit/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bbmap/bbmap_bbsplit"
  executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
@@ -199,13 +199,8 @@ function ViashHelp {
  echo "        If set, only builds the index. Otherwise, mapping is performed."
  echo ""
  echo "    --build"
-  echo "        type: string"
-  echo "        example: 1"
-  echo "        Designate index to use. Corresponds to the number specified when"
-  echo "        building the index."
-  echo "        If building the index, this will be the build's id. If multiple"
-  echo "        references are indexed"
-  echo "        in the same directory, each needs a unique build ID. Default: 1."
+  echo "        type: file, file must exist"
+  echo "        Index to be used for mapping."
  echo ""
  echo "    --qin"
  echo "        type: string"
@@ -277,6 +272,11 @@ function ViashHelp {
  echo "        cigar strings."
  echo ""
  echo "Output:"
+  echo "    --index"
+  echo "        type: file, output, file must exist"
+  echo "        example: BBSplit_index"
+  echo "        Location to write the index."
+  echo ""
  echo "    --fastq_1"
  echo "        type: file, output, file must exist"
  echo "        example: read_out1.fastq"
@@ -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="2024-11-02T09:32:13Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:33Z"
 LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -895,6 +895,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_UNTRIM=true
            shift 1
            ;;
+        --index)
+            [ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INDEX="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --index. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --index=*)
+            [ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index=*\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INDEX=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --fastq_1)
            [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_1="$2"
@@ -1211,6 +1222,10 @@ if [ ! -z "$VIASH_PAR_REF" ]; then
  done
  set +f
 fi
+if [ ! -z "$VIASH_PAR_BUILD" ] && [ ! -e "$VIASH_PAR_BUILD" ]; then
+  ViashError "Input file '$VIASH_PAR_BUILD' does not exist."
+  exit 1
+fi

 # check whether parameters values are of the right type
 if [[ -n "$VIASH_PAR_PAIRED" ]]; then
@@ -1372,6 +1387,9 @@ if [ ! -z "$VIASH_PAR_QTRIM" ]; then
 fi

 # create parent directories of output files, if so desired
+if [ ! -z "$VIASH_PAR_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_INDEX")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_INDEX")"
+fi
 if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_1")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_FASTQ_1")"
 fi
@@ -1422,6 +1440,15 @@ if [ ! -z "$VIASH_PAR_REF" ]; then
  done
  VIASH_PAR_REF=$(IFS=';' ; echo "${VIASH_TEST_REF[*]}")
 fi
+if [ ! -z "$VIASH_PAR_BUILD" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BUILD")" )
+  VIASH_PAR_BUILD=$(ViashDockerAutodetectMount "$VIASH_PAR_BUILD")
+fi
+if [ ! -z "$VIASH_PAR_INDEX" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
+  VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_INDEX" )
+fi
 if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_1")" )
  VIASH_PAR_FASTQ_1=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_1")
@@ -1533,6 +1560,7 @@ $( if [ ! -z ${VIASH_PAR_AMBIGUOUS+x} ]; then echo "${VIASH_PAR_AMBIGUOUS}" | se
 $( if [ ! -z ${VIASH_PAR_AMBIGUOUS2+x} ]; then echo "${VIASH_PAR_AMBIGUOUS2}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous2='&'#" ; else echo "# par_ambiguous2="; fi )
 $( if [ ! -z ${VIASH_PAR_QTRIM+x} ]; then echo "${VIASH_PAR_QTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_qtrim='&'#" ; else echo "# par_qtrim="; fi )
 $( if [ ! -z ${VIASH_PAR_UNTRIM+x} ]; then echo "${VIASH_PAR_UNTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_untrim='&'#" ; else echo "# par_untrim="; fi )
+$( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
 $( if [ ! -z ${VIASH_PAR_FASTQ_1+x} ]; then echo "${VIASH_PAR_FASTQ_1}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_1='&'#" ; else echo "# par_fastq_1="; fi )
 $( if [ ! -z ${VIASH_PAR_FASTQ_2+x} ]; then echo "${VIASH_PAR_FASTQ_2}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_2='&'#" ; else echo "# par_fastq_2="; fi )
 $( if [ ! -z ${VIASH_PAR_SAM2BAM+x} ]; then echo "${VIASH_PAR_SAM2BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_sam2bam='&'#" ; else echo "# par_sam2bam="; fi )
@@ -1588,17 +1616,17 @@ if [ ! -d "\$par_build" ]; then
 fi

 if \$par_only_build_index; then
-    if [ \${#refs[@]} -gt 1 ]; then
+    if [ "\${#refs[@]}" -gt 1 ]; then
        bbsplit.sh \\
            --ref_primary="\$primary_ref" \\
            "\${refs[@]}" \\
-            path=\$par_build
+            path=\$par_index
    else
        echo "ERROR: Please specify at least two reference fasta files."
    fi
 else
    IFS=";" read -ra input <<< "\$par_input"
-    tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_functionality_name-XXXXXXXX")
+    tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
    index_files=''
    if [ -d "\$par_build" ]; then
        index_files="path=\$par_build"
@@ -1609,7 +1637,7 @@ else
    fi

    extra_args=""
-    if [ -n "\$par_refstats" ]; then extra_args+=" --refstats \$par_refstats"; fi
+    if [ -f "\$par_refstats" ]; then extra_args+=" --refstats \$par_refstats"; fi
    if [ -n "\$par_ambiguous" ]; then extra_args+=" --ambiguous \$par_ambiguous"; fi
    if [ -n "\$par_ambiguous2" ]; then extra_args+=" --ambiguous2 \$par_ambiguous2"; fi
    if [ -n "\$par_minratio" ]; then extra_args+=" --minratio \$par_minratio"; fi
@@ -1683,6 +1711,12 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
    done
    VIASH_PAR_REF="$VIASH_TEST_REF"
  fi
+  if [ ! -z "$VIASH_PAR_BUILD" ]; then
+    VIASH_PAR_BUILD=$(ViashDockerStripAutomount "$VIASH_PAR_BUILD")
+  fi
+  if [ ! -z "$VIASH_PAR_INDEX" ]; then
+    VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
+  fi
  if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then
    VIASH_PAR_FASTQ_1=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_1")
  fi
@@ -1714,6 +1748,10 @@ fi


 # check whether required files exist
+if [ ! -z "$VIASH_PAR_INDEX" ] && [ ! -e "$VIASH_PAR_INDEX" ]; then
+  ViashError "Output file '$VIASH_PAR_INDEX' does not exist."
+  exit 1
+fi
 if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then
  ViashError "Output file '$VIASH_PAR_FASTQ_1' does not exist."
  exit 1
--- 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:22Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:21Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:21Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:20Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:21Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:19Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:23Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:42Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:22Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:42Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:19Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:39Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:20Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:21Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:22Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:22Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:20Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:19Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:21Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:21Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:22Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:20Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:19Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:39Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:18Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:38Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:18Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:38Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:14Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:34Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:10Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:31Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:23Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:42Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:24Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:44Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:08Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:28Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-11-02T09:32:17Z"
+LABEL org.opencontainers.image.created="2024-11-08T09:17:37Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="06005a79b49911f1197ccfddf066fc566d5b1def"
+LABEL org.opencontainers.image.revision="b3fcd52f2039056907160baf85fd84ac9c5b96be"
 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: "06005a79b49911f1197ccfddf066fc566d5b1def"
-  git_remote: "https://x-access-token:ghs_s2VchCFPnGFkJ2bOWXBcoeam5dPxgi4UR0W2@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-22-g06005a7"
+  git_commit: "b3fcd52f2039056907160baf85fd84ac9c5b96be"
+  git_remote: "https://x-access-token:ghs_ZC0rzL9dZoRAoQQFaSrx6tuZSkKgI83FPAmh@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-23-gb3fcd52"
 package_config:
  name: "biobox"
  version: "main"
--- a/Show More
+++ b/Show More