From 55de3a494d7cbc20b97331afdff475e8b2850108 Mon Sep 17 00:00:00 2001
From: CI <toni@data-intuitive.com>
Date: Wed, 16 Oct 2024 09:18:30 +0000
Subject: [PATCH] Build branch main with version main (86333c1)

Build pipeline: meta-vsh-ci-template-tpwsr

Source commit: https://github.com/viash-hub/biobox/commit/86333c1a465db45facd936695f1f33b186ccf0fc

Source message: SnpEff (#153)

* Help file

* config file

* config file

* runners script

* config file

* test script

* test

* test

* runners script

* snake case

* snake case

* output parameters

* modify argument formatting, container setup

* fix buf with mv command

* avoid boolean_false and fix bug with output files

---------

Co-authored-by: Emma Rousseau <emmarou1@icloud.com>
---
 src/snpeff/config.vsh.yaml                    |  297 ++
 src/snpeff/help.txt                           |   79 +
 src/snpeff/script.sh                          |  148 +
 src/snpeff/test.sh                            |  129 +
 src/snpeff/test_data/cancer.vcf               |    2 +
 src/snpeff/test_data/my_annotations.bed       |    1 +
 src/snpeff/test_data/script.sh                |   15 +
 src/snpeff/test_data/test.vcf                 |    1 +
 .../agat_convert_bed2gff/.config.vsh.yaml     |    6 +-
 .../agat_convert_bed2gff/agat_convert_bed2gff |    4 +-
 .../agat_convert_embl2gff/.config.vsh.yaml    |    6 +-
 .../agat_convert_embl2gff                     |    4 +-
 .../agat_convert_genscan2gff/.config.vsh.yaml |    6 +-
 .../agat_convert_genscan2gff                  |    4 +-
 .../agat_convert_sp_gff2gtf/.config.vsh.yaml  |    6 +-
 .../agat_convert_sp_gff2gtf                   |    4 +-
 .../agat_convert_sp_gff2tsv/.config.vsh.yaml  |    6 +-
 .../agat_convert_sp_gff2tsv                   |    4 +-
 .../agat_convert_sp_gxf2gxf/.config.vsh.yaml  |    6 +-
 .../agat_convert_sp_gxf2gxf                   |    4 +-
 target/executable/arriba/.config.vsh.yaml     |    6 +-
 target/executable/arriba/arriba               |    4 +-
 .../bcftools_annotate/.config.vsh.yaml        |    6 +-
 .../bcftools_annotate/bcftools_annotate       |    4 +-
 .../bcftools/bcftools_concat/.config.vsh.yaml |    6 +-
 .../bcftools/bcftools_concat/bcftools_concat  |    4 +-
 .../bcftools/bcftools_norm/.config.vsh.yaml   |    6 +-
 .../bcftools/bcftools_norm/bcftools_norm      |    4 +-
 .../bcftools/bcftools_sort/.config.vsh.yaml   |    6 +-
 .../bcftools/bcftools_sort/bcftools_sort      |    4 +-
 .../bcftools/bcftools_stats/.config.vsh.yaml  |    6 +-
 .../bcftools/bcftools_stats/bcftools_stats    |    4 +-
 .../executable/bcl_convert/.config.vsh.yaml   |    6 +-
 target/executable/bcl_convert/bcl_convert     |    4 +-
 .../.config.vsh.yaml                          |    6 +-
 .../bd_rhapsody_make_reference                |    4 +-
 .../.config.vsh.yaml                          |    6 +-
 .../bd_rhapsody_sequence_analysis             |    4 +-
 .../bedtools_bamtofastq/.config.vsh.yaml      |    6 +-
 .../bedtools_bamtofastq/bedtools_bamtofastq   |    4 +-
 .../bedtools_bed12tobed6/.config.vsh.yaml     |    6 +-
 .../bedtools_bed12tobed6/bedtools_bed12tobed6 |    4 +-
 .../bedtools_bedtobam/.config.vsh.yaml        |    6 +-
 .../bedtools_bedtobam/bedtools_bedtobam       |    4 +-
 .../bedtools_genomecov/.config.vsh.yaml       |    6 +-
 .../bedtools_genomecov/bedtools_genomecov     |    4 +-
 .../bedtools_getfasta/.config.vsh.yaml        |    6 +-
 .../bedtools_getfasta/bedtools_getfasta       |    4 +-
 .../bedtools_groupby/.config.vsh.yaml         |    6 +-
 .../bedtools_groupby/bedtools_groupby         |    4 +-
 .../bedtools_intersect/.config.vsh.yaml       |    6 +-
 .../bedtools_intersect/bedtools_intersect     |    4 +-
 .../bedtools/bedtools_links/.config.vsh.yaml  |    6 +-
 .../bedtools/bedtools_links/bedtools_links    |    4 +-
 .../bedtools/bedtools_merge/.config.vsh.yaml  |    6 +-
 .../bedtools/bedtools_merge/bedtools_merge    |    4 +-
 .../bedtools/bedtools_sort/.config.vsh.yaml   |    6 +-
 .../bedtools/bedtools_sort/bedtools_sort      |    4 +-
 .../busco_download_datasets/.config.vsh.yaml  |    6 +-
 .../busco_download_datasets                   |    4 +-
 .../busco_list_datasets/.config.vsh.yaml      |    6 +-
 .../busco_list_datasets/busco_list_datasets   |    4 +-
 .../busco/busco_run/.config.vsh.yaml          |    6 +-
 target/executable/busco/busco_run/busco_run   |    4 +-
 target/executable/cutadapt/.config.vsh.yaml   |    6 +-
 target/executable/cutadapt/cutadapt           |    4 +-
 target/executable/falco/.config.vsh.yaml      |    6 +-
 target/executable/falco/falco                 |    4 +-
 target/executable/fastp/.config.vsh.yaml      |    6 +-
 target/executable/fastp/fastp                 |    4 +-
 target/executable/fastqc/.config.vsh.yaml     |    6 +-
 target/executable/fastqc/fastqc               |    4 +-
 .../executable/featurecounts/.config.vsh.yaml |    6 +-
 target/executable/featurecounts/featurecounts |    4 +-
 .../executable/fq_subsample/.config.vsh.yaml  |    6 +-
 target/executable/fq_subsample/fq_subsample   |    4 +-
 target/executable/gffread/.config.vsh.yaml    |    6 +-
 target/executable/gffread/gffread             |    4 +-
 .../kallisto/kallisto_index/.config.vsh.yaml  |    6 +-
 .../kallisto/kallisto_index/kallisto_index    |    4 +-
 .../kallisto/kallisto_quant/.config.vsh.yaml  |    6 +-
 .../kallisto/kallisto_quant/kallisto_quant    |    4 +-
 .../lofreq/lofreq_call/.config.vsh.yaml       |    6 +-
 .../executable/lofreq/lofreq_call/lofreq_call |    4 +-
 .../lofreq/lofreq_indelqual/.config.vsh.yaml  |    6 +-
 .../lofreq/lofreq_indelqual/lofreq_indelqual  |    4 +-
 target/executable/multiqc/.config.vsh.yaml    |    6 +-
 target/executable/multiqc/multiqc             |    4 +-
 target/executable/pear/.config.vsh.yaml       |    6 +-
 target/executable/pear/pear                   |    4 +-
 .../qualimap/qualimap_rnaseq/.config.vsh.yaml |    6 +-
 .../qualimap/qualimap_rnaseq/qualimap_rnaseq  |    4 +-
 .../.config.vsh.yaml                          |    6 +-
 .../rsem_calculate_expression                 |    4 +-
 .../rsem_prepare_reference/.config.vsh.yaml   |    6 +-
 .../rsem_prepare_reference                    |    4 +-
 .../salmon/salmon_index/.config.vsh.yaml      |    6 +-
 .../salmon/salmon_index/salmon_index          |    4 +-
 .../salmon/salmon_quant/.config.vsh.yaml      |    6 +-
 .../salmon/salmon_quant/salmon_quant          |    4 +-
 .../samtools_collate/.config.vsh.yaml         |    6 +-
 .../samtools_collate/samtools_collate         |    4 +-
 .../samtools/samtools_faidx/.config.vsh.yaml  |    6 +-
 .../samtools/samtools_faidx/samtools_faidx    |    4 +-
 .../samtools/samtools_fasta/.config.vsh.yaml  |    6 +-
 .../samtools/samtools_fasta/samtools_fasta    |    4 +-
 .../samtools/samtools_fastq/.config.vsh.yaml  |    6 +-
 .../samtools/samtools_fastq/samtools_fastq    |    4 +-
 .../samtools_flagstat/.config.vsh.yaml        |    6 +-
 .../samtools_flagstat/samtools_flagstat       |    4 +-
 .../samtools_idxstats/.config.vsh.yaml        |    6 +-
 .../samtools_idxstats/samtools_idxstats       |    4 +-
 .../samtools/samtools_index/.config.vsh.yaml  |    6 +-
 .../samtools/samtools_index/samtools_index    |    4 +-
 .../samtools/samtools_sort/.config.vsh.yaml   |    6 +-
 .../samtools/samtools_sort/samtools_sort      |    4 +-
 .../samtools/samtools_stats/.config.vsh.yaml  |    6 +-
 .../samtools/samtools_stats/samtools_stats    |    4 +-
 .../samtools/samtools_view/.config.vsh.yaml   |    6 +-
 .../samtools/samtools_view/samtools_view      |    4 +-
 .../seqtk/seqtk_sample/.config.vsh.yaml       |    6 +-
 .../seqtk/seqtk_sample/seqtk_sample           |    4 +-
 .../seqtk/seqtk_subseq/.config.vsh.yaml       |    6 +-
 .../seqtk/seqtk_subseq/seqtk_subseq           |    4 +-
 target/executable/snpeff/.config.vsh.yaml     |  655 +++
 target/executable/snpeff/snpeff               | 2656 ++++++++++
 target/executable/sortmerna/.config.vsh.yaml  |    6 +-
 target/executable/sortmerna/sortmerna         |    4 +-
 .../star/star_align_reads/.config.vsh.yaml    |    6 +-
 .../star/star_align_reads/star_align_reads    |    4 +-
 .../star_genome_generate/.config.vsh.yaml     |    6 +-
 .../star_genome_generate/star_genome_generate |    4 +-
 target/executable/trimgalore/.config.vsh.yaml |    6 +-
 target/executable/trimgalore/trimgalore       |    4 +-
 .../umi_tools_dedup/.config.vsh.yaml          |    6 +-
 .../umi_tools/umi_tools_dedup/umi_tools_dedup |    4 +-
 .../umi_tools_extract/.config.vsh.yaml        |    6 +-
 .../umi_tools_extract/umi_tools_extract       |    4 +-
 .../umi_tools_prepareforrsem/.config.vsh.yaml |    6 +-
 .../umi_tools_prepareforrsem                  |    4 +-
 .../agat_convert_bed2gff/.config.vsh.yaml     |    6 +-
 .../agat/agat_convert_bed2gff/main.nf         |    6 +-
 .../agat_convert_embl2gff/.config.vsh.yaml    |    6 +-
 .../agat/agat_convert_embl2gff/main.nf        |    6 +-
 .../agat_convert_genscan2gff/.config.vsh.yaml |    6 +-
 .../agat/agat_convert_genscan2gff/main.nf     |    6 +-
 .../agat_convert_sp_gff2gtf/.config.vsh.yaml  |    6 +-
 .../agat/agat_convert_sp_gff2gtf/main.nf      |    6 +-
 .../agat_convert_sp_gff2tsv/.config.vsh.yaml  |    6 +-
 .../agat/agat_convert_sp_gff2tsv/main.nf      |    6 +-
 .../agat_convert_sp_gxf2gxf/.config.vsh.yaml  |    6 +-
 .../agat/agat_convert_sp_gxf2gxf/main.nf      |    6 +-
 target/nextflow/arriba/.config.vsh.yaml       |    6 +-
 target/nextflow/arriba/main.nf                |    6 +-
 .../bcftools_annotate/.config.vsh.yaml        |    6 +-
 .../bcftools/bcftools_annotate/main.nf        |    6 +-
 .../bcftools/bcftools_concat/.config.vsh.yaml |    6 +-
 .../nextflow/bcftools/bcftools_concat/main.nf |    6 +-
 .../bcftools/bcftools_norm/.config.vsh.yaml   |    6 +-
 .../nextflow/bcftools/bcftools_norm/main.nf   |    6 +-
 .../bcftools/bcftools_sort/.config.vsh.yaml   |    6 +-
 .../nextflow/bcftools/bcftools_sort/main.nf   |    6 +-
 .../bcftools/bcftools_stats/.config.vsh.yaml  |    6 +-
 .../nextflow/bcftools/bcftools_stats/main.nf  |    6 +-
 target/nextflow/bcl_convert/.config.vsh.yaml  |    6 +-
 target/nextflow/bcl_convert/main.nf           |    6 +-
 .../.config.vsh.yaml                          |    6 +-
 .../bd_rhapsody_make_reference/main.nf        |    6 +-
 .../.config.vsh.yaml                          |    6 +-
 .../bd_rhapsody_sequence_analysis/main.nf     |    6 +-
 .../bedtools_bamtofastq/.config.vsh.yaml      |    6 +-
 .../bedtools/bedtools_bamtofastq/main.nf      |    6 +-
 .../bedtools_bed12tobed6/.config.vsh.yaml     |    6 +-
 .../bedtools/bedtools_bed12tobed6/main.nf     |    6 +-
 .../bedtools_bedtobam/.config.vsh.yaml        |    6 +-
 .../bedtools/bedtools_bedtobam/main.nf        |    6 +-
 .../bedtools_genomecov/.config.vsh.yaml       |    6 +-
 .../bedtools/bedtools_genomecov/main.nf       |    6 +-
 .../bedtools_getfasta/.config.vsh.yaml        |    6 +-
 .../bedtools/bedtools_getfasta/main.nf        |    6 +-
 .../bedtools_groupby/.config.vsh.yaml         |    6 +-
 .../bedtools/bedtools_groupby/main.nf         |    6 +-
 .../bedtools_intersect/.config.vsh.yaml       |    6 +-
 .../bedtools/bedtools_intersect/main.nf       |    6 +-
 .../bedtools/bedtools_links/.config.vsh.yaml  |    6 +-
 .../nextflow/bedtools/bedtools_links/main.nf  |    6 +-
 .../bedtools/bedtools_merge/.config.vsh.yaml  |    6 +-
 .../nextflow/bedtools/bedtools_merge/main.nf  |    6 +-
 .../bedtools/bedtools_sort/.config.vsh.yaml   |    6 +-
 .../nextflow/bedtools/bedtools_sort/main.nf   |    6 +-
 .../busco_download_datasets/.config.vsh.yaml  |    6 +-
 .../busco/busco_download_datasets/main.nf     |    6 +-
 .../busco_list_datasets/.config.vsh.yaml      |    6 +-
 .../busco/busco_list_datasets/main.nf         |    6 +-
 .../nextflow/busco/busco_run/.config.vsh.yaml |    6 +-
 target/nextflow/busco/busco_run/main.nf       |    6 +-
 target/nextflow/cutadapt/.config.vsh.yaml     |    6 +-
 target/nextflow/cutadapt/main.nf              |    6 +-
 target/nextflow/falco/.config.vsh.yaml        |    6 +-
 target/nextflow/falco/main.nf                 |    6 +-
 target/nextflow/fastp/.config.vsh.yaml        |    6 +-
 target/nextflow/fastp/main.nf                 |    6 +-
 target/nextflow/fastqc/.config.vsh.yaml       |    6 +-
 target/nextflow/fastqc/main.nf                |    6 +-
 .../nextflow/featurecounts/.config.vsh.yaml   |    6 +-
 target/nextflow/featurecounts/main.nf         |    6 +-
 target/nextflow/fq_subsample/.config.vsh.yaml |    6 +-
 target/nextflow/fq_subsample/main.nf          |    6 +-
 target/nextflow/gffread/.config.vsh.yaml      |    6 +-
 target/nextflow/gffread/main.nf               |    6 +-
 .../kallisto/kallisto_index/.config.vsh.yaml  |    6 +-
 .../nextflow/kallisto/kallisto_index/main.nf  |    6 +-
 .../kallisto/kallisto_quant/.config.vsh.yaml  |    6 +-
 .../nextflow/kallisto/kallisto_quant/main.nf  |    6 +-
 .../lofreq/lofreq_call/.config.vsh.yaml       |    6 +-
 target/nextflow/lofreq/lofreq_call/main.nf    |    6 +-
 .../lofreq/lofreq_indelqual/.config.vsh.yaml  |    6 +-
 .../nextflow/lofreq/lofreq_indelqual/main.nf  |    6 +-
 target/nextflow/multiqc/.config.vsh.yaml      |    6 +-
 target/nextflow/multiqc/main.nf               |    6 +-
 target/nextflow/pear/.config.vsh.yaml         |    6 +-
 target/nextflow/pear/main.nf                  |    6 +-
 .../qualimap/qualimap_rnaseq/.config.vsh.yaml |    6 +-
 .../nextflow/qualimap/qualimap_rnaseq/main.nf |    6 +-
 .../.config.vsh.yaml                          |    6 +-
 .../rsem/rsem_calculate_expression/main.nf    |    6 +-
 .../rsem_prepare_reference/.config.vsh.yaml   |    6 +-
 .../rsem/rsem_prepare_reference/main.nf       |    6 +-
 .../salmon/salmon_index/.config.vsh.yaml      |    6 +-
 target/nextflow/salmon/salmon_index/main.nf   |    6 +-
 .../salmon/salmon_quant/.config.vsh.yaml      |    6 +-
 target/nextflow/salmon/salmon_quant/main.nf   |    6 +-
 .../samtools_collate/.config.vsh.yaml         |    6 +-
 .../samtools/samtools_collate/main.nf         |    6 +-
 .../samtools/samtools_faidx/.config.vsh.yaml  |    6 +-
 .../nextflow/samtools/samtools_faidx/main.nf  |    6 +-
 .../samtools/samtools_fasta/.config.vsh.yaml  |    6 +-
 .../nextflow/samtools/samtools_fasta/main.nf  |    6 +-
 .../samtools/samtools_fastq/.config.vsh.yaml  |    6 +-
 .../nextflow/samtools/samtools_fastq/main.nf  |    6 +-
 .../samtools_flagstat/.config.vsh.yaml        |    6 +-
 .../samtools/samtools_flagstat/main.nf        |    6 +-
 .../samtools_idxstats/.config.vsh.yaml        |    6 +-
 .../samtools/samtools_idxstats/main.nf        |    6 +-
 .../samtools/samtools_index/.config.vsh.yaml  |    6 +-
 .../nextflow/samtools/samtools_index/main.nf  |    6 +-
 .../samtools/samtools_sort/.config.vsh.yaml   |    6 +-
 .../nextflow/samtools/samtools_sort/main.nf   |    6 +-
 .../samtools/samtools_stats/.config.vsh.yaml  |    6 +-
 .../nextflow/samtools/samtools_stats/main.nf  |    6 +-
 .../samtools/samtools_view/.config.vsh.yaml   |    6 +-
 .../nextflow/samtools/samtools_view/main.nf   |    6 +-
 .../seqtk/seqtk_sample/.config.vsh.yaml       |    6 +-
 target/nextflow/seqtk/seqtk_sample/main.nf    |    6 +-
 .../seqtk/seqtk_subseq/.config.vsh.yaml       |    6 +-
 target/nextflow/seqtk/seqtk_subseq/main.nf    |    6 +-
 target/nextflow/snpeff/.config.vsh.yaml       |  655 +++
 target/nextflow/snpeff/main.nf                | 4315 +++++++++++++++++
 target/nextflow/snpeff/nextflow.config        |  125 +
 target/nextflow/snpeff/nextflow_schema.json   |  868 ++++
 target/nextflow/sortmerna/.config.vsh.yaml    |    6 +-
 target/nextflow/sortmerna/main.nf             |    6 +-
 .../star/star_align_reads/.config.vsh.yaml    |    6 +-
 target/nextflow/star/star_align_reads/main.nf |    6 +-
 .../star_genome_generate/.config.vsh.yaml     |    6 +-
 .../star/star_genome_generate/main.nf         |    6 +-
 target/nextflow/trimgalore/.config.vsh.yaml   |    6 +-
 target/nextflow/trimgalore/main.nf            |    6 +-
 .../umi_tools_dedup/.config.vsh.yaml          |    6 +-
 .../umi_tools/umi_tools_dedup/main.nf         |    6 +-
 .../umi_tools_extract/.config.vsh.yaml        |    6 +-
 .../umi_tools/umi_tools_extract/main.nf       |    6 +-
 .../umi_tools_prepareforrsem/.config.vsh.yaml |    6 +-
 .../umi_tools_prepareforrsem/main.nf          |    6 +-
 274 files changed, 10661 insertions(+), 715 deletions(-)
 create mode 100644 src/snpeff/config.vsh.yaml
 create mode 100644 src/snpeff/help.txt
 create mode 100644 src/snpeff/script.sh
 create mode 100644 src/snpeff/test.sh
 create mode 100644 src/snpeff/test_data/cancer.vcf
 create mode 100644 src/snpeff/test_data/my_annotations.bed
 create mode 100644 src/snpeff/test_data/script.sh
 create mode 100644 src/snpeff/test_data/test.vcf
 create mode 100644 target/executable/snpeff/.config.vsh.yaml
 create mode 100755 target/executable/snpeff/snpeff
 create mode 100644 target/nextflow/snpeff/.config.vsh.yaml
 create mode 100644 target/nextflow/snpeff/main.nf
 create mode 100644 target/nextflow/snpeff/nextflow.config
 create mode 100644 target/nextflow/snpeff/nextflow_schema.json

diff --git a/src/snpeff/config.vsh.yaml b/src/snpeff/config.vsh.yaml
new file mode 100644
index 00000000..5fb8622d
--- /dev/null
+++ b/src/snpeff/config.vsh.yaml
@@ -0,0 +1,297 @@
+name: snpeff
+description: |
+  Genetic variant annotation, and functional effect prediction toolbox. 
+  It annotates and predicts the effects of genetic variants on genes and 
+  proteins (such as amino acid changes).
+keywords: [ "annotation", "effect prediction", "snp", "variant", "vcf"]
+
+links:
+  repository: https://github.com/pcingola/SnpEff
+  homepage: https://pcingola.github.io/SnpEff/
+  documentation: https://pcingola.github.io/SnpEff/
+references:
+  doi: 10.3389/fgene.2012.00035
+license: MIT
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file
+        description: Input variants file.
+        example: test.vcf
+        required: true
+      - name: --genome_version
+        type: string
+        description: Reference genome version.
+        example: GRCh37.75
+        required: true
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        description: The output file.
+        example: out.vcf
+        direction: output
+        required: true
+      - name: --summary
+        type: file
+        description: Summary file directory.
+        example: summary_dir
+        direction: output
+      - name: --genes
+        type: file
+        description: Txt file directory.
+        example: genes_dir
+        direction: output
+  - name: Options
+    arguments:
+      - name: --chr
+        type: string
+        description: |
+          Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
+      - name: --classic
+        type: boolean_true
+        description: Use old style annotations instead of Sequence Ontology and Hgvs.
+      - name: --csv_stats
+        type: file
+        description: Create CSV summary file.
+      - name: --download
+        type: boolean_true
+        description: Download reference genome if not available.
+      - name: --input_format
+        alternatives: [-i]
+        type: string
+        description: |
+          Input format [ vcf, bed ]. Default: VCF.
+          example: "VCF"
+      - name: --file_list
+        type: boolean_true
+        description: Input actually contains a list of files to process.
+      - name: --output_format
+        alternatives: [-o]
+        type: string
+        description: |
+          Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
+        example: "VCF"
+      - name: --stats
+        alternatives: [-s, --htmlStats]
+        type: boolean_true
+        description: Create HTML summary file.
+      - name: --no_stats
+        type: boolean_true
+        description: Do not create stats (summary) file.
+  - name: Results filter options
+    arguments:
+      - name: --fi
+        alternatives: [--filterInterval]
+        type: file
+        description: |
+          Only analyze changes that intersect with the intervals 
+          specified in this file. This option can be used several times.
+      - name: --no_downstream 
+        type: boolean_true
+        description: Do not show DOWNSTREAM changes
+      - name: --no_intergenic
+        type: boolean_true
+        description: Do not show INTERGENIC changes.
+      - name: --no_intron
+        type: boolean_true
+        description: Do not show INTRON changes.
+      - name: --no_upstream
+        type: boolean_true
+        description: Do not show UPSTREAM changes.
+      - name: --no_utr
+        type: boolean_true
+        description: Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.
+      - name: --no
+        type: string
+        description: |
+          Do not show 'EffectType'. This option can be used several times.
+  - name: Annotations options
+    arguments:
+      - name: --cancer 
+        type: boolean_true
+        description: Perform 'cancer' comparisons (Somatic vs Germline).
+      - name: --cancer_samples
+        type: file
+        description: Two column TXT file defining 'original \t derived' samples.
+      - name: --fastaprot
+        type: file
+        description: |
+          Create an output file containing the resulting protein sequences.
+      - name: --format_eff
+        type: boolean_true
+        description: |
+          Use 'EFF' field compatible with older versions (instead of 'ANN').
+      - name: --gene_id
+        type: boolean_true
+        description: Use gene ID instead of gene name (VCF output).
+      - name: --hgvs
+        type: boolean_true
+        description: Use HGVS annotations for amino acid sub-field.
+      - name: --hgvs_old
+        type: boolean_true
+        description: Use old HGVS notation.
+      - name: --hgvs1_letter_aa 
+        type: boolean_true
+        description: Use one letter Amino acid codes in HGVS notation.
+      - name: --hgvs_tr_id
+        type: boolean_true
+        description: Use transcript ID in HGVS notation.
+      - name: --lof
+        type: boolean_true
+        description: |
+          Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
+      - name: -no_hgvs
+        type: boolean_true
+        description: Do not add HGVS annotations.
+      - name: --no_lof
+        type: boolean_true
+        description: Do not add LOF and NMD annotations.
+      - name: --no_shift_hgvs
+        type: boolean_true
+        description: |
+          Do not shift variants according to HGVS notation (most 3prime end).
+      - name: --oicr
+        type: boolean_true
+        description: Add OICR tag in VCF file.
+      - name: --sequence_ontology
+        type: boolean_true
+        description: Use Sequence Ontology terms.
+  - name: Generic options
+    arguments:
+      - name: --config
+        alternatives: [-c]
+        type: file
+        description: Specify config file
+      - name: --config_option
+        type: string
+        description: Override a config file option (name=value).
+      - name: --debug
+        alternatives: [-d]
+        type: boolean_true
+        description: Debug mode (very verbose).
+      - name: --data_dir
+        type: file
+        description: Override data_dir parameter from config file.
+      - name: --no_download
+        type: boolean_true
+        description: Do not download a SnpEff database, if not available locally.
+      - name: --no_log
+        type: boolean_true
+        description: Do not report usage statistics to server.
+      - name: --quiet
+        alternatives: [-q]
+        type: boolean_true
+        description: Quiet mode (do not show any messages or errors)
+      - name: --verbose
+        alternatives: [-v]
+        type: boolean_true
+        description: Verbose mode.
+  - name: Database options
+    arguments:
+      - name: --canon 
+        type: boolean_true
+        description: Only use canonical transcripts.
+      - name: --canon_list
+        type: file
+        description: |
+          Only use canonical transcripts, replace some transcripts using the 'gene_id         
+          transcript_id' entries in <file>.
+      - name: --tag
+        type: string
+        description: |
+          Only use transcript having a tag 'tagName'. This option can be used multiple times.
+      - name: --no_tag
+        type: boolean_true
+        description: |
+          Filter out transcript having a tag 'tagName'. This option can be used multiple times.
+      - name: --interaction
+        type: boolean_true
+        description: Annotate using interactions (requires interaction database).
+      - name: --interval
+        type: file
+        description: |
+          Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).
+      - name: --max_tsl
+        type: integer
+        description: Only use transcripts having Transcript Support Level lower than <TSL_number>.
+      - name: --motif 
+        type: boolean_true
+        description: Annotate using motifs (requires Motif database).
+      - name: --nextprot
+        type: boolean_true
+        description: Annotate using NextProt (requires NextProt database).
+      - name: --no_genome
+        type: boolean_true
+        description: Do not load any genomic database (e.g. annotate using custom files).
+      - name: --no_expand_iub
+        type: boolean_true
+        description: Disable IUB code expansion in input variants.
+      - name: --no_interaction
+        type: boolean_true
+        description: Disable inteaction annotations.
+      - name: --no_motif
+        type: boolean_true
+        description: Disable motif annotations.
+      - name: --no_nextprot
+        type: boolean_true
+        description: Disable NextProt annotations.
+      - name: --only_reg
+        type: boolean_true
+        description: Only use regulation tracks.
+      - name: --only_protein
+        type: boolean_true
+        description: Only use protein coding transcripts.
+      - name: --only_tr
+        type: file
+        description: |
+          Only use the transcripts in this file. Format: One transcript ID per line.
+        example: file.txt
+      - name: --reg
+        type: string
+        description: Regulation track to use (this option can be used add several times).
+      - name: --ss
+        alternatives: [--spliceSiteSize]
+        type: integer
+        description: |
+          Set size for splice sites (donor and acceptor) in bases. Default: 2.
+      - name: --splice_region_exon_size
+        type: integer
+        description: |
+          Set size for splice site region within exons. Default: 3 bases.
+      - name: --splice_region_intron_min
+        type: integer
+        description: |
+          Set minimum number of bases for splice site region within intron. Default: 3 bases.
+      - name: --splice_region_intron_max
+        type: integer
+        description: |
+          Set maximum number of bases for splice site region within intron. Default: 8 bases.
+      - name: --strict
+        type: boolean_true
+        description: Only use 'validated' transcripts (i.e. sequence has been checked).
+      - name: --ud
+        alternatives: [--upDownStreamLen]
+        type: integer
+        description: Set upstream downstream interval length (in bases).
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/staphb/snpeff:5.2a
+    setup:
+      - type: docker
+        run: |
+          version=$(snpEff -version) && \
+          version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
+          echo "$version_trimmed" > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
\ No newline at end of file
diff --git a/src/snpeff/help.txt b/src/snpeff/help.txt
new file mode 100644
index 00000000..d1950220
--- /dev/null
+++ b/src/snpeff/help.txt
@@ -0,0 +1,79 @@
+Usage: snpEff [eff] [options] genome_version [input_file]
+
+        variants_file                   : Default is STDIN
+
+Options:
+        -chr <string>                   : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
+        -classic                        : Use old style annotations instead of Sequence Ontology and Hgvs.
+        -csvStats <file>                : Create CSV summary file.
+        -download                       : Download reference genome if not available. Default: true
+        -i <format>                     : Input format [ vcf, bed ]. Default: VCF.
+        -fileList                       : Input actually contains a list of files to process.
+        -o <format>                     : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
+        -s , -stats, -htmlStats         : Create HTML summary file.  Default is 'snpEff_summary.html'
+        -noStats                        : Do not create stats (summary) file      
+
+Results filter options:
+        -fi , -filterInterval  <file>   : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)        
+        -no-downstream                  : Do not show DOWNSTREAM changes
+        -no-intergenic                  : Do not show INTERGENIC changes
+        -no-intron                      : Do not show INTRON changes
+        -no-upstream                    : Do not show UPSTREAM changes
+        -no-utr                         : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
+        -no <effectType>                : Do not show 'EffectType'. This option can be used several times.
+
+Annotations options:
+        -cancer                         : Perform 'cancer' comparisons (Somatic vs Germline). Default: false
+        -cancerSamples <file>           : Two column TXT file defining 'oringinal \t derived' samples.
+        -fastaProt <file>               : Create an output file containing the resulting protein sequences.
+        -formatEff                      : Use 'EFF' field compatible with older versions (instead of 'ANN').
+        -geneId                         : Use gene ID instead of gene name (VCF output). Default: false
+        -hgvs                           : Use HGVS annotations for amino acid sub-field. Default: true
+        -hgvsOld                        : Use old HGVS notation. Default: false   
+        -hgvs1LetterAa                  : Use one letter Amino acid codes in HGVS notation. Default: false
+        -hgvsTrId                       : Use transcript ID in HGVS notation. Default: false
+        -lof                            : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
+        -noHgvs                         : Do not add HGVS annotations.
+        -noLof                          : Do not add LOF and NMD annotations.     
+        -noShiftHgvs                    : Do not shift variants according to HGVS notation (most 3prime end).
+        -oicr                           : Add OICR tag in VCF file. Default: false
+        -sequenceOntology               : Use Sequence Ontology terms. Default: true
+
+Generic options:
+        -c , -config                 : Specify config file
+        -configOption name=value     : Override a config file option
+        -d , -debug                  : Debug mode (very verbose).
+        -dataDir <path>              : Override data_dir parameter from config file.
+        -download                    : Download a SnpEff database, if not available locally. Default: true
+        -nodownload                  : Do not download a SnpEff database, if not available locally.
+        -h , -help                   : Show this help and exit
+        -noLog                       : Do not report usage statistics to server   
+        -q , -quiet                  : Quiet mode (do not show any messages or errors)
+        -v , -verbose                : Verbose mode
+        -version                     : Show version number and exit
+
+Database options:
+        -canon                       : Only use canonical transcripts.
+        -canonList <file>            : Only use canonical transcripts, replace some transcripts using the 'gene_id         transcript_id' entries in <file>.        
+        -tag <tagName>               : Only use transcript having a tag 'tagName'. This option can be used multiple times.
+        -notag <tagName>             : Filter out transcript having a tag 'tagName'. This option can be used multiple times.
+        -interaction                 : Annotate using interactions (requires interaction database). Default: true
+        -interval <file>             : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
+        -maxTSL <TSL_number>         : Only use transcripts having Transcript Support Level lower than <TSL_number>.
+        -motif                       : Annotate using motifs (requires Motif database). Default: true
+        -nextProt                    : Annotate using NextProt (requires NextProt database).
+        -noGenome                    : Do not load any genomic database (e.g. annotate using custom files).
+        -noExpandIUB                 : Disable IUB code expansion in input variants
+        -noInteraction               : Disable inteaction annotations
+        -noMotif                     : Disable motif annotations.
+        -noNextProt                  : Disable NextProt annotations.
+        -onlyReg                     : Only use regulation tracks.
+        -onlyProtein                 : Only use protein coding transcripts. Default: false
+        -onlyTr <file.txt>           : Only use the transcripts in this file. Format: One transcript ID per line.
+        -reg <name>                  : Regulation track to use (this option can be used add several times).
+        -ss , -spliceSiteSize <int>  : Set size for splice sites (donor and acceptor) in bases. Default: 2
+        -spliceRegionExonSize <int>  : Set size for splice site region within exons. Default: 3 bases
+        -spliceRegionIntronMin <int> : Set minimum number of bases for splice site region within intron. Default: 3 bases
+        -spliceRegionIntronMax <int> : Set maximum number of bases for splice site region within intron. Default: 8 bases
+        -strict                      : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
+        -ud , -upDownStreamLen <int> : Set upstream downstream interval length (in bases)
\ No newline at end of file
diff --git a/src/snpeff/script.sh b/src/snpeff/script.sh
new file mode 100644
index 00000000..bf3914bb
--- /dev/null
+++ b/src/snpeff/script.sh
@@ -0,0 +1,148 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# Unset flags if 'false'
+unset_if_false=(
+    par_classic
+    par_download
+    par_file_list
+    par_stats
+    par_cancer
+    par_format_eff
+    par_gene_id
+    par_hgvs
+    par_hgvs_old
+    par_hgvs1_letter_aa
+    par_hgvs_tr_id
+    par_lof
+    par_oicr
+    par_sequence_ontology
+    par_debug
+    par_quiet
+    par_verbose
+    par_canon
+    par_interaction
+    par_motif
+    par_nextprot
+    par_only_reg
+    par_only_protein
+    par_strict
+    par_no_stats
+    par_no_downstream
+    par_no_intergenic
+    par_no_intron
+    par_no_upstream
+    par_no_utr
+    par_no_hgvs
+    par_no_lof
+    par_no_shift_hgvs
+    par_no_download
+    par_no_log
+    par_no_tag
+    par_no_genome
+    par_no_expand_iub
+    par_no_interaction
+    par_no_motif
+    par_no_nextprot
+)
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}" # contains the value of the 'par'
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+
+# Run SnpEff
+snpEff \
+    ${par_chr:+-chr "$par_chr"} \
+    ${par_classic:+-classic} \
+    ${par_csv_stats:+-csvStats "$par_csv_stats"} \
+    ${par_download:+-download} \
+    ${par_input_format:+-i "$par_input_format"} \
+    ${par_file_list:+-fileList} \
+    ${par_output_format:+-o "$par_output_format"} \
+    ${par_stats:+-stats} \
+    ${par_no_stats:+-noStats} \
+    ${par_fi:+-fi "$par_fi"} \
+    ${par_no_downstream:+-no-downstream} \
+    ${par_no_intergenic:+-no-intergenic} \
+    ${par_no_intron:+-no-intron} \
+    ${par_no_upstream:+-no-upstream} \
+    ${par_no_utr:+-no-utr} \
+    ${par_no:+-no "$par_no"} \
+    ${par_cancer:+-cancer} \
+    ${par_cancer_samples:+-cancerSamples "$par_cancer_samples]"} \
+    ${par_fastaprot:+-fastaProt "$par_fastaprot]"} \
+    ${par_format_eff:+-formatEff} \
+    ${par_gene_id:+-geneId} \
+    ${par_hgvs:+-hgvs} \
+    ${par_hgvs_old:+-hgvsOld} \
+    ${par_hgvs1_letter_aa:+-hgvs1LetterAa} \
+    ${par_hgvs_tr_id:+-hgvsTrId} \
+    ${par_lof:+-lof} \
+    ${par_no_hgvs:+-noHgvs} \
+    ${par_no_lof:+-noLof} \
+    ${par_no_shift_hgvs:+-noShiftHgvs} \
+    ${par_oicr:+-oicr} \
+    ${par_sequence_ontology:+-sequenceOntology} \
+    ${par_config:+-config "$par_config"} \
+    ${par_config_option:+-configOption "$par_config_option"} \
+    ${par_debug:+-debug} \
+    ${par_data_dir:+-dataDir "$par_data_dir"} \
+    ${par_no_download:+-nodownload} \
+    ${par_no_log:+-noLog} \
+    ${par_quiet:+-quiet} \
+    ${par_verbose:+-verbose} \
+    ${par_canon:+-canon} \
+    ${par_canon_list:+-canonList "$par_canon_list"} \
+    ${par_tag:+-tag "$par_tag"} \
+    ${par_no_tag:+-notag} \
+    ${par_interaction:+-interaction} \
+    ${par_interval:+-interval "$par_interval"} \
+    ${par_max_tsl:+-maxTSL "$par_max_tsl"} \
+    ${par_motif:+-motif} \
+    ${par_nextprot:+-nextProt} \
+    ${par_no_genome:+-noGenome} \
+    ${par_no_expand_iub:+-noExpandIUB} \
+    ${par_no_interaction:+-noInteraction} \
+    ${par_no_motif:+-noMotif} \
+    ${par_no_nextprot:+-noNextProt} \
+    ${par_only_reg:+-onlyReg} \
+    ${par_only_protein:+-onlyProtein} \
+    ${par_only_tr:+-onlyTr "$par_onlyTr"} \
+    ${par_reg:+-reg "$par_reg"} \
+    ${par_ss:+-ss "$par_ss"} \
+    ${par_splice_region_exon_size:+-spliceRegionExonSize "$par_splice_region_exon_size"} \
+    ${par_splice_region_intron_min:+-spliceRegionIntronMin "$par_splice_region_intron_min"} \
+    ${par_splice_region_intron_max:+-spliceRegionIntronMax "$par_splice_region_intron_max"} \
+    ${par_strict:+-strict} \
+    ${par_ud:+-ud "$par_ud"} \
+    "$par_genome_version" \
+    "$par_input" \
+    > "$par_output"
+
+# Path of the output file (par_output)
+absolute_path=$(realpath "$par_output")
+directory_path=$(dirname "$absolute_path")
+
+# Move the automatically generated outputs to their locations
+if [ -z "$par_no_stats" ]; then
+    if [ ! -z "$par_summary" ]; then
+        mv -n snpEff_summary.html "$par_summary"
+    else
+        mv -n snpEff_summary.html "$directory_path"
+    fi
+fi 
+
+if [ -z "$par_no_stats" ]; then
+    if [ ! -z "$par_genes" ]; then
+        mv -n snpEff_genes.txt "$par_genes"
+    else
+        mv -n snpEff_genes.txt "$directory_path"
+    fi
+fi
+
+exit 0
diff --git a/src/snpeff/test.sh b/src/snpeff/test.sh
new file mode 100644
index 00000000..d8c72c20
--- /dev/null
+++ b/src/snpeff/test.sh
@@ -0,0 +1,129 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+###########################################################################
+
+# Test 1: Run SnpEff with only required parameters
+
+mkdir test1
+pushd test1 > /dev/null # cd test1 (stack)
+
+echo "> Run Test 1: required parameters"
+"$meta_executable" \
+  --genome_version GRCh37.75 \
+  --input "$meta_resources_dir/test_data/cancer.vcf" \
+  --output out.vcf
+
+# Check if output files are generated
+output_files=("out.vcf" "snpEff_genes.txt" "snpEff_summary.html")
+
+# Check if any of the files do not exist
+for file in "${output_files[@]}"; do
+    if [ ! -e "$file" ]; then
+        echo "File $file does not exist."
+    fi
+done
+
+# Check if files are empty
+for file in "${output_files[@]}"; do
+    if [ ! -s "$file" ]; then
+        echo "File $file is empty."
+    fi
+done
+
+popd > /dev/null # Remove directory from stack (LIFO)
+
+echo "Test 1 succeeded."
+
+###########################################################################
+
+# Test 2: Run SnpEff with a different input + options
+
+mkdir test2
+pushd test2 > /dev/null
+
+echo "> Run Test 2: different input + options"
+"$meta_executable" \
+  --genome_version GRCh37.75 \
+  --input "$meta_resources_dir/test_data/test.vcf" \
+  --interval "$meta_resources_dir/test_data/my_annotations.bed" \
+  --no_stats \
+  --output output.vcf
+
+# Check if output.vcf exists
+if [ ! -e "output.vcf" ]; then
+    echo "File output.vcf does not exist."
+fi
+
+# These files should not exist
+files=("snpEff_genes.txt" "snpEff_summary.html")
+for file in "${files[@]}"; do
+    if [ -e "$file" ]; then
+        echo "Error: File $file exists."
+    fi
+done
+
+# Check if output.vcf is empty
+if [ ! -s "output.vcf" ]; then
+    echo "File output.vcf is empty."
+fi
+
+popd > /dev/null
+
+echo "Test 2 succeeded."
+
+###########################################################################
+
+# Test 3: Move the output files to other locations
+
+mkdir test3
+pushd test3 > /dev/null
+
+mkdir temp
+
+echo "> Run Test 3: move output files"
+"$meta_executable" \
+  --genome_version GRCh37.75 \
+  --input "$meta_resources_dir/test_data/test.vcf" \
+  --output output.vcf \
+  --summary temp \
+  --genes temp
+
+# Check if output.vcf exists
+if [ ! -e "output.vcf" ]; then
+    echo "File output.vcf does not exist."
+fi
+
+# Check if the other output files have been moved to temp folder
+output_files=("snpEff_genes.txt" "snpEff_summary.html")
+
+# Check if any of the files do not exist
+for file in "${output_files[@]}"; do
+    if [ ! -e "temp/$file" ]; then
+        echo "File $file does not exist in 'temp' folder."
+    fi
+done
+
+# Check if output.vcf is empty
+if [ ! -s "output.vcf" ]; then
+    echo "File output.vcf is empty."
+fi
+
+# Check if the other output files in temp folder are empty
+for file in "${output_files[@]}"; do
+    if [ ! -s "temp/$file" ]; then
+        echo "File $file is empty."
+    fi
+done
+
+popd > /dev/null
+
+echo "Test 3 succeeded."
+
+###########################################################################
+
+echo "All tests successfully completed!"
\ No newline at end of file
diff --git a/src/snpeff/test_data/cancer.vcf b/src/snpeff/test_data/cancer.vcf
new file mode 100644
index 00000000..f37ad8c3
--- /dev/null
+++ b/src/snpeff/test_data/cancer.vcf
@@ -0,0 +1,2 @@
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
+1	69091	.	A	C,G	.	PASS	AC=1	GT	1/0	2/1
diff --git a/src/snpeff/test_data/my_annotations.bed b/src/snpeff/test_data/my_annotations.bed
new file mode 100644
index 00000000..a5247f97
--- /dev/null
+++ b/src/snpeff/test_data/my_annotations.bed
@@ -0,0 +1 @@
+1	10000	20000	MY_ANNOTATION
diff --git a/src/snpeff/test_data/script.sh b/src/snpeff/test_data/script.sh
new file mode 100644
index 00000000..a47ec136
--- /dev/null
+++ b/src/snpeff/test_data/script.sh
@@ -0,0 +1,15 @@
+# Test files from SnpEff examples
+if [ ! -f snpEff_latest_core.zip ]; then
+    wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
+fi
+
+if [ ! -d snpEff ]; then
+    unzip snpEff_latest_core.zip
+fi
+
+mv snpEff/examples/test.vcf src/snpeff/test_data/
+mv snpEff/examples/cancer.vcf src/snpeff/test_data/
+mv snpEff/examples/my_annotations.bed src/snpeff/test_data/
+
+rm -rf snpEff_latest_core.zip
+rm -rf snpEff
\ No newline at end of file
diff --git a/src/snpeff/test_data/test.vcf b/src/snpeff/test_data/test.vcf
new file mode 100644
index 00000000..d552ef18
--- /dev/null
+++ b/src/snpeff/test_data/test.vcf
@@ -0,0 +1 @@
+1	10469	.	C	G	365.78	PASS	AC=30;AF=0.0732
diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
index 1f58b4dc..6d5842b3 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
index 131d6650..96c47390 100755
--- 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="2024-10-07T09:07:56Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
index aea6afeb..080dd19a 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
index 8ef88126..7e9d14eb 100755
--- 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="2024-10-07T09:07:56Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
index d1f831a7..506a8bd8 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
index e6887ec6..87ba31d1 100755
--- 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="2024-10-07T09:07:57Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index 5b59f542..17c91a03 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
index aad0cb4e..3c7849e4 100755
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -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="2024-10-07T09:07:56Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index 5f85535e..504e5f29 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
index 457c7c9a..ec79ce76 100755
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -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="2024-10-07T09:07:55Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index 665cdc30..76855cd1 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
index 1205c174..0b2e9506 100755
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -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="2024-10-07T09:07:55Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml
index 377335b5..88edafcc 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba
index 6de980c7..6dfa6e45 100755
--- 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="2024-10-07T09:07:59Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
index fad6420e..2ba2e6d0 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
index 56272a7c..f9a44dad 100755
--- 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="2024-10-07T09:07:49Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
index 8499c979..de2bc144 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat
index 1fedda36..24f54c6c 100755
--- 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="2024-10-07T09:07:49Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
index 83f9708c..8a4f08f5 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm
index d4d19059..eafce02b 100755
--- 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="2024-10-07T09:07:50Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
index ea255a4f..b1438e05 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort
index c19adee4..7cf7e81b 100755
--- 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="2024-10-07T09:07:48Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
index 9eb2c5b6..cdd93b4b 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats
index 0153322a..7fa2f90b 100755
--- 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="2024-10-07T09:07:49Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml
index 7a9e8280..717ab6b8 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert
index 9939f4c6..09fa58fc 100755
--- 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="2024-10-07T09:07:58Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index b60d763b..0d45449e 100644
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
index 0c2c3b2d..c103b1d1 100755
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -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="2024-10-07T09:08:02Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:47Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
index 77b2f4dc..3ce38aa6 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git 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
index fe01cdbc..6b8c57a9 100755
--- 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="2024-10-07T09:08:01Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:47Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index b74a39f9..d3bea49c 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
index 8c9673aa..ca3627cd 100755
--- 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="2024-10-07T09:07:41Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
index 8a8ce77e..a99986ac 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
index fd10b66a..5171f565 100755
--- 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="2024-10-07T09:07:40Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
index c67cb108..b51233af 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
index 9b849555..9ce671cc 100755
--- 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="2024-10-07T09:07:42Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
index 24134700..049cac36 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
index 538b922e..e19d98fb 100755
--- 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="2024-10-07T09:07:40Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
index f17fc680..fb814adb 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
index 617af4a2..ffe46b94 100755
--- 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="2024-10-07T09:07:40Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
index 8c5c679d..9d970ae6 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
index 8005f950..e1ab1d1d 100755
--- 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="2024-10-07T09:07:42Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
index 1213f995..5145017e 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
index 325c329d..87e47ee0 100755
--- 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="2024-10-07T09:07:40Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
index 83b1372f..66038234 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links
index 85978d2d..c321dead 100755
--- 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="2024-10-07T09:07:41Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
index 0803bdc6..f42602dc 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge
index f962808d..14287c5b 100755
--- 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="2024-10-07T09:07:39Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
index 75655609..2a204915 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort
index 68a39a47..b531a8a8 100755
--- 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="2024-10-07T09:07:42Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
index 4c37cf82..8d702428 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets
index f5b6baf8..982aabc5 100755
--- 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="2024-10-07T09:07:53Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
index 1ce0a8a5..a3733e1b 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets
index 74ad299e..48671c03 100755
--- 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="2024-10-07T09:07:53Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml
index aedd311f..e21312df 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run
index 7e97f26d..27520568 100755
--- 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="2024-10-07T09:07:53Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml
index 4532c8b2..437916b0 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt
index 272519fb..0b52cf31 100755
--- 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="2024-10-07T09:08:00Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml
index 409784da..ad2e11d5 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/falco/falco b/target/executable/falco/falco
index 6d4d7623..143d92ea 100755
--- 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="2024-10-07T09:08:01Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml
index 2188ea01..a28befd6 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp
index 70412881..8d67cced 100755
--- 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="2024-10-07T09:07:57Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml
index b5f70490..7bc18283 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc
index b034eb4e..9b109f32 100755
--- 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="2024-10-07T09:07:47Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml
index 43c4a1c3..421d69f1 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts
index 401aa969..391e6860 100755
--- 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="2024-10-07T09:07:51Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml
index 82bde9bc..708e3370 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample
index 78781c10..928b2e12 100755
--- 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="2024-10-07T09:07:47Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml
index 95ee32c6..a7568d03 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread
index b14b316d..d5cd0889 100755
--- 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="2024-10-07T09:07:39Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
index 95533d8f..1f625ee6 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index
index 764e94c8..5942c8df 100755
--- 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="2024-10-07T09:07:55Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
index 295e5c5e..db647cce 100644
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -234,9 +234,9 @@ build_info:
   output: "target/executable/kallisto/kallisto_quant"
   executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant
index 1bd35e09..392c23a1 100755
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -518,9 +518,9 @@ 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="2024-10-07T09:07:55Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
index c86e5975..cb7cf288 100644
--- 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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call
index 442b46a3..ceea54ad 100755
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -656,9 +656,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:50Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
index eedab650..36c1b1aa 100644
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
index 0963d69a..b022f0f5 100755
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -501,9 +501,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:50Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml
index 38d0e93f..42fe9796 100644
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc
index 95c49d52..4eeb22c5 100755
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -637,9 +637,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-10-07T09:08:00Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml
index b4ee2a80..d89289fb 100644
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,9 +398,9 @@ build_info:
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/pear/pear b/target/executable/pear/pear
index 48060033..e6961f8c 100755
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -597,9 +597,9 @@ echo "pear: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:43Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:39Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
index 0f412f0e..e94a7ad5 100644
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -264,9 +264,9 @@ build_info:
   output: "target/executable/qualimap/qualimap_rnaseq"
   executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
index 9eb3d53c..c6f3cf0a 100755
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:46Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
index 08d4e919..c9c3368c 100644
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -852,9 +852,9 @@ build_info:
   output: "target/executable/rsem/rsem_calculate_expression"
   executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
index ce727e23..ea0c6986 100755
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -991,9 +991,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\
 echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:54Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
index f9b68bcf..c80b5646 100644
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
   output: "target/executable/rsem/rsem_prepare_reference"
   executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
index ca429cdf..b9d3bd44 100755
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:54Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml
index 4f5e78f3..503888bd 100644
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,9 +277,9 @@ build_info:
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index
index 52f9c4c7..f1f60607 100755
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -546,9 +546,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:59Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml
index 5f6d0f92..e223d01f 100644
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,9 +1173,9 @@ build_info:
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant
index 04de2580..5b226d9c 100755
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1168,9 +1168,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:59Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml
index 037cd9a4..a9998269 100644
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -264,9 +264,9 @@ build_info:
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate
index 4ea7ff87..02e24718 100755
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -519,9 +519,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:45Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
index a1d679e7..7ea62dec 100644
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,9 +243,9 @@ build_info:
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx
index 58e6a085..2ba23246 100755
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -512,9 +512,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:45Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
index 6f0addef..a7743544 100644
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,9 +433,9 @@ build_info:
   output: "target/executable/samtools/samtools_fasta"
   executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta
index d8482873..a2d8a86b 100755
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:45Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
index 923cadd7..ed9b24ec 100644
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,9 +433,9 @@ build_info:
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq
index 61bba02a..fc15b466 100755
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -626,9 +626,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:44Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
index a13aeed8..dff8a3d3 100644
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,9 +173,9 @@ build_info:
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat
index 4b78c4b4..bfeffd01 100755
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -474,9 +474,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:44Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
index b944c2ae..c173f04b 100644
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats
index 9916b948..92748376 100755
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -478,9 +478,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:43Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml
index bc9e8f5a..d6a9b4bf 100644
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -189,9 +189,9 @@ build_info:
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index
index c68a7feb..49ab00a2 100755
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -485,9 +485,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:43Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml
index 9f19b707..971af32d 100644
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -332,9 +332,9 @@ build_info:
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort
index 20568b56..7b0c9271 100755
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -556,9 +556,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:46Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml
index bab33a5c..011c6798 100644
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -401,9 +401,9 @@ build_info:
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats
index 90ec5221..90fcebf7 100755
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -575,9 +575,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:46Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml
index 393aba39..392fb83f 100644
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -665,9 +665,9 @@ build_info:
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view
index 244e97ad..1ecddb5f 100755
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -825,9 +825,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:44Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
index 23a239ff..a15d3a29 100644
--- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,9 +173,9 @@ build_info:
   output: "target/executable/seqtk/seqtk_sample"
   executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample
index c90db98d..b5bd1dc2 100755
--- a/target/executable/seqtk/seqtk_sample/seqtk_sample
+++ b/target/executable/seqtk/seqtk_sample/seqtk_sample
@@ -481,9 +481,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-10-07T09:08:02Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
index 3f55a1d9..8419794f 100644
--- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,9 +196,9 @@ build_info:
   output: "target/executable/seqtk/seqtk_subseq"
   executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
index 2441152c..db0ca1d1 100755
--- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq
+++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
@@ -491,9 +491,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-10-07T09:08:02Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/.config.vsh.yaml
new file mode 100644
index 00000000..5fca32ca
--- /dev/null
+++ b/target/executable/snpeff/.config.vsh.yaml
@@ -0,0 +1,655 @@
+name: "snpeff"
+version: "main"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input variants file."
+    info: null
+    example:
+    - "test.vcf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--genome_version"
+    description: "Reference genome version."
+    info: null
+    example:
+    - "GRCh37.75"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The output file."
+    info: null
+    example:
+    - "out.vcf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary"
+    description: "Summary file directory."
+    info: null
+    example:
+    - "summary_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genes"
+    description: "Txt file directory."
+    info: null
+    example:
+    - "genes_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "string"
+    name: "--chr"
+    description: "Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1').\
+      \ Only on TXT output.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--classic"
+    description: "Use old style annotations instead of Sequence Ontology and Hgvs."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--csv_stats"
+    description: "Create CSV summary file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--download"
+    description: "Download reference genome if not available."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--input_format"
+    alternatives:
+    - "-i"
+    description: "Input format [ vcf, bed ]. Default: VCF.\nexample: \"VCF\"\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--file_list"
+    description: "Input actually contains a list of files to process."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--output_format"
+    alternatives:
+    - "-o"
+    description: "Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n"
+    info: null
+    example:
+    - "VCF"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--stats"
+    alternatives:
+    - "-s"
+    - "--htmlStats"
+    description: "Create HTML summary file."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_stats"
+    description: "Do not create stats (summary) file."
+    info: null
+    direction: "input"
+- name: "Results filter options"
+  arguments:
+  - type: "file"
+    name: "--fi"
+    alternatives:
+    - "--filterInterval"
+    description: "Only analyze changes that intersect with the intervals \nspecified\
+      \ in this file. This option can be used several times.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_downstream"
+    description: "Do not show DOWNSTREAM changes"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_intergenic"
+    description: "Do not show INTERGENIC changes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_intron"
+    description: "Do not show INTRON changes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_upstream"
+    description: "Do not show UPSTREAM changes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_utr"
+    description: "Do not show 5_PRIME_UTR or 3_PRIME_UTR changes."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--no"
+    description: "Do not show 'EffectType'. This option can be used several times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Annotations options"
+  arguments:
+  - type: "boolean_true"
+    name: "--cancer"
+    description: "Perform 'cancer' comparisons (Somatic vs Germline)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--cancer_samples"
+    description: "Two column TXT file defining 'original \\t derived' samples."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastaprot"
+    description: "Create an output file containing the resulting protein sequences.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--format_eff"
+    description: "Use 'EFF' field compatible with older versions (instead of 'ANN').\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--gene_id"
+    description: "Use gene ID instead of gene name (VCF output)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs"
+    description: "Use HGVS annotations for amino acid sub-field."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs_old"
+    description: "Use old HGVS notation."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs1_letter_aa"
+    description: "Use one letter Amino acid codes in HGVS notation."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs_tr_id"
+    description: "Use transcript ID in HGVS notation."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--lof"
+    description: "Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "-no_hgvs"
+    description: "Do not add HGVS annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_lof"
+    description: "Do not add LOF and NMD annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_shift_hgvs"
+    description: "Do not shift variants according to HGVS notation (most 3prime end).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--oicr"
+    description: "Add OICR tag in VCF file."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sequence_ontology"
+    description: "Use Sequence Ontology terms."
+    info: null
+    direction: "input"
+- name: "Generic options"
+  arguments:
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Specify config file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--config_option"
+    description: "Override a config file option (name=value)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--debug"
+    alternatives:
+    - "-d"
+    description: "Debug mode (very verbose)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--data_dir"
+    description: "Override data_dir parameter from config file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_download"
+    description: "Do not download a SnpEff database, if not available locally."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_log"
+    description: "Do not report usage statistics to server."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--quiet"
+    alternatives:
+    - "-q"
+    description: "Quiet mode (do not show any messages or errors)"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--verbose"
+    alternatives:
+    - "-v"
+    description: "Verbose mode."
+    info: null
+    direction: "input"
+- name: "Database options"
+  arguments:
+  - type: "boolean_true"
+    name: "--canon"
+    description: "Only use canonical transcripts."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--canon_list"
+    description: "Only use canonical transcripts, replace some transcripts using the\
+      \ 'gene_id         \ntranscript_id' entries in <file>.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--tag"
+    description: "Only use transcript having a tag 'tagName'. This option can be used\
+      \ multiple times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_tag"
+    description: "Filter out transcript having a tag 'tagName'. This option can be\
+      \ used multiple times.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--interaction"
+    description: "Annotate using interactions (requires interaction database)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--interval"
+    description: "Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use\
+      \ this option many times).\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_tsl"
+    description: "Only use transcripts having Transcript Support Level lower than\
+      \ <TSL_number>."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--motif"
+    description: "Annotate using motifs (requires Motif database)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nextprot"
+    description: "Annotate using NextProt (requires NextProt database)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_genome"
+    description: "Do not load any genomic database (e.g. annotate using custom files)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_expand_iub"
+    description: "Disable IUB code expansion in input variants."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_interaction"
+    description: "Disable inteaction annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_motif"
+    description: "Disable motif annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_nextprot"
+    description: "Disable NextProt annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--only_reg"
+    description: "Only use regulation tracks."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--only_protein"
+    description: "Only use protein coding transcripts."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--only_tr"
+    description: "Only use the transcripts in this file. Format: One transcript ID\
+      \ per line.\n"
+    info: null
+    example:
+    - "file.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reg"
+    description: "Regulation track to use (this option can be used add several times)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--ss"
+    alternatives:
+    - "--spliceSiteSize"
+    description: "Set size for splice sites (donor and acceptor) in bases. Default:\
+      \ 2.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--splice_region_exon_size"
+    description: "Set size for splice site region within exons. Default: 3 bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--splice_region_intron_min"
+    description: "Set minimum number of bases for splice site region within intron.\
+      \ Default: 3 bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--splice_region_intron_max"
+    description: "Set maximum number of bases for splice site region within intron.\
+      \ Default: 8 bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--strict"
+    description: "Only use 'validated' transcripts (i.e. sequence has been checked)."
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--ud"
+    alternatives:
+    - "--upDownStreamLen"
+    description: "Set upstream downstream interval length (in bases)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Genetic variant annotation, and functional effect prediction toolbox.\
+  \ \nIt annotates and predicts the effects of genetic variants on genes and \nproteins\
+  \ (such as amino acid changes).\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "annotation"
+- "effect prediction"
+- "snp"
+- "variant"
+- "vcf"
+license: "MIT"
+references:
+  doi:
+  - "10.3389/fgene.2012.00035"
+links:
+  repository: "https://github.com/pcingola/SnpEff"
+  homepage: "https://pcingola.github.io/SnpEff/"
+  documentation: "https://pcingola.github.io/SnpEff/"
+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: "quay.io/staphb/snpeff:5.2a"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "version=$(snpEff -version) && \\\nversion_trimmed=$(echo \"$version\" | awk\
+      \ '{print $1, $2}') && \\\necho \"$version_trimmed\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/snpeff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/snpeff"
+  executable: "target/executable/snpeff/snpeff"
+  viash_version: "0.9.0"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
+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"
diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff
new file mode 100755
index 00000000..54747663
--- /dev/null
+++ b/target/executable/snpeff/snpeff
@@ -0,0 +1,2656 @@
+#!/usr/bin/env bash
+
+# snpeff main
+# 
+# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+# Intuitive.
+# 
+# The component may contain files which fall under a different license. The
+# authors of this component should specify the license in the header of such
+# files, or include a separate license file detailing the licenses of all included
+# files.
+
+set -e
+
+if [ -z "$VIASH_TEMP" ]; then
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
+  VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$TMP}
+  VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$TEMP}
+  VIASH_TEMP=${VIASH_TEMP:-/tmp}
+fi
+
+# define helper functions
+# ViashQuote: put quotes around non flag values
+# $1     : unquoted string
+# return : possibly quoted string
+# examples:
+#   ViashQuote --foo      # returns --foo
+#   ViashQuote bar        # returns 'bar'
+#   Viashquote --foo=bar  # returns --foo='bar'
+function ViashQuote {
+  if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
+    echo "$1" | sed "s#=\(.*\)#='\1'#"
+  elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
+    echo "$1"
+  else
+    echo "'$1'"
+  fi
+}
+# ViashRemoveFlags: Remove leading flag
+# $1     : string with a possible leading flag
+# return : string without possible leading flag
+# examples:
+#   ViashRemoveFlags --foo=bar  # returns bar
+function ViashRemoveFlags {
+  echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
+}
+# ViashSourceDir: return the path of a bash file, following symlinks
+# usage   : ViashSourceDir ${BASH_SOURCE[0]}
+# $1      : Should always be set to ${BASH_SOURCE[0]}
+# returns : The absolute path of the bash file
+function ViashSourceDir {
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
+  done
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
+}
+# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
+# usage   : ViashFindTargetDir 'ScriptPath'
+# $1      : The location from where to start the upward search
+# returns : The absolute path of the '.build.yaml' file
+function ViashFindTargetDir {
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
+  done
+  echo $source
+}
+# see https://en.wikipedia.org/wiki/Syslog#Severity_level
+VIASH_LOGCODE_EMERGENCY=0
+VIASH_LOGCODE_ALERT=1
+VIASH_LOGCODE_CRITICAL=2
+VIASH_LOGCODE_ERROR=3
+VIASH_LOGCODE_WARNING=4
+VIASH_LOGCODE_NOTICE=5
+VIASH_LOGCODE_INFO=6
+VIASH_LOGCODE_DEBUG=7
+VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
+
+# ViashLog: Log events depending on the verbosity level
+# usage: ViashLog 1 alert Oh no something went wrong!
+# $1: required verbosity level
+# $2: display tag
+# $3+: messages to display
+# stdout: Your input, prepended by '[$2] '.
+function ViashLog {
+  local required_level="$1"
+  local display_tag="$2"
+  shift 2
+  if [ $VIASH_VERBOSITY -ge $required_level ]; then
+    >&2 echo "[$display_tag]" "$@"
+  fi
+}
+
+# ViashEmergency: log events when the system is unstable
+# usage: ViashEmergency Oh no something went wrong.
+# stdout: Your input, prepended by '[emergency] '.
+function ViashEmergency {
+  ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
+}
+
+# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
+# usage: ViashAlert Oh no something went wrong.
+# stdout: Your input, prepended by '[alert] '.
+function ViashAlert {
+  ViashLog $VIASH_LOGCODE_ALERT alert "$@"
+}
+
+# ViashCritical: log events when a critical condition occurs
+# usage: ViashCritical Oh no something went wrong.
+# stdout: Your input, prepended by '[critical] '.
+function ViashCritical {
+  ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
+}
+
+# ViashError: log events when an error condition occurs
+# usage: ViashError Oh no something went wrong.
+# stdout: Your input, prepended by '[error] '.
+function ViashError {
+  ViashLog $VIASH_LOGCODE_ERROR error "$@"
+}
+
+# ViashWarning: log potentially abnormal events
+# usage: ViashWarning Something may have gone wrong.
+# stdout: Your input, prepended by '[warning] '.
+function ViashWarning {
+  ViashLog $VIASH_LOGCODE_WARNING warning "$@"
+}
+
+# ViashNotice: log significant but normal events
+# usage: ViashNotice This just happened.
+# stdout: Your input, prepended by '[notice] '.
+function ViashNotice {
+  ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
+}
+
+# ViashInfo: log normal events
+# usage: ViashInfo This just happened.
+# stdout: Your input, prepended by '[info] '.
+function ViashInfo {
+  ViashLog $VIASH_LOGCODE_INFO info "$@"
+}
+
+# ViashDebug: log all events, for debugging purposes
+# usage: ViashDebug This just happened.
+# stdout: Your input, prepended by '[debug] '.
+function ViashDebug {
+  ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
+}
+
+# find source folder of this component
+VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
+
+# find the root of the built components & dependencies
+VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
+
+# define meta fields
+VIASH_META_NAME="snpeff"
+VIASH_META_FUNCTIONALITY_NAME="snpeff"
+VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
+VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
+VIASH_META_TEMP_DIR="$VIASH_TEMP"
+
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "snpeff main"
+  echo ""
+  echo "Genetic variant annotation, and functional effect prediction toolbox."
+  echo "It annotates and predicts the effects of genetic variants on genes and"
+  echo "proteins (such as amino acid changes)."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: test.vcf"
+  echo "        Input variants file."
+  echo ""
+  echo "    --genome_version"
+  echo "        type: string, required parameter"
+  echo "        example: GRCh37.75"
+  echo "        Reference genome version."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: out.vcf"
+  echo "        The output file."
+  echo ""
+  echo "    --summary"
+  echo "        type: file, output, file must exist"
+  echo "        example: summary_dir"
+  echo "        Summary file directory."
+  echo ""
+  echo "    --genes"
+  echo "        type: file, output, file must exist"
+  echo "        example: genes_dir"
+  echo "        Txt file directory."
+  echo ""
+  echo "Options:"
+  echo "    --chr"
+  echo "        type: string"
+  echo "        Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only"
+  echo "        on TXT output."
+  echo ""
+  echo "    --classic"
+  echo "        type: boolean_true"
+  echo "        Use old style annotations instead of Sequence Ontology and Hgvs."
+  echo ""
+  echo "    --csv_stats"
+  echo "        type: file, file must exist"
+  echo "        Create CSV summary file."
+  echo ""
+  echo "    --download"
+  echo "        type: boolean_true"
+  echo "        Download reference genome if not available."
+  echo ""
+  echo "    -i, --input_format"
+  echo "        type: string"
+  echo "        Input format [ vcf, bed ]. Default: VCF."
+  echo "        example: \"VCF\""
+  echo ""
+  echo "    --file_list"
+  echo "        type: boolean_true"
+  echo "        Input actually contains a list of files to process."
+  echo ""
+  echo "    -o, --output_format"
+  echo "        type: string"
+  echo "        example: VCF"
+  echo "        Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF."
+  echo ""
+  echo "    -s, --htmlStats, --stats"
+  echo "        type: boolean_true"
+  echo "        Create HTML summary file."
+  echo ""
+  echo "    --no_stats"
+  echo "        type: boolean_true"
+  echo "        Do not create stats (summary) file."
+  echo ""
+  echo "Results filter options:"
+  echo "    --filterInterval, --fi"
+  echo "        type: file, file must exist"
+  echo "        Only analyze changes that intersect with the intervals"
+  echo "        specified in this file. This option can be used several times."
+  echo ""
+  echo "    --no_downstream"
+  echo "        type: boolean_true"
+  echo "        Do not show DOWNSTREAM changes"
+  echo ""
+  echo "    --no_intergenic"
+  echo "        type: boolean_true"
+  echo "        Do not show INTERGENIC changes."
+  echo ""
+  echo "    --no_intron"
+  echo "        type: boolean_true"
+  echo "        Do not show INTRON changes."
+  echo ""
+  echo "    --no_upstream"
+  echo "        type: boolean_true"
+  echo "        Do not show UPSTREAM changes."
+  echo ""
+  echo "    --no_utr"
+  echo "        type: boolean_true"
+  echo "        Do not show 5_PRIME_UTR or 3_PRIME_UTR changes."
+  echo ""
+  echo "    --no"
+  echo "        type: string"
+  echo "        Do not show 'EffectType'. This option can be used several times."
+  echo ""
+  echo "Annotations options:"
+  echo "    --cancer"
+  echo "        type: boolean_true"
+  echo "        Perform 'cancer' comparisons (Somatic vs Germline)."
+  echo ""
+  echo "    --cancer_samples"
+  echo "        type: file, file must exist"
+  echo "        Two column TXT file defining 'original \\t derived' samples."
+  echo ""
+  echo "    --fastaprot"
+  echo "        type: file, file must exist"
+  echo "        Create an output file containing the resulting protein sequences."
+  echo ""
+  echo "    --format_eff"
+  echo "        type: boolean_true"
+  echo "        Use 'EFF' field compatible with older versions (instead of 'ANN')."
+  echo ""
+  echo "    --gene_id"
+  echo "        type: boolean_true"
+  echo "        Use gene ID instead of gene name (VCF output)."
+  echo ""
+  echo "    --hgvs"
+  echo "        type: boolean_true"
+  echo "        Use HGVS annotations for amino acid sub-field."
+  echo ""
+  echo "    --hgvs_old"
+  echo "        type: boolean_true"
+  echo "        Use old HGVS notation."
+  echo ""
+  echo "    --hgvs1_letter_aa"
+  echo "        type: boolean_true"
+  echo "        Use one letter Amino acid codes in HGVS notation."
+  echo ""
+  echo "    --hgvs_tr_id"
+  echo "        type: boolean_true"
+  echo "        Use transcript ID in HGVS notation."
+  echo ""
+  echo "    --lof"
+  echo "        type: boolean_true"
+  echo "        Add loss of function (LOF) and Nonsense mediated decay (NMD) tags."
+  echo ""
+  echo "    -no_hgvs"
+  echo "        type: boolean_true"
+  echo "        Do not add HGVS annotations."
+  echo ""
+  echo "    --no_lof"
+  echo "        type: boolean_true"
+  echo "        Do not add LOF and NMD annotations."
+  echo ""
+  echo "    --no_shift_hgvs"
+  echo "        type: boolean_true"
+  echo "        Do not shift variants according to HGVS notation (most 3prime end)."
+  echo ""
+  echo "    --oicr"
+  echo "        type: boolean_true"
+  echo "        Add OICR tag in VCF file."
+  echo ""
+  echo "    --sequence_ontology"
+  echo "        type: boolean_true"
+  echo "        Use Sequence Ontology terms."
+  echo ""
+  echo "Generic options:"
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        Specify config file"
+  echo ""
+  echo "    --config_option"
+  echo "        type: string"
+  echo "        Override a config file option (name=value)."
+  echo ""
+  echo "    -d, --debug"
+  echo "        type: boolean_true"
+  echo "        Debug mode (very verbose)."
+  echo ""
+  echo "    --data_dir"
+  echo "        type: file, file must exist"
+  echo "        Override data_dir parameter from config file."
+  echo ""
+  echo "    --no_download"
+  echo "        type: boolean_true"
+  echo "        Do not download a SnpEff database, if not available locally."
+  echo ""
+  echo "    --no_log"
+  echo "        type: boolean_true"
+  echo "        Do not report usage statistics to server."
+  echo ""
+  echo "    -q, --quiet"
+  echo "        type: boolean_true"
+  echo "        Quiet mode (do not show any messages or errors)"
+  echo ""
+  echo "    -v, --verbose"
+  echo "        type: boolean_true"
+  echo "        Verbose mode."
+  echo ""
+  echo "Database options:"
+  echo "    --canon"
+  echo "        type: boolean_true"
+  echo "        Only use canonical transcripts."
+  echo ""
+  echo "    --canon_list"
+  echo "        type: file, file must exist"
+  echo "        Only use canonical transcripts, replace some transcripts using the"
+  echo "        'gene_id"
+  echo "        transcript_id' entries in <file>."
+  echo ""
+  echo "    --tag"
+  echo "        type: string"
+  echo "        Only use transcript having a tag 'tagName'. This option can be used"
+  echo "        multiple times."
+  echo ""
+  echo "    --no_tag"
+  echo "        type: boolean_true"
+  echo "        Filter out transcript having a tag 'tagName'. This option can be used"
+  echo "        multiple times."
+  echo ""
+  echo "    --interaction"
+  echo "        type: boolean_true"
+  echo "        Annotate using interactions (requires interaction database)."
+  echo ""
+  echo "    --interval"
+  echo "        type: file, file must exist"
+  echo "        Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this"
+  echo "        option many times)."
+  echo ""
+  echo "    --max_tsl"
+  echo "        type: integer"
+  echo "        Only use transcripts having Transcript Support Level lower than"
+  echo "        <TSL_number>."
+  echo ""
+  echo "    --motif"
+  echo "        type: boolean_true"
+  echo "        Annotate using motifs (requires Motif database)."
+  echo ""
+  echo "    --nextprot"
+  echo "        type: boolean_true"
+  echo "        Annotate using NextProt (requires NextProt database)."
+  echo ""
+  echo "    --no_genome"
+  echo "        type: boolean_true"
+  echo "        Do not load any genomic database (e.g. annotate using custom files)."
+  echo ""
+  echo "    --no_expand_iub"
+  echo "        type: boolean_true"
+  echo "        Disable IUB code expansion in input variants."
+  echo ""
+  echo "    --no_interaction"
+  echo "        type: boolean_true"
+  echo "        Disable inteaction annotations."
+  echo ""
+  echo "    --no_motif"
+  echo "        type: boolean_true"
+  echo "        Disable motif annotations."
+  echo ""
+  echo "    --no_nextprot"
+  echo "        type: boolean_true"
+  echo "        Disable NextProt annotations."
+  echo ""
+  echo "    --only_reg"
+  echo "        type: boolean_true"
+  echo "        Only use regulation tracks."
+  echo ""
+  echo "    --only_protein"
+  echo "        type: boolean_true"
+  echo "        Only use protein coding transcripts."
+  echo ""
+  echo "    --only_tr"
+  echo "        type: file, file must exist"
+  echo "        example: file.txt"
+  echo "        Only use the transcripts in this file. Format: One transcript ID per"
+  echo "        line."
+  echo ""
+  echo "    --reg"
+  echo "        type: string"
+  echo "        Regulation track to use (this option can be used add several times)."
+  echo ""
+  echo "    --spliceSiteSize, --ss"
+  echo "        type: integer"
+  echo "        Set size for splice sites (donor and acceptor) in bases. Default: 2."
+  echo ""
+  echo "    --splice_region_exon_size"
+  echo "        type: integer"
+  echo "        Set size for splice site region within exons. Default: 3 bases."
+  echo ""
+  echo "    --splice_region_intron_min"
+  echo "        type: integer"
+  echo "        Set minimum number of bases for splice site region within intron."
+  echo "        Default: 3 bases."
+  echo ""
+  echo "    --splice_region_intron_max"
+  echo "        type: integer"
+  echo "        Set maximum number of bases for splice site region within intron."
+  echo "        Default: 8 bases."
+  echo ""
+  echo "    --strict"
+  echo "        type: boolean_true"
+  echo "        Only use 'validated' transcripts (i.e. sequence has been checked)."
+  echo ""
+  echo "    --upDownStreamLen, --ud"
+  echo "        type: integer"
+  echo "        Set upstream downstream interval length (in bases)."
+}
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/staphb/snpeff:5.2a
+ENTRYPOINT []
+RUN version=$(snpEff -version) && \
+version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
+echo "$version_trimmed" > /var/software_versions.txt
+
+LABEL org.opencontainers.image.description="Companion container for running component snpeff"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+# initialise array
+VIASH_POSITIONAL_ARGS=''
+
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        -h|--help)
+            ViashHelp
+            exit
+            ;;
+        ---v|---verbose)
+            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
+            shift 1
+            ;;
+        ---verbosity)
+            VIASH_VERBOSITY="$2"
+            shift 2
+            ;;
+        ---verbosity=*)
+            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        --version)
+            echo "snpeff main"
+            exit
+            ;;
+        --input)
+            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --input=*)
+            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --genome_version)
+            [ -n "$VIASH_PAR_GENOME_VERSION" ] && ViashError Bad arguments for option \'--genome_version\': \'$VIASH_PAR_GENOME_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GENOME_VERSION="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_version. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --genome_version=*)
+            [ -n "$VIASH_PAR_GENOME_VERSION" ] && ViashError Bad arguments for option \'--genome_version=*\': \'$VIASH_PAR_GENOME_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GENOME_VERSION=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --output)
+            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --output=*)
+            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --summary)
+            [ -n "$VIASH_PAR_SUMMARY" ] && ViashError Bad arguments for option \'--summary\': \'$VIASH_PAR_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SUMMARY="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --summary. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --summary=*)
+            [ -n "$VIASH_PAR_SUMMARY" ] && ViashError Bad arguments for option \'--summary=*\': \'$VIASH_PAR_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SUMMARY=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --genes)
+            [ -n "$VIASH_PAR_GENES" ] && ViashError Bad arguments for option \'--genes\': \'$VIASH_PAR_GENES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GENES="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genes. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --genes=*)
+            [ -n "$VIASH_PAR_GENES" ] && ViashError Bad arguments for option \'--genes=*\': \'$VIASH_PAR_GENES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GENES=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --chr)
+            [ -n "$VIASH_PAR_CHR" ] && ViashError Bad arguments for option \'--chr\': \'$VIASH_PAR_CHR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CHR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chr. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --chr=*)
+            [ -n "$VIASH_PAR_CHR" ] && ViashError Bad arguments for option \'--chr=*\': \'$VIASH_PAR_CHR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CHR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --classic)
+            [ -n "$VIASH_PAR_CLASSIC" ] && ViashError Bad arguments for option \'--classic\': \'$VIASH_PAR_CLASSIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CLASSIC=true
+            shift 1
+            ;;
+        --csv_stats)
+            [ -n "$VIASH_PAR_CSV_STATS" ] && ViashError Bad arguments for option \'--csv_stats\': \'$VIASH_PAR_CSV_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CSV_STATS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --csv_stats. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --csv_stats=*)
+            [ -n "$VIASH_PAR_CSV_STATS" ] && ViashError Bad arguments for option \'--csv_stats=*\': \'$VIASH_PAR_CSV_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CSV_STATS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --download)
+            [ -n "$VIASH_PAR_DOWNLOAD" ] && ViashError Bad arguments for option \'--download\': \'$VIASH_PAR_DOWNLOAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DOWNLOAD=true
+            shift 1
+            ;;
+        --input_format)
+            [ -n "$VIASH_PAR_INPUT_FORMAT" ] && ViashError Bad arguments for option \'--input_format\': \'$VIASH_PAR_INPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_FORMAT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_format. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --input_format=*)
+            [ -n "$VIASH_PAR_INPUT_FORMAT" ] && ViashError Bad arguments for option \'--input_format=*\': \'$VIASH_PAR_INPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_FORMAT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        -i)
+            [ -n "$VIASH_PAR_INPUT_FORMAT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_FORMAT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --file_list)
+            [ -n "$VIASH_PAR_FILE_LIST" ] && ViashError Bad arguments for option \'--file_list\': \'$VIASH_PAR_FILE_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FILE_LIST=true
+            shift 1
+            ;;
+        --output_format)
+            [ -n "$VIASH_PAR_OUTPUT_FORMAT" ] && ViashError Bad arguments for option \'--output_format\': \'$VIASH_PAR_OUTPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_FORMAT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_format. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --output_format=*)
+            [ -n "$VIASH_PAR_OUTPUT_FORMAT" ] && ViashError Bad arguments for option \'--output_format=*\': \'$VIASH_PAR_OUTPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_FORMAT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        -o)
+            [ -n "$VIASH_PAR_OUTPUT_FORMAT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_FORMAT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --stats)
+            [ -n "$VIASH_PAR_STATS" ] && ViashError Bad arguments for option \'--stats\': \'$VIASH_PAR_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STATS=true
+            shift 1
+            ;;
+        -s)
+            [ -n "$VIASH_PAR_STATS" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STATS=true
+            shift 1
+            ;;
+        --htmlStats)
+            [ -n "$VIASH_PAR_STATS" ] && ViashError Bad arguments for option \'--htmlStats\': \'$VIASH_PAR_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STATS=true
+            shift 1
+            ;;
+        --no_stats)
+            [ -n "$VIASH_PAR_NO_STATS" ] && ViashError Bad arguments for option \'--no_stats\': \'$VIASH_PAR_NO_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_STATS=true
+            shift 1
+            ;;
+        --fi)
+            [ -n "$VIASH_PAR_FI" ] && ViashError Bad arguments for option \'--fi\': \'$VIASH_PAR_FI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FI="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fi. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --fi=*)
+            [ -n "$VIASH_PAR_FI" ] && ViashError Bad arguments for option \'--fi=*\': \'$VIASH_PAR_FI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FI=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --filterInterval)
+            [ -n "$VIASH_PAR_FI" ] && ViashError Bad arguments for option \'--filterInterval\': \'$VIASH_PAR_FI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FI="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --filterInterval. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --no_downstream)
+            [ -n "$VIASH_PAR_NO_DOWNSTREAM" ] && ViashError Bad arguments for option \'--no_downstream\': \'$VIASH_PAR_NO_DOWNSTREAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_DOWNSTREAM=true
+            shift 1
+            ;;
+        --no_intergenic)
+            [ -n "$VIASH_PAR_NO_INTERGENIC" ] && ViashError Bad arguments for option \'--no_intergenic\': \'$VIASH_PAR_NO_INTERGENIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_INTERGENIC=true
+            shift 1
+            ;;
+        --no_intron)
+            [ -n "$VIASH_PAR_NO_INTRON" ] && ViashError Bad arguments for option \'--no_intron\': \'$VIASH_PAR_NO_INTRON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_INTRON=true
+            shift 1
+            ;;
+        --no_upstream)
+            [ -n "$VIASH_PAR_NO_UPSTREAM" ] && ViashError Bad arguments for option \'--no_upstream\': \'$VIASH_PAR_NO_UPSTREAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_UPSTREAM=true
+            shift 1
+            ;;
+        --no_utr)
+            [ -n "$VIASH_PAR_NO_UTR" ] && ViashError Bad arguments for option \'--no_utr\': \'$VIASH_PAR_NO_UTR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_UTR=true
+            shift 1
+            ;;
+        --no)
+            [ -n "$VIASH_PAR_NO" ] && ViashError Bad arguments for option \'--no\': \'$VIASH_PAR_NO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --no. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --no=*)
+            [ -n "$VIASH_PAR_NO" ] && ViashError Bad arguments for option \'--no=*\': \'$VIASH_PAR_NO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --cancer)
+            [ -n "$VIASH_PAR_CANCER" ] && ViashError Bad arguments for option \'--cancer\': \'$VIASH_PAR_CANCER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CANCER=true
+            shift 1
+            ;;
+        --cancer_samples)
+            [ -n "$VIASH_PAR_CANCER_SAMPLES" ] && ViashError Bad arguments for option \'--cancer_samples\': \'$VIASH_PAR_CANCER_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CANCER_SAMPLES="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cancer_samples. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --cancer_samples=*)
+            [ -n "$VIASH_PAR_CANCER_SAMPLES" ] && ViashError Bad arguments for option \'--cancer_samples=*\': \'$VIASH_PAR_CANCER_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CANCER_SAMPLES=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --fastaprot)
+            [ -n "$VIASH_PAR_FASTAPROT" ] && ViashError Bad arguments for option \'--fastaprot\': \'$VIASH_PAR_FASTAPROT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FASTAPROT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastaprot. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --fastaprot=*)
+            [ -n "$VIASH_PAR_FASTAPROT" ] && ViashError Bad arguments for option \'--fastaprot=*\': \'$VIASH_PAR_FASTAPROT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FASTAPROT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --format_eff)
+            [ -n "$VIASH_PAR_FORMAT_EFF" ] && ViashError Bad arguments for option \'--format_eff\': \'$VIASH_PAR_FORMAT_EFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FORMAT_EFF=true
+            shift 1
+            ;;
+        --gene_id)
+            [ -n "$VIASH_PAR_GENE_ID" ] && ViashError Bad arguments for option \'--gene_id\': \'$VIASH_PAR_GENE_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GENE_ID=true
+            shift 1
+            ;;
+        --hgvs)
+            [ -n "$VIASH_PAR_HGVS" ] && ViashError Bad arguments for option \'--hgvs\': \'$VIASH_PAR_HGVS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_HGVS=true
+            shift 1
+            ;;
+        --hgvs_old)
+            [ -n "$VIASH_PAR_HGVS_OLD" ] && ViashError Bad arguments for option \'--hgvs_old\': \'$VIASH_PAR_HGVS_OLD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_HGVS_OLD=true
+            shift 1
+            ;;
+        --hgvs1_letter_aa)
+            [ -n "$VIASH_PAR_HGVS1_LETTER_AA" ] && ViashError Bad arguments for option \'--hgvs1_letter_aa\': \'$VIASH_PAR_HGVS1_LETTER_AA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_HGVS1_LETTER_AA=true
+            shift 1
+            ;;
+        --hgvs_tr_id)
+            [ -n "$VIASH_PAR_HGVS_TR_ID" ] && ViashError Bad arguments for option \'--hgvs_tr_id\': \'$VIASH_PAR_HGVS_TR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_HGVS_TR_ID=true
+            shift 1
+            ;;
+        --lof)
+            [ -n "$VIASH_PAR_LOF" ] && ViashError Bad arguments for option \'--lof\': \'$VIASH_PAR_LOF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_LOF=true
+            shift 1
+            ;;
+        -no_hgvs)
+            [ -n "$VIASH_PAR_NO_HGVS" ] && ViashError Bad arguments for option \'-no_hgvs\': \'$VIASH_PAR_NO_HGVS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_HGVS=true
+            shift 1
+            ;;
+        --no_lof)
+            [ -n "$VIASH_PAR_NO_LOF" ] && ViashError Bad arguments for option \'--no_lof\': \'$VIASH_PAR_NO_LOF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_LOF=true
+            shift 1
+            ;;
+        --no_shift_hgvs)
+            [ -n "$VIASH_PAR_NO_SHIFT_HGVS" ] && ViashError Bad arguments for option \'--no_shift_hgvs\': \'$VIASH_PAR_NO_SHIFT_HGVS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_SHIFT_HGVS=true
+            shift 1
+            ;;
+        --oicr)
+            [ -n "$VIASH_PAR_OICR" ] && ViashError Bad arguments for option \'--oicr\': \'$VIASH_PAR_OICR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OICR=true
+            shift 1
+            ;;
+        --sequence_ontology)
+            [ -n "$VIASH_PAR_SEQUENCE_ONTOLOGY" ] && ViashError Bad arguments for option \'--sequence_ontology\': \'$VIASH_PAR_SEQUENCE_ONTOLOGY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SEQUENCE_ONTOLOGY=true
+            shift 1
+            ;;
+        --config)
+            [ -n "$VIASH_PAR_CONFIG" ] && ViashError Bad arguments for option \'--config\': \'$VIASH_PAR_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CONFIG="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --config. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --config=*)
+            [ -n "$VIASH_PAR_CONFIG" ] && ViashError Bad arguments for option \'--config=*\': \'$VIASH_PAR_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CONFIG=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        -c)
+            [ -n "$VIASH_PAR_CONFIG" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CONFIG="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --config_option)
+            [ -n "$VIASH_PAR_CONFIG_OPTION" ] && ViashError Bad arguments for option \'--config_option\': \'$VIASH_PAR_CONFIG_OPTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CONFIG_OPTION="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --config_option. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --config_option=*)
+            [ -n "$VIASH_PAR_CONFIG_OPTION" ] && ViashError Bad arguments for option \'--config_option=*\': \'$VIASH_PAR_CONFIG_OPTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CONFIG_OPTION=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --debug)
+            [ -n "$VIASH_PAR_DEBUG" ] && ViashError Bad arguments for option \'--debug\': \'$VIASH_PAR_DEBUG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DEBUG=true
+            shift 1
+            ;;
+        -d)
+            [ -n "$VIASH_PAR_DEBUG" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_DEBUG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DEBUG=true
+            shift 1
+            ;;
+        --data_dir)
+            [ -n "$VIASH_PAR_DATA_DIR" ] && ViashError Bad arguments for option \'--data_dir\': \'$VIASH_PAR_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DATA_DIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --data_dir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --data_dir=*)
+            [ -n "$VIASH_PAR_DATA_DIR" ] && ViashError Bad arguments for option \'--data_dir=*\': \'$VIASH_PAR_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DATA_DIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --no_download)
+            [ -n "$VIASH_PAR_NO_DOWNLOAD" ] && ViashError Bad arguments for option \'--no_download\': \'$VIASH_PAR_NO_DOWNLOAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_DOWNLOAD=true
+            shift 1
+            ;;
+        --no_log)
+            [ -n "$VIASH_PAR_NO_LOG" ] && ViashError Bad arguments for option \'--no_log\': \'$VIASH_PAR_NO_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_LOG=true
+            shift 1
+            ;;
+        --quiet)
+            [ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'--quiet\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QUIET=true
+            shift 1
+            ;;
+        -q)
+            [ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QUIET=true
+            shift 1
+            ;;
+        --verbose)
+            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_VERBOSE=true
+            shift 1
+            ;;
+        -v)
+            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_VERBOSE=true
+            shift 1
+            ;;
+        --canon)
+            [ -n "$VIASH_PAR_CANON" ] && ViashError Bad arguments for option \'--canon\': \'$VIASH_PAR_CANON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CANON=true
+            shift 1
+            ;;
+        --canon_list)
+            [ -n "$VIASH_PAR_CANON_LIST" ] && ViashError Bad arguments for option \'--canon_list\': \'$VIASH_PAR_CANON_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CANON_LIST="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --canon_list. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --canon_list=*)
+            [ -n "$VIASH_PAR_CANON_LIST" ] && ViashError Bad arguments for option \'--canon_list=*\': \'$VIASH_PAR_CANON_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_CANON_LIST=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --tag)
+            [ -n "$VIASH_PAR_TAG" ] && ViashError Bad arguments for option \'--tag\': \'$VIASH_PAR_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_TAG="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --tag. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --tag=*)
+            [ -n "$VIASH_PAR_TAG" ] && ViashError Bad arguments for option \'--tag=*\': \'$VIASH_PAR_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_TAG=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --no_tag)
+            [ -n "$VIASH_PAR_NO_TAG" ] && ViashError Bad arguments for option \'--no_tag\': \'$VIASH_PAR_NO_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_TAG=true
+            shift 1
+            ;;
+        --interaction)
+            [ -n "$VIASH_PAR_INTERACTION" ] && ViashError Bad arguments for option \'--interaction\': \'$VIASH_PAR_INTERACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INTERACTION=true
+            shift 1
+            ;;
+        --interval)
+            [ -n "$VIASH_PAR_INTERVAL" ] && ViashError Bad arguments for option \'--interval\': \'$VIASH_PAR_INTERVAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INTERVAL="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --interval. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --interval=*)
+            [ -n "$VIASH_PAR_INTERVAL" ] && ViashError Bad arguments for option \'--interval=*\': \'$VIASH_PAR_INTERVAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INTERVAL=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --max_tsl)
+            [ -n "$VIASH_PAR_MAX_TSL" ] && ViashError Bad arguments for option \'--max_tsl\': \'$VIASH_PAR_MAX_TSL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_MAX_TSL="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_tsl. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --max_tsl=*)
+            [ -n "$VIASH_PAR_MAX_TSL" ] && ViashError Bad arguments for option \'--max_tsl=*\': \'$VIASH_PAR_MAX_TSL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_MAX_TSL=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --motif)
+            [ -n "$VIASH_PAR_MOTIF" ] && ViashError Bad arguments for option \'--motif\': \'$VIASH_PAR_MOTIF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_MOTIF=true
+            shift 1
+            ;;
+        --nextprot)
+            [ -n "$VIASH_PAR_NEXTPROT" ] && ViashError Bad arguments for option \'--nextprot\': \'$VIASH_PAR_NEXTPROT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NEXTPROT=true
+            shift 1
+            ;;
+        --no_genome)
+            [ -n "$VIASH_PAR_NO_GENOME" ] && ViashError Bad arguments for option \'--no_genome\': \'$VIASH_PAR_NO_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_GENOME=true
+            shift 1
+            ;;
+        --no_expand_iub)
+            [ -n "$VIASH_PAR_NO_EXPAND_IUB" ] && ViashError Bad arguments for option \'--no_expand_iub\': \'$VIASH_PAR_NO_EXPAND_IUB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_EXPAND_IUB=true
+            shift 1
+            ;;
+        --no_interaction)
+            [ -n "$VIASH_PAR_NO_INTERACTION" ] && ViashError Bad arguments for option \'--no_interaction\': \'$VIASH_PAR_NO_INTERACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_INTERACTION=true
+            shift 1
+            ;;
+        --no_motif)
+            [ -n "$VIASH_PAR_NO_MOTIF" ] && ViashError Bad arguments for option \'--no_motif\': \'$VIASH_PAR_NO_MOTIF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_MOTIF=true
+            shift 1
+            ;;
+        --no_nextprot)
+            [ -n "$VIASH_PAR_NO_NEXTPROT" ] && ViashError Bad arguments for option \'--no_nextprot\': \'$VIASH_PAR_NO_NEXTPROT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NO_NEXTPROT=true
+            shift 1
+            ;;
+        --only_reg)
+            [ -n "$VIASH_PAR_ONLY_REG" ] && ViashError Bad arguments for option \'--only_reg\': \'$VIASH_PAR_ONLY_REG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ONLY_REG=true
+            shift 1
+            ;;
+        --only_protein)
+            [ -n "$VIASH_PAR_ONLY_PROTEIN" ] && ViashError Bad arguments for option \'--only_protein\': \'$VIASH_PAR_ONLY_PROTEIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ONLY_PROTEIN=true
+            shift 1
+            ;;
+        --only_tr)
+            [ -n "$VIASH_PAR_ONLY_TR" ] && ViashError Bad arguments for option \'--only_tr\': \'$VIASH_PAR_ONLY_TR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ONLY_TR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --only_tr. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --only_tr=*)
+            [ -n "$VIASH_PAR_ONLY_TR" ] && ViashError Bad arguments for option \'--only_tr=*\': \'$VIASH_PAR_ONLY_TR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ONLY_TR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --reg)
+            [ -n "$VIASH_PAR_REG" ] && ViashError Bad arguments for option \'--reg\': \'$VIASH_PAR_REG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_REG="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reg. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --reg=*)
+            [ -n "$VIASH_PAR_REG" ] && ViashError Bad arguments for option \'--reg=*\': \'$VIASH_PAR_REG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_REG=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --ss)
+            [ -n "$VIASH_PAR_SS" ] && ViashError Bad arguments for option \'--ss\': \'$VIASH_PAR_SS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ss. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --ss=*)
+            [ -n "$VIASH_PAR_SS" ] && ViashError Bad arguments for option \'--ss=*\': \'$VIASH_PAR_SS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --spliceSiteSize)
+            [ -n "$VIASH_PAR_SS" ] && ViashError Bad arguments for option \'--spliceSiteSize\': \'$VIASH_PAR_SS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --spliceSiteSize. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --splice_region_exon_size)
+            [ -n "$VIASH_PAR_SPLICE_REGION_EXON_SIZE" ] && ViashError Bad arguments for option \'--splice_region_exon_size\': \'$VIASH_PAR_SPLICE_REGION_EXON_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SPLICE_REGION_EXON_SIZE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --splice_region_exon_size. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --splice_region_exon_size=*)
+            [ -n "$VIASH_PAR_SPLICE_REGION_EXON_SIZE" ] && ViashError Bad arguments for option \'--splice_region_exon_size=*\': \'$VIASH_PAR_SPLICE_REGION_EXON_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SPLICE_REGION_EXON_SIZE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --splice_region_intron_min)
+            [ -n "$VIASH_PAR_SPLICE_REGION_INTRON_MIN" ] && ViashError Bad arguments for option \'--splice_region_intron_min\': \'$VIASH_PAR_SPLICE_REGION_INTRON_MIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SPLICE_REGION_INTRON_MIN="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --splice_region_intron_min. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --splice_region_intron_min=*)
+            [ -n "$VIASH_PAR_SPLICE_REGION_INTRON_MIN" ] && ViashError Bad arguments for option \'--splice_region_intron_min=*\': \'$VIASH_PAR_SPLICE_REGION_INTRON_MIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SPLICE_REGION_INTRON_MIN=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --splice_region_intron_max)
+            [ -n "$VIASH_PAR_SPLICE_REGION_INTRON_MAX" ] && ViashError Bad arguments for option \'--splice_region_intron_max\': \'$VIASH_PAR_SPLICE_REGION_INTRON_MAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SPLICE_REGION_INTRON_MAX="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --splice_region_intron_max. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --splice_region_intron_max=*)
+            [ -n "$VIASH_PAR_SPLICE_REGION_INTRON_MAX" ] && ViashError Bad arguments for option \'--splice_region_intron_max=*\': \'$VIASH_PAR_SPLICE_REGION_INTRON_MAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SPLICE_REGION_INTRON_MAX=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --strict)
+            [ -n "$VIASH_PAR_STRICT" ] && ViashError Bad arguments for option \'--strict\': \'$VIASH_PAR_STRICT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_STRICT=true
+            shift 1
+            ;;
+        --ud)
+            [ -n "$VIASH_PAR_UD" ] && ViashError Bad arguments for option \'--ud\': \'$VIASH_PAR_UD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_UD="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ud. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --ud=*)
+            [ -n "$VIASH_PAR_UD" ] && ViashError Bad arguments for option \'--ud=*\': \'$VIASH_PAR_UD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_UD=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --upDownStreamLen)
+            [ -n "$VIASH_PAR_UD" ] && ViashError Bad arguments for option \'--upDownStreamLen\': \'$VIASH_PAR_UD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_UD="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --upDownStreamLen. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---engine)
+            VIASH_ENGINE_ID="$2"
+            shift 2
+            ;;
+        ---engine=*)
+            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        ---setup)
+            VIASH_MODE='setup'
+            VIASH_SETUP_STRATEGY="$2"
+            shift 2
+            ;;
+        ---setup=*)
+            VIASH_MODE='setup'
+            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        ---dockerfile)
+            VIASH_MODE='dockerfile'
+            shift 1
+            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
+        ---debug)
+            VIASH_MODE='debug'
+            shift 1
+            ;;
+        ---cpus)
+            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_CPUS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---cpus=*)
+            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        ---memory)
+            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_MEMORY="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---memory=*)
+            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        *)  # positional arg or unknown option
+            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
+            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
+            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
+            shift # past argument
+            ;;
+    esac
+done
+
+# parse positional parameters
+eval set -- $VIASH_POSITIONAL_ARGS
+
+
+if   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+  VIASH_ENGINE_TYPE='native'
+elif   [ "$VIASH_ENGINE_ID" == "docker" ]  ; then
+  VIASH_ENGINE_TYPE='docker'
+else
+  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
+  exit 1
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # check if docker is installed properly
+  ViashDockerInstallationCheck
+
+  # determine docker image id
+  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/snpeff:main'
+  fi
+
+  # print dockerfile
+  if [ "$VIASH_MODE" == "dockerfile" ]; then
+    ViashDockerfile "$VIASH_ENGINE_ID"
+    exit 0
+
+  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
+    echo "$VIASH_DOCKER_IMAGE_ID"
+    exit 0
+  
+  # enter docker container
+  elif [[ "$VIASH_MODE" == "debug" ]]; then
+    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
+    ViashNotice "+ $VIASH_CMD"
+    eval $VIASH_CMD
+    exit 
+
+  # build docker image
+  elif [ "$VIASH_MODE" == "setup" ]; then
+    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
+    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
+    exit 0
+  fi
+
+  # check if docker image exists
+  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
+  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
+fi
+
+# setting computational defaults
+
+# helper function for parsing memory strings
+function ViashMemoryAsBytes {
+  local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
+  local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
+  if [[ $memory =~ $memory_regex ]]; then
+    local number=${memory/[^0-9]*/}
+    local symbol=${memory/*[0-9]/}
+    
+    case $symbol in
+      b)      memory_b=$number ;;
+      kb|k)   memory_b=$(( $number * 1000 )) ;;
+      mb|m)   memory_b=$(( $number * 1000 * 1000 )) ;;
+      gb|g)   memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
+      tb|t)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
+      pb|p)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
+      kib|ki)   memory_b=$(( $number * 1024 )) ;;
+      mib|mi)   memory_b=$(( $number * 1024 * 1024 )) ;;
+      gib|gi)   memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
+      tib|ti)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
+      pib|pi)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
+    esac
+    echo "$memory_b"
+  fi
+}
+# compute memory in different units
+if [ ! -z ${VIASH_META_MEMORY+x} ]; then
+  VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
+  # do not define other variables if memory_b is an empty string
+  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
+    VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
+    VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
+    VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
+    VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
+    VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
+    VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
+    VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
+    VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
+    VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
+    VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
+  else
+    # unset memory if string is empty
+    unset $VIASH_META_MEMORY_B
+  fi
+fi
+# unset nproc if string is empty
+if [ -z "$VIASH_META_CPUS" ]; then
+  unset $VIASH_META_CPUS
+fi
+
+
+# check whether required parameters exist
+if [ -z ${VIASH_PAR_INPUT+x} ]; then
+  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_PAR_GENOME_VERSION+x} ]; then
+  ViashError '--genome_version' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
+  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_NAME+x} ]; then
+  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
+  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
+  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
+  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_CONFIG+x} ]; then
+  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
+  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+
+# filling in defaults
+if [ -z ${VIASH_PAR_CLASSIC+x} ]; then
+  VIASH_PAR_CLASSIC="false"
+fi
+if [ -z ${VIASH_PAR_DOWNLOAD+x} ]; then
+  VIASH_PAR_DOWNLOAD="false"
+fi
+if [ -z ${VIASH_PAR_FILE_LIST+x} ]; then
+  VIASH_PAR_FILE_LIST="false"
+fi
+if [ -z ${VIASH_PAR_STATS+x} ]; then
+  VIASH_PAR_STATS="false"
+fi
+if [ -z ${VIASH_PAR_NO_STATS+x} ]; then
+  VIASH_PAR_NO_STATS="false"
+fi
+if [ -z ${VIASH_PAR_NO_DOWNSTREAM+x} ]; then
+  VIASH_PAR_NO_DOWNSTREAM="false"
+fi
+if [ -z ${VIASH_PAR_NO_INTERGENIC+x} ]; then
+  VIASH_PAR_NO_INTERGENIC="false"
+fi
+if [ -z ${VIASH_PAR_NO_INTRON+x} ]; then
+  VIASH_PAR_NO_INTRON="false"
+fi
+if [ -z ${VIASH_PAR_NO_UPSTREAM+x} ]; then
+  VIASH_PAR_NO_UPSTREAM="false"
+fi
+if [ -z ${VIASH_PAR_NO_UTR+x} ]; then
+  VIASH_PAR_NO_UTR="false"
+fi
+if [ -z ${VIASH_PAR_CANCER+x} ]; then
+  VIASH_PAR_CANCER="false"
+fi
+if [ -z ${VIASH_PAR_FORMAT_EFF+x} ]; then
+  VIASH_PAR_FORMAT_EFF="false"
+fi
+if [ -z ${VIASH_PAR_GENE_ID+x} ]; then
+  VIASH_PAR_GENE_ID="false"
+fi
+if [ -z ${VIASH_PAR_HGVS+x} ]; then
+  VIASH_PAR_HGVS="false"
+fi
+if [ -z ${VIASH_PAR_HGVS_OLD+x} ]; then
+  VIASH_PAR_HGVS_OLD="false"
+fi
+if [ -z ${VIASH_PAR_HGVS1_LETTER_AA+x} ]; then
+  VIASH_PAR_HGVS1_LETTER_AA="false"
+fi
+if [ -z ${VIASH_PAR_HGVS_TR_ID+x} ]; then
+  VIASH_PAR_HGVS_TR_ID="false"
+fi
+if [ -z ${VIASH_PAR_LOF+x} ]; then
+  VIASH_PAR_LOF="false"
+fi
+if [ -z ${VIASH_PAR_NO_HGVS+x} ]; then
+  VIASH_PAR_NO_HGVS="false"
+fi
+if [ -z ${VIASH_PAR_NO_LOF+x} ]; then
+  VIASH_PAR_NO_LOF="false"
+fi
+if [ -z ${VIASH_PAR_NO_SHIFT_HGVS+x} ]; then
+  VIASH_PAR_NO_SHIFT_HGVS="false"
+fi
+if [ -z ${VIASH_PAR_OICR+x} ]; then
+  VIASH_PAR_OICR="false"
+fi
+if [ -z ${VIASH_PAR_SEQUENCE_ONTOLOGY+x} ]; then
+  VIASH_PAR_SEQUENCE_ONTOLOGY="false"
+fi
+if [ -z ${VIASH_PAR_DEBUG+x} ]; then
+  VIASH_PAR_DEBUG="false"
+fi
+if [ -z ${VIASH_PAR_NO_DOWNLOAD+x} ]; then
+  VIASH_PAR_NO_DOWNLOAD="false"
+fi
+if [ -z ${VIASH_PAR_NO_LOG+x} ]; then
+  VIASH_PAR_NO_LOG="false"
+fi
+if [ -z ${VIASH_PAR_QUIET+x} ]; then
+  VIASH_PAR_QUIET="false"
+fi
+if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
+  VIASH_PAR_VERBOSE="false"
+fi
+if [ -z ${VIASH_PAR_CANON+x} ]; then
+  VIASH_PAR_CANON="false"
+fi
+if [ -z ${VIASH_PAR_NO_TAG+x} ]; then
+  VIASH_PAR_NO_TAG="false"
+fi
+if [ -z ${VIASH_PAR_INTERACTION+x} ]; then
+  VIASH_PAR_INTERACTION="false"
+fi
+if [ -z ${VIASH_PAR_MOTIF+x} ]; then
+  VIASH_PAR_MOTIF="false"
+fi
+if [ -z ${VIASH_PAR_NEXTPROT+x} ]; then
+  VIASH_PAR_NEXTPROT="false"
+fi
+if [ -z ${VIASH_PAR_NO_GENOME+x} ]; then
+  VIASH_PAR_NO_GENOME="false"
+fi
+if [ -z ${VIASH_PAR_NO_EXPAND_IUB+x} ]; then
+  VIASH_PAR_NO_EXPAND_IUB="false"
+fi
+if [ -z ${VIASH_PAR_NO_INTERACTION+x} ]; then
+  VIASH_PAR_NO_INTERACTION="false"
+fi
+if [ -z ${VIASH_PAR_NO_MOTIF+x} ]; then
+  VIASH_PAR_NO_MOTIF="false"
+fi
+if [ -z ${VIASH_PAR_NO_NEXTPROT+x} ]; then
+  VIASH_PAR_NO_NEXTPROT="false"
+fi
+if [ -z ${VIASH_PAR_ONLY_REG+x} ]; then
+  VIASH_PAR_ONLY_REG="false"
+fi
+if [ -z ${VIASH_PAR_ONLY_PROTEIN+x} ]; then
+  VIASH_PAR_ONLY_PROTEIN="false"
+fi
+if [ -z ${VIASH_PAR_STRICT+x} ]; then
+  VIASH_PAR_STRICT="false"
+fi
+
+# check whether required files exist
+if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
+  ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_CSV_STATS" ] && [ ! -e "$VIASH_PAR_CSV_STATS" ]; then
+  ViashError "Input file '$VIASH_PAR_CSV_STATS' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_FI" ] && [ ! -e "$VIASH_PAR_FI" ]; then
+  ViashError "Input file '$VIASH_PAR_FI' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_CANCER_SAMPLES" ] && [ ! -e "$VIASH_PAR_CANCER_SAMPLES" ]; then
+  ViashError "Input file '$VIASH_PAR_CANCER_SAMPLES' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_FASTAPROT" ] && [ ! -e "$VIASH_PAR_FASTAPROT" ]; then
+  ViashError "Input file '$VIASH_PAR_FASTAPROT' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_CONFIG" ] && [ ! -e "$VIASH_PAR_CONFIG" ]; then
+  ViashError "Input file '$VIASH_PAR_CONFIG' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_DATA_DIR" ] && [ ! -e "$VIASH_PAR_DATA_DIR" ]; then
+  ViashError "Input file '$VIASH_PAR_DATA_DIR' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_CANON_LIST" ] && [ ! -e "$VIASH_PAR_CANON_LIST" ]; then
+  ViashError "Input file '$VIASH_PAR_CANON_LIST' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_INTERVAL" ] && [ ! -e "$VIASH_PAR_INTERVAL" ]; then
+  ViashError "Input file '$VIASH_PAR_INTERVAL' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_ONLY_TR" ] && [ ! -e "$VIASH_PAR_ONLY_TR" ]; then
+  ViashError "Input file '$VIASH_PAR_ONLY_TR' does not exist."
+  exit 1
+fi
+
+# check whether parameters values are of the right type
+if [[ -n "$VIASH_PAR_CLASSIC" ]]; then
+  if ! [[ "$VIASH_PAR_CLASSIC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--classic' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_DOWNLOAD" ]]; then
+  if ! [[ "$VIASH_PAR_DOWNLOAD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--download' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_FILE_LIST" ]]; then
+  if ! [[ "$VIASH_PAR_FILE_LIST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--file_list' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_STATS" ]]; then
+  if ! [[ "$VIASH_PAR_STATS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--stats' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_STATS" ]]; then
+  if ! [[ "$VIASH_PAR_NO_STATS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_stats' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_DOWNSTREAM" ]]; then
+  if ! [[ "$VIASH_PAR_NO_DOWNSTREAM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_downstream' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_INTERGENIC" ]]; then
+  if ! [[ "$VIASH_PAR_NO_INTERGENIC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_intergenic' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_INTRON" ]]; then
+  if ! [[ "$VIASH_PAR_NO_INTRON" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_intron' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_UPSTREAM" ]]; then
+  if ! [[ "$VIASH_PAR_NO_UPSTREAM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_upstream' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_UTR" ]]; then
+  if ! [[ "$VIASH_PAR_NO_UTR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_utr' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_CANCER" ]]; then
+  if ! [[ "$VIASH_PAR_CANCER" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--cancer' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_FORMAT_EFF" ]]; then
+  if ! [[ "$VIASH_PAR_FORMAT_EFF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--format_eff' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_GENE_ID" ]]; then
+  if ! [[ "$VIASH_PAR_GENE_ID" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--gene_id' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_HGVS" ]]; then
+  if ! [[ "$VIASH_PAR_HGVS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--hgvs' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_HGVS_OLD" ]]; then
+  if ! [[ "$VIASH_PAR_HGVS_OLD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--hgvs_old' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_HGVS1_LETTER_AA" ]]; then
+  if ! [[ "$VIASH_PAR_HGVS1_LETTER_AA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--hgvs1_letter_aa' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_HGVS_TR_ID" ]]; then
+  if ! [[ "$VIASH_PAR_HGVS_TR_ID" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--hgvs_tr_id' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_LOF" ]]; then
+  if ! [[ "$VIASH_PAR_LOF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--lof' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_HGVS" ]]; then
+  if ! [[ "$VIASH_PAR_NO_HGVS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '-no_hgvs' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_LOF" ]]; then
+  if ! [[ "$VIASH_PAR_NO_LOF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_lof' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_SHIFT_HGVS" ]]; then
+  if ! [[ "$VIASH_PAR_NO_SHIFT_HGVS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_shift_hgvs' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_OICR" ]]; then
+  if ! [[ "$VIASH_PAR_OICR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--oicr' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_SEQUENCE_ONTOLOGY" ]]; then
+  if ! [[ "$VIASH_PAR_SEQUENCE_ONTOLOGY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--sequence_ontology' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_DEBUG" ]]; then
+  if ! [[ "$VIASH_PAR_DEBUG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--debug' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_DOWNLOAD" ]]; then
+  if ! [[ "$VIASH_PAR_NO_DOWNLOAD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_download' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_LOG" ]]; then
+  if ! [[ "$VIASH_PAR_NO_LOG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_log' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_QUIET" ]]; then
+  if ! [[ "$VIASH_PAR_QUIET" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--quiet' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
+  if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--verbose' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_CANON" ]]; then
+  if ! [[ "$VIASH_PAR_CANON" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--canon' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_TAG" ]]; then
+  if ! [[ "$VIASH_PAR_NO_TAG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_tag' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_INTERACTION" ]]; then
+  if ! [[ "$VIASH_PAR_INTERACTION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--interaction' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_MAX_TSL" ]]; then
+  if ! [[ "$VIASH_PAR_MAX_TSL" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--max_tsl' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_MOTIF" ]]; then
+  if ! [[ "$VIASH_PAR_MOTIF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--motif' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NEXTPROT" ]]; then
+  if ! [[ "$VIASH_PAR_NEXTPROT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--nextprot' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_GENOME" ]]; then
+  if ! [[ "$VIASH_PAR_NO_GENOME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_genome' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_EXPAND_IUB" ]]; then
+  if ! [[ "$VIASH_PAR_NO_EXPAND_IUB" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_expand_iub' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_INTERACTION" ]]; then
+  if ! [[ "$VIASH_PAR_NO_INTERACTION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_interaction' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_MOTIF" ]]; then
+  if ! [[ "$VIASH_PAR_NO_MOTIF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_motif' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NO_NEXTPROT" ]]; then
+  if ! [[ "$VIASH_PAR_NO_NEXTPROT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--no_nextprot' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_ONLY_REG" ]]; then
+  if ! [[ "$VIASH_PAR_ONLY_REG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--only_reg' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_ONLY_PROTEIN" ]]; then
+  if ! [[ "$VIASH_PAR_ONLY_PROTEIN" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--only_protein' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_SS" ]]; then
+  if ! [[ "$VIASH_PAR_SS" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--ss' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_SPLICE_REGION_EXON_SIZE" ]]; then
+  if ! [[ "$VIASH_PAR_SPLICE_REGION_EXON_SIZE" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--splice_region_exon_size' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_SPLICE_REGION_INTRON_MIN" ]]; then
+  if ! [[ "$VIASH_PAR_SPLICE_REGION_INTRON_MIN" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--splice_region_intron_min' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_SPLICE_REGION_INTRON_MAX" ]]; then
+  if ! [[ "$VIASH_PAR_SPLICE_REGION_INTRON_MAX" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--splice_region_intron_max' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_STRICT" ]]; then
+  if ! [[ "$VIASH_PAR_STRICT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--strict' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_UD" ]]; then
+  if ! [[ "$VIASH_PAR_UD" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--ud' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_CPUS" ]]; then
+  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_B" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+
+# create parent directories of output files, if so desired
+if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
+fi
+if [ ! -z "$VIASH_PAR_SUMMARY" ] && [ ! -d "$(dirname "$VIASH_PAR_SUMMARY")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_SUMMARY")"
+fi
+if [ ! -z "$VIASH_PAR_GENES" ] && [ ! -d "$(dirname "$VIASH_PAR_GENES")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_GENES")"
+fi
+
+if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+  if [ "$VIASH_MODE" == "run" ]; then
+    VIASH_CMD="bash"
+  else
+    ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
+    exit 1
+  fi
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # detect volumes from file arguments
+  VIASH_CHOWN_VARS=()
+if [ ! -z "$VIASH_PAR_INPUT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
+  VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
+fi
+if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
+  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
+fi
+if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SUMMARY")" )
+  VIASH_PAR_SUMMARY=$(ViashDockerAutodetectMount "$VIASH_PAR_SUMMARY")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_SUMMARY" )
+fi
+if [ ! -z "$VIASH_PAR_GENES" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENES")" )
+  VIASH_PAR_GENES=$(ViashDockerAutodetectMount "$VIASH_PAR_GENES")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_GENES" )
+fi
+if [ ! -z "$VIASH_PAR_CSV_STATS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CSV_STATS")" )
+  VIASH_PAR_CSV_STATS=$(ViashDockerAutodetectMount "$VIASH_PAR_CSV_STATS")
+fi
+if [ ! -z "$VIASH_PAR_FI" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FI")" )
+  VIASH_PAR_FI=$(ViashDockerAutodetectMount "$VIASH_PAR_FI")
+fi
+if [ ! -z "$VIASH_PAR_CANCER_SAMPLES" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CANCER_SAMPLES")" )
+  VIASH_PAR_CANCER_SAMPLES=$(ViashDockerAutodetectMount "$VIASH_PAR_CANCER_SAMPLES")
+fi
+if [ ! -z "$VIASH_PAR_FASTAPROT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTAPROT")" )
+  VIASH_PAR_FASTAPROT=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTAPROT")
+fi
+if [ ! -z "$VIASH_PAR_CONFIG" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CONFIG")" )
+  VIASH_PAR_CONFIG=$(ViashDockerAutodetectMount "$VIASH_PAR_CONFIG")
+fi
+if [ ! -z "$VIASH_PAR_DATA_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DATA_DIR")" )
+  VIASH_PAR_DATA_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_DATA_DIR")
+fi
+if [ ! -z "$VIASH_PAR_CANON_LIST" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CANON_LIST")" )
+  VIASH_PAR_CANON_LIST=$(ViashDockerAutodetectMount "$VIASH_PAR_CANON_LIST")
+fi
+if [ ! -z "$VIASH_PAR_INTERVAL" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INTERVAL")" )
+  VIASH_PAR_INTERVAL=$(ViashDockerAutodetectMount "$VIASH_PAR_INTERVAL")
+fi
+if [ ! -z "$VIASH_PAR_ONLY_TR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ONLY_TR")" )
+  VIASH_PAR_ONLY_TR=$(ViashDockerAutodetectMount "$VIASH_PAR_ONLY_TR")
+fi
+if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
+  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
+fi
+if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
+  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
+fi
+if [ ! -z "$VIASH_META_CONFIG" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
+  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
+fi
+if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
+  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
+fi
+  
+  # get unique mounts
+  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # change file ownership
+  function ViashPerformChown {
+    if (( ${#VIASH_CHOWN_VARS[@]} )); then
+      set +e
+      VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
+      ViashDebug "+ $VIASH_CMD"
+      eval $VIASH_CMD
+      set -e
+    fi
+  }
+  trap ViashPerformChown EXIT
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # helper function for filling in extra docker args
+  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
+    VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
+  fi
+  if [ ! -z "$VIASH_META_CPUS" ]; then
+    VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
+  fi
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
+fi
+
+
+# set dependency paths
+
+
+ViashDebug "Running command: $(echo $VIASH_CMD)"
+cat << VIASHEOF | eval $VIASH_CMD
+set -e
+tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-snpeff-XXXXXX").sh
+function clean_up {
+  rm "\$tempscript"
+}
+function interrupt {
+  echo -e "\nCTRL-C Pressed..."
+  exit 1
+}
+trap clean_up EXIT
+trap interrupt INT SIGINT
+cat > "\$tempscript" << 'VIASHMAIN'
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+# The following code has been auto-generated by Viash.
+$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
+$( if [ ! -z ${VIASH_PAR_GENOME_VERSION+x} ]; then echo "${VIASH_PAR_GENOME_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_genome_version='&'#" ; else echo "# par_genome_version="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
+$( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\"'\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
+$( if [ ! -z ${VIASH_PAR_GENES+x} ]; then echo "${VIASH_PAR_GENES}" | sed "s#'#'\"'\"'#g;s#.*#par_genes='&'#" ; else echo "# par_genes="; fi )
+$( if [ ! -z ${VIASH_PAR_CHR+x} ]; then echo "${VIASH_PAR_CHR}" | sed "s#'#'\"'\"'#g;s#.*#par_chr='&'#" ; else echo "# par_chr="; fi )
+$( if [ ! -z ${VIASH_PAR_CLASSIC+x} ]; then echo "${VIASH_PAR_CLASSIC}" | sed "s#'#'\"'\"'#g;s#.*#par_classic='&'#" ; else echo "# par_classic="; fi )
+$( if [ ! -z ${VIASH_PAR_CSV_STATS+x} ]; then echo "${VIASH_PAR_CSV_STATS}" | sed "s#'#'\"'\"'#g;s#.*#par_csv_stats='&'#" ; else echo "# par_csv_stats="; fi )
+$( if [ ! -z ${VIASH_PAR_DOWNLOAD+x} ]; then echo "${VIASH_PAR_DOWNLOAD}" | sed "s#'#'\"'\"'#g;s#.*#par_download='&'#" ; else echo "# par_download="; fi )
+$( if [ ! -z ${VIASH_PAR_INPUT_FORMAT+x} ]; then echo "${VIASH_PAR_INPUT_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_input_format='&'#" ; else echo "# par_input_format="; fi )
+$( if [ ! -z ${VIASH_PAR_FILE_LIST+x} ]; then echo "${VIASH_PAR_FILE_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_file_list='&'#" ; else echo "# par_file_list="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT_FORMAT+x} ]; then echo "${VIASH_PAR_OUTPUT_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_output_format='&'#" ; else echo "# par_output_format="; fi )
+$( if [ ! -z ${VIASH_PAR_STATS+x} ]; then echo "${VIASH_PAR_STATS}" | sed "s#'#'\"'\"'#g;s#.*#par_stats='&'#" ; else echo "# par_stats="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_STATS+x} ]; then echo "${VIASH_PAR_NO_STATS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_stats='&'#" ; else echo "# par_no_stats="; fi )
+$( if [ ! -z ${VIASH_PAR_FI+x} ]; then echo "${VIASH_PAR_FI}" | sed "s#'#'\"'\"'#g;s#.*#par_fi='&'#" ; else echo "# par_fi="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_DOWNSTREAM+x} ]; then echo "${VIASH_PAR_NO_DOWNSTREAM}" | sed "s#'#'\"'\"'#g;s#.*#par_no_downstream='&'#" ; else echo "# par_no_downstream="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_INTERGENIC+x} ]; then echo "${VIASH_PAR_NO_INTERGENIC}" | sed "s#'#'\"'\"'#g;s#.*#par_no_intergenic='&'#" ; else echo "# par_no_intergenic="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_INTRON+x} ]; then echo "${VIASH_PAR_NO_INTRON}" | sed "s#'#'\"'\"'#g;s#.*#par_no_intron='&'#" ; else echo "# par_no_intron="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_UPSTREAM+x} ]; then echo "${VIASH_PAR_NO_UPSTREAM}" | sed "s#'#'\"'\"'#g;s#.*#par_no_upstream='&'#" ; else echo "# par_no_upstream="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_UTR+x} ]; then echo "${VIASH_PAR_NO_UTR}" | sed "s#'#'\"'\"'#g;s#.*#par_no_utr='&'#" ; else echo "# par_no_utr="; fi )
+$( if [ ! -z ${VIASH_PAR_NO+x} ]; then echo "${VIASH_PAR_NO}" | sed "s#'#'\"'\"'#g;s#.*#par_no='&'#" ; else echo "# par_no="; fi )
+$( if [ ! -z ${VIASH_PAR_CANCER+x} ]; then echo "${VIASH_PAR_CANCER}" | sed "s#'#'\"'\"'#g;s#.*#par_cancer='&'#" ; else echo "# par_cancer="; fi )
+$( if [ ! -z ${VIASH_PAR_CANCER_SAMPLES+x} ]; then echo "${VIASH_PAR_CANCER_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_cancer_samples='&'#" ; else echo "# par_cancer_samples="; fi )
+$( if [ ! -z ${VIASH_PAR_FASTAPROT+x} ]; then echo "${VIASH_PAR_FASTAPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_fastaprot='&'#" ; else echo "# par_fastaprot="; fi )
+$( if [ ! -z ${VIASH_PAR_FORMAT_EFF+x} ]; then echo "${VIASH_PAR_FORMAT_EFF}" | sed "s#'#'\"'\"'#g;s#.*#par_format_eff='&'#" ; else echo "# par_format_eff="; fi )
+$( if [ ! -z ${VIASH_PAR_GENE_ID+x} ]; then echo "${VIASH_PAR_GENE_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_gene_id='&'#" ; else echo "# par_gene_id="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS+x} ]; then echo "${VIASH_PAR_HGVS}" | sed "s#'#'\"'\"'#g;s#.*#par_hgvs='&'#" ; else echo "# par_hgvs="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS_OLD+x} ]; then echo "${VIASH_PAR_HGVS_OLD}" | sed "s#'#'\"'\"'#g;s#.*#par_hgvs_old='&'#" ; else echo "# par_hgvs_old="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS1_LETTER_AA+x} ]; then echo "${VIASH_PAR_HGVS1_LETTER_AA}" | sed "s#'#'\"'\"'#g;s#.*#par_hgvs1_letter_aa='&'#" ; else echo "# par_hgvs1_letter_aa="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS_TR_ID+x} ]; then echo "${VIASH_PAR_HGVS_TR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_hgvs_tr_id='&'#" ; else echo "# par_hgvs_tr_id="; fi )
+$( if [ ! -z ${VIASH_PAR_LOF+x} ]; then echo "${VIASH_PAR_LOF}" | sed "s#'#'\"'\"'#g;s#.*#par_lof='&'#" ; else echo "# par_lof="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_HGVS+x} ]; then echo "${VIASH_PAR_NO_HGVS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_hgvs='&'#" ; else echo "# par_no_hgvs="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_LOF+x} ]; then echo "${VIASH_PAR_NO_LOF}" | sed "s#'#'\"'\"'#g;s#.*#par_no_lof='&'#" ; else echo "# par_no_lof="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_SHIFT_HGVS+x} ]; then echo "${VIASH_PAR_NO_SHIFT_HGVS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_shift_hgvs='&'#" ; else echo "# par_no_shift_hgvs="; fi )
+$( if [ ! -z ${VIASH_PAR_OICR+x} ]; then echo "${VIASH_PAR_OICR}" | sed "s#'#'\"'\"'#g;s#.*#par_oicr='&'#" ; else echo "# par_oicr="; fi )
+$( if [ ! -z ${VIASH_PAR_SEQUENCE_ONTOLOGY+x} ]; then echo "${VIASH_PAR_SEQUENCE_ONTOLOGY}" | sed "s#'#'\"'\"'#g;s#.*#par_sequence_ontology='&'#" ; else echo "# par_sequence_ontology="; fi )
+$( if [ ! -z ${VIASH_PAR_CONFIG+x} ]; then echo "${VIASH_PAR_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#par_config='&'#" ; else echo "# par_config="; fi )
+$( if [ ! -z ${VIASH_PAR_CONFIG_OPTION+x} ]; then echo "${VIASH_PAR_CONFIG_OPTION}" | sed "s#'#'\"'\"'#g;s#.*#par_config_option='&'#" ; else echo "# par_config_option="; fi )
+$( if [ ! -z ${VIASH_PAR_DEBUG+x} ]; then echo "${VIASH_PAR_DEBUG}" | sed "s#'#'\"'\"'#g;s#.*#par_debug='&'#" ; else echo "# par_debug="; fi )
+$( if [ ! -z ${VIASH_PAR_DATA_DIR+x} ]; then echo "${VIASH_PAR_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_data_dir='&'#" ; else echo "# par_data_dir="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_DOWNLOAD+x} ]; then echo "${VIASH_PAR_NO_DOWNLOAD}" | sed "s#'#'\"'\"'#g;s#.*#par_no_download='&'#" ; else echo "# par_no_download="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_LOG+x} ]; then echo "${VIASH_PAR_NO_LOG}" | sed "s#'#'\"'\"'#g;s#.*#par_no_log='&'#" ; else echo "# par_no_log="; fi )
+$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\"'\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
+$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
+$( if [ ! -z ${VIASH_PAR_CANON+x} ]; then echo "${VIASH_PAR_CANON}" | sed "s#'#'\"'\"'#g;s#.*#par_canon='&'#" ; else echo "# par_canon="; fi )
+$( if [ ! -z ${VIASH_PAR_CANON_LIST+x} ]; then echo "${VIASH_PAR_CANON_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_canon_list='&'#" ; else echo "# par_canon_list="; fi )
+$( if [ ! -z ${VIASH_PAR_TAG+x} ]; then echo "${VIASH_PAR_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_tag='&'#" ; else echo "# par_tag="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_TAG+x} ]; then echo "${VIASH_PAR_NO_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_no_tag='&'#" ; else echo "# par_no_tag="; fi )
+$( if [ ! -z ${VIASH_PAR_INTERACTION+x} ]; then echo "${VIASH_PAR_INTERACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_interaction='&'#" ; else echo "# par_interaction="; fi )
+$( if [ ! -z ${VIASH_PAR_INTERVAL+x} ]; then echo "${VIASH_PAR_INTERVAL}" | sed "s#'#'\"'\"'#g;s#.*#par_interval='&'#" ; else echo "# par_interval="; fi )
+$( if [ ! -z ${VIASH_PAR_MAX_TSL+x} ]; then echo "${VIASH_PAR_MAX_TSL}" | sed "s#'#'\"'\"'#g;s#.*#par_max_tsl='&'#" ; else echo "# par_max_tsl="; fi )
+$( if [ ! -z ${VIASH_PAR_MOTIF+x} ]; then echo "${VIASH_PAR_MOTIF}" | sed "s#'#'\"'\"'#g;s#.*#par_motif='&'#" ; else echo "# par_motif="; fi )
+$( if [ ! -z ${VIASH_PAR_NEXTPROT+x} ]; then echo "${VIASH_PAR_NEXTPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_nextprot='&'#" ; else echo "# par_nextprot="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_GENOME+x} ]; then echo "${VIASH_PAR_NO_GENOME}" | sed "s#'#'\"'\"'#g;s#.*#par_no_genome='&'#" ; else echo "# par_no_genome="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_EXPAND_IUB+x} ]; then echo "${VIASH_PAR_NO_EXPAND_IUB}" | sed "s#'#'\"'\"'#g;s#.*#par_no_expand_iub='&'#" ; else echo "# par_no_expand_iub="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_INTERACTION+x} ]; then echo "${VIASH_PAR_NO_INTERACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_no_interaction='&'#" ; else echo "# par_no_interaction="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_MOTIF+x} ]; then echo "${VIASH_PAR_NO_MOTIF}" | sed "s#'#'\"'\"'#g;s#.*#par_no_motif='&'#" ; else echo "# par_no_motif="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_NEXTPROT+x} ]; then echo "${VIASH_PAR_NO_NEXTPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_no_nextprot='&'#" ; else echo "# par_no_nextprot="; fi )
+$( if [ ! -z ${VIASH_PAR_ONLY_REG+x} ]; then echo "${VIASH_PAR_ONLY_REG}" | sed "s#'#'\"'\"'#g;s#.*#par_only_reg='&'#" ; else echo "# par_only_reg="; fi )
+$( if [ ! -z ${VIASH_PAR_ONLY_PROTEIN+x} ]; then echo "${VIASH_PAR_ONLY_PROTEIN}" | sed "s#'#'\"'\"'#g;s#.*#par_only_protein='&'#" ; else echo "# par_only_protein="; fi )
+$( if [ ! -z ${VIASH_PAR_ONLY_TR+x} ]; then echo "${VIASH_PAR_ONLY_TR}" | sed "s#'#'\"'\"'#g;s#.*#par_only_tr='&'#" ; else echo "# par_only_tr="; fi )
+$( if [ ! -z ${VIASH_PAR_REG+x} ]; then echo "${VIASH_PAR_REG}" | sed "s#'#'\"'\"'#g;s#.*#par_reg='&'#" ; else echo "# par_reg="; fi )
+$( if [ ! -z ${VIASH_PAR_SS+x} ]; then echo "${VIASH_PAR_SS}" | sed "s#'#'\"'\"'#g;s#.*#par_ss='&'#" ; else echo "# par_ss="; fi )
+$( if [ ! -z ${VIASH_PAR_SPLICE_REGION_EXON_SIZE+x} ]; then echo "${VIASH_PAR_SPLICE_REGION_EXON_SIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_splice_region_exon_size='&'#" ; else echo "# par_splice_region_exon_size="; fi )
+$( if [ ! -z ${VIASH_PAR_SPLICE_REGION_INTRON_MIN+x} ]; then echo "${VIASH_PAR_SPLICE_REGION_INTRON_MIN}" | sed "s#'#'\"'\"'#g;s#.*#par_splice_region_intron_min='&'#" ; else echo "# par_splice_region_intron_min="; fi )
+$( if [ ! -z ${VIASH_PAR_SPLICE_REGION_INTRON_MAX+x} ]; then echo "${VIASH_PAR_SPLICE_REGION_INTRON_MAX}" | sed "s#'#'\"'\"'#g;s#.*#par_splice_region_intron_max='&'#" ; else echo "# par_splice_region_intron_max="; fi )
+$( if [ ! -z ${VIASH_PAR_STRICT+x} ]; then echo "${VIASH_PAR_STRICT}" | sed "s#'#'\"'\"'#g;s#.*#par_strict='&'#" ; else echo "# par_strict="; fi )
+$( if [ ! -z ${VIASH_PAR_UD+x} ]; then echo "${VIASH_PAR_UD}" | sed "s#'#'\"'\"'#g;s#.*#par_ud='&'#" ; else echo "# par_ud="; fi )
+$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
+$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
+$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
+$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
+$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
+$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
+$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
+
+## VIASH END
+
+# Unset flags if 'false'
+unset_if_false=(
+    par_classic
+    par_download
+    par_file_list
+    par_stats
+    par_cancer
+    par_format_eff
+    par_gene_id
+    par_hgvs
+    par_hgvs_old
+    par_hgvs1_letter_aa
+    par_hgvs_tr_id
+    par_lof
+    par_oicr
+    par_sequence_ontology
+    par_debug
+    par_quiet
+    par_verbose
+    par_canon
+    par_interaction
+    par_motif
+    par_nextprot
+    par_only_reg
+    par_only_protein
+    par_strict
+    par_no_stats
+    par_no_downstream
+    par_no_intergenic
+    par_no_intron
+    par_no_upstream
+    par_no_utr
+    par_no_hgvs
+    par_no_lof
+    par_no_shift_hgvs
+    par_no_download
+    par_no_log
+    par_no_tag
+    par_no_genome
+    par_no_expand_iub
+    par_no_interaction
+    par_no_motif
+    par_no_nextprot
+)
+for par in \${unset_if_false[@]}; do
+    test_val="\${!par}" # contains the value of the 'par'
+    [[ "\$test_val" == "false" ]] && unset \$par
+done
+
+
+# Run SnpEff
+snpEff \\
+    \${par_chr:+-chr "\$par_chr"} \\
+    \${par_classic:+-classic} \\
+    \${par_csv_stats:+-csvStats "\$par_csv_stats"} \\
+    \${par_download:+-download} \\
+    \${par_input_format:+-i "\$par_input_format"} \\
+    \${par_file_list:+-fileList} \\
+    \${par_output_format:+-o "\$par_output_format"} \\
+    \${par_stats:+-stats} \\
+    \${par_no_stats:+-noStats} \\
+    \${par_fi:+-fi "\$par_fi"} \\
+    \${par_no_downstream:+-no-downstream} \\
+    \${par_no_intergenic:+-no-intergenic} \\
+    \${par_no_intron:+-no-intron} \\
+    \${par_no_upstream:+-no-upstream} \\
+    \${par_no_utr:+-no-utr} \\
+    \${par_no:+-no "\$par_no"} \\
+    \${par_cancer:+-cancer} \\
+    \${par_cancer_samples:+-cancerSamples "\$par_cancer_samples]"} \\
+    \${par_fastaprot:+-fastaProt "\$par_fastaprot]"} \\
+    \${par_format_eff:+-formatEff} \\
+    \${par_gene_id:+-geneId} \\
+    \${par_hgvs:+-hgvs} \\
+    \${par_hgvs_old:+-hgvsOld} \\
+    \${par_hgvs1_letter_aa:+-hgvs1LetterAa} \\
+    \${par_hgvs_tr_id:+-hgvsTrId} \\
+    \${par_lof:+-lof} \\
+    \${par_no_hgvs:+-noHgvs} \\
+    \${par_no_lof:+-noLof} \\
+    \${par_no_shift_hgvs:+-noShiftHgvs} \\
+    \${par_oicr:+-oicr} \\
+    \${par_sequence_ontology:+-sequenceOntology} \\
+    \${par_config:+-config "\$par_config"} \\
+    \${par_config_option:+-configOption "\$par_config_option"} \\
+    \${par_debug:+-debug} \\
+    \${par_data_dir:+-dataDir "\$par_data_dir"} \\
+    \${par_no_download:+-nodownload} \\
+    \${par_no_log:+-noLog} \\
+    \${par_quiet:+-quiet} \\
+    \${par_verbose:+-verbose} \\
+    \${par_canon:+-canon} \\
+    \${par_canon_list:+-canonList "\$par_canon_list"} \\
+    \${par_tag:+-tag "\$par_tag"} \\
+    \${par_no_tag:+-notag} \\
+    \${par_interaction:+-interaction} \\
+    \${par_interval:+-interval "\$par_interval"} \\
+    \${par_max_tsl:+-maxTSL "\$par_max_tsl"} \\
+    \${par_motif:+-motif} \\
+    \${par_nextprot:+-nextProt} \\
+    \${par_no_genome:+-noGenome} \\
+    \${par_no_expand_iub:+-noExpandIUB} \\
+    \${par_no_interaction:+-noInteraction} \\
+    \${par_no_motif:+-noMotif} \\
+    \${par_no_nextprot:+-noNextProt} \\
+    \${par_only_reg:+-onlyReg} \\
+    \${par_only_protein:+-onlyProtein} \\
+    \${par_only_tr:+-onlyTr "\$par_onlyTr"} \\
+    \${par_reg:+-reg "\$par_reg"} \\
+    \${par_ss:+-ss "\$par_ss"} \\
+    \${par_splice_region_exon_size:+-spliceRegionExonSize "\$par_splice_region_exon_size"} \\
+    \${par_splice_region_intron_min:+-spliceRegionIntronMin "\$par_splice_region_intron_min"} \\
+    \${par_splice_region_intron_max:+-spliceRegionIntronMax "\$par_splice_region_intron_max"} \\
+    \${par_strict:+-strict} \\
+    \${par_ud:+-ud "\$par_ud"} \\
+    "\$par_genome_version" \\
+    "\$par_input" \\
+    > "\$par_output"
+
+# Path of the output file (par_output)
+absolute_path=\$(realpath "\$par_output")
+directory_path=\$(dirname "\$absolute_path")
+
+# Move the automatically generated outputs to their locations
+if [ -z "\$par_no_stats" ]; then
+    if [ ! -z "\$par_summary" ]; then
+        mv -n snpEff_summary.html "\$par_summary"
+    else
+        mv -n snpEff_summary.html "\$directory_path"
+    fi
+fi 
+
+if [ -z "\$par_no_stats" ]; then
+    if [ ! -z "\$par_genes" ]; then
+        mv -n snpEff_genes.txt "\$par_genes"
+    else
+        mv -n snpEff_genes.txt "\$directory_path"
+    fi
+fi
+
+exit 0
+VIASHMAIN
+bash "\$tempscript" &
+wait "\$!"
+
+VIASHEOF
+
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # strip viash automount from file paths
+  
+  if [ ! -z "$VIASH_PAR_INPUT" ]; then
+    VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
+  fi
+  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
+    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
+  fi
+  if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
+    VIASH_PAR_SUMMARY=$(ViashDockerStripAutomount "$VIASH_PAR_SUMMARY")
+  fi
+  if [ ! -z "$VIASH_PAR_GENES" ]; then
+    VIASH_PAR_GENES=$(ViashDockerStripAutomount "$VIASH_PAR_GENES")
+  fi
+  if [ ! -z "$VIASH_PAR_CSV_STATS" ]; then
+    VIASH_PAR_CSV_STATS=$(ViashDockerStripAutomount "$VIASH_PAR_CSV_STATS")
+  fi
+  if [ ! -z "$VIASH_PAR_FI" ]; then
+    VIASH_PAR_FI=$(ViashDockerStripAutomount "$VIASH_PAR_FI")
+  fi
+  if [ ! -z "$VIASH_PAR_CANCER_SAMPLES" ]; then
+    VIASH_PAR_CANCER_SAMPLES=$(ViashDockerStripAutomount "$VIASH_PAR_CANCER_SAMPLES")
+  fi
+  if [ ! -z "$VIASH_PAR_FASTAPROT" ]; then
+    VIASH_PAR_FASTAPROT=$(ViashDockerStripAutomount "$VIASH_PAR_FASTAPROT")
+  fi
+  if [ ! -z "$VIASH_PAR_CONFIG" ]; then
+    VIASH_PAR_CONFIG=$(ViashDockerStripAutomount "$VIASH_PAR_CONFIG")
+  fi
+  if [ ! -z "$VIASH_PAR_DATA_DIR" ]; then
+    VIASH_PAR_DATA_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_DATA_DIR")
+  fi
+  if [ ! -z "$VIASH_PAR_CANON_LIST" ]; then
+    VIASH_PAR_CANON_LIST=$(ViashDockerStripAutomount "$VIASH_PAR_CANON_LIST")
+  fi
+  if [ ! -z "$VIASH_PAR_INTERVAL" ]; then
+    VIASH_PAR_INTERVAL=$(ViashDockerStripAutomount "$VIASH_PAR_INTERVAL")
+  fi
+  if [ ! -z "$VIASH_PAR_ONLY_TR" ]; then
+    VIASH_PAR_ONLY_TR=$(ViashDockerStripAutomount "$VIASH_PAR_ONLY_TR")
+  fi
+  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
+    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
+  fi
+  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
+    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
+  fi
+  if [ ! -z "$VIASH_META_CONFIG" ]; then
+    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
+  fi
+  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
+    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
+  fi
+fi
+
+
+# check whether required files exist
+if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
+  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_SUMMARY" ] && [ ! -e "$VIASH_PAR_SUMMARY" ]; then
+  ViashError "Output file '$VIASH_PAR_SUMMARY' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_GENES" ] && [ ! -e "$VIASH_PAR_GENES" ]; then
+  ViashError "Output file '$VIASH_PAR_GENES' does not exist."
+  exit 1
+fi
+
+
+exit 0
diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml
index 2273fb6a..77864c64 100644
--- a/target/executable/sortmerna/.config.vsh.yaml
+++ b/target/executable/sortmerna/.config.vsh.yaml
@@ -591,9 +591,9 @@ build_info:
   output: "target/executable/sortmerna"
   executable: "target/executable/sortmerna/sortmerna"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna
index c0ae6e54..d0dd2c56 100755
--- a/target/executable/sortmerna/sortmerna
+++ b/target/executable/sortmerna/sortmerna
@@ -744,9 +744,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
 bash sortmerna-4.3.6-Linux.sh --skip-license
 
 LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:58Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml
index 7a7323bb..016cb33f 100644
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2663,9 +2663,9 @@ build_info:
   output: "target/executable/star/star_align_reads"
   executable: "target/executable/star/star_align_reads/star_align_reads"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads
index 4783d5c7..903e2441 100755
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1920,9 +1920,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:52Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml
index 868d53b6..cbecc328 100644
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -333,9 +333,9 @@ build_info:
   output: "target/executable/star/star_genome_generate"
   executable: "target/executable/star/star_genome_generate/star_genome_generate"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate
index 91d5f854..1f211397 100755
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -577,9 +577,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:51Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml
index f281c3b0..393d2294 100644
--- a/target/executable/trimgalore/.config.vsh.yaml
+++ b/target/executable/trimgalore/.config.vsh.yaml
@@ -770,9 +770,9 @@ build_info:
   output: "target/executable/trimgalore"
   executable: "target/executable/trimgalore/trimgalore"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore
index a6845d0c..ddc48234 100755
--- a/target/executable/trimgalore/trimgalore
+++ b/target/executable/trimgalore/trimgalore
@@ -881,9 +881,9 @@ RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:57Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
 LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
index 244e5a2b..66119970 100644
--- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,9 +611,9 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_dedup"
   executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
index 71b86cc4..2373dac7 100755
--- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
+++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
@@ -770,9 +770,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:48Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
index 0ca55ead..5a06cd00 100644
--- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,9 +449,9 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_extract"
   executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
index 0bcb7ca3..3ba9db0e 100755
--- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
+++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
@@ -637,9 +637,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:47Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
index 4b4a92e4..3a38e82c 100644
--- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
@@ -256,9 +256,9 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_prepareforrsem"
   executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem
index 99601c5a..48ab393f 100755
--- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem
+++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem
@@ -519,9 +519,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem"
-LABEL org.opencontainers.image.created="2024-10-07T09:07:48Z"
+LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
index 43570422..99030b48 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,9 +235,9 @@ build_info:
   output: "target/nextflow/agat/agat_convert_bed2gff"
   executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf
index 9e7fcd4a..30a022e0 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf
@@ -3092,9 +3092,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_bed2gff",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
index f37cabe9..38450003 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,9 +225,9 @@ build_info:
   output: "target/nextflow/agat/agat_convert_embl2gff"
   executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf
index 36407741..5af54d74 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf
@@ -3085,9 +3085,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_embl2gff",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml
index 9911e8f6..fc1bffa0 100644
--- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -230,9 +230,9 @@ build_info:
   output: "target/nextflow/agat/agat_convert_genscan2gff"
   executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf
index 585a4cf9..806bfad1 100644
--- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf
@@ -3087,9 +3087,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_genscan2gff",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index ff1b8cc7..7a092537 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,9 +228,9 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2gtf"
   executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
index 57e2c2a6..4aee64f2 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
@@ -3068,9 +3068,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index 3721b4d9..d077c854 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,9 +188,9 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2tsv"
   executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
index cc828778..9c41c532 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
@@ -3046,9 +3046,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index 19e44d9d..554505e1 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,9 +195,9 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gxf2gxf"
   executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
index 75232487..89813b41 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
@@ -3046,9 +3046,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml
index e3a08b94..fb154e50 100644
--- a/target/nextflow/arriba/.config.vsh.yaml
+++ b/target/nextflow/arriba/.config.vsh.yaml
@@ -706,9 +706,9 @@ build_info:
   output: "target/nextflow/arriba"
   executable: "target/nextflow/arriba/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf
index c7538fd1..82b3570f 100644
--- a/target/nextflow/arriba/main.nf
+++ b/target/nextflow/arriba/main.nf
@@ -3592,9 +3592,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/arriba",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml
index 749afaa8..abc96b1e 100644
--- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -469,9 +469,9 @@ build_info:
   output: "target/nextflow/bcftools/bcftools_annotate"
   executable: "target/nextflow/bcftools/bcftools_annotate/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf
index 2fe18432..85a50724 100644
--- a/target/nextflow/bcftools/bcftools_annotate/main.nf
+++ b/target/nextflow/bcftools/bcftools_annotate/main.nf
@@ -3335,9 +3335,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_annotate",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml
index 43d6f870..052f1a54 100644
--- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml
@@ -335,9 +335,9 @@ build_info:
   output: "target/nextflow/bcftools/bcftools_concat"
   executable: "target/nextflow/bcftools/bcftools_concat/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf
index 2c59142b..f5826d9b 100644
--- a/target/nextflow/bcftools/bcftools_concat/main.nf
+++ b/target/nextflow/bcftools/bcftools_concat/main.nf
@@ -3207,9 +3207,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_concat",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml
index 718817b0..2a115151 100644
--- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
   output: "target/nextflow/bcftools/bcftools_norm"
   executable: "target/nextflow/bcftools/bcftools_norm/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf
index 3e89c7f9..9552c727 100644
--- a/target/nextflow/bcftools/bcftools_norm/main.nf
+++ b/target/nextflow/bcftools/bcftools_norm/main.nf
@@ -3300,9 +3300,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_norm",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
index c8301102..c0541845 100644
--- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,9 +185,9 @@ build_info:
   output: "target/nextflow/bcftools/bcftools_sort"
   executable: "target/nextflow/bcftools/bcftools_sort/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf
index 2e0bb7c0..eab6f206 100644
--- a/target/nextflow/bcftools/bcftools_sort/main.nf
+++ b/target/nextflow/bcftools/bcftools_sort/main.nf
@@ -3048,9 +3048,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_sort",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml
index 51369ee7..b1e8a4ba 100644
--- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml
@@ -458,9 +458,9 @@ build_info:
   output: "target/nextflow/bcftools/bcftools_stats"
   executable: "target/nextflow/bcftools/bcftools_stats/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf
index 159d4739..84e79426 100644
--- a/target/nextflow/bcftools/bcftools_stats/main.nf
+++ b/target/nextflow/bcftools/bcftools_stats/main.nf
@@ -3337,9 +3337,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_stats",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml
index 236bc69f..07e32490 100644
--- a/target/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/nextflow/bcl_convert/.config.vsh.yaml
@@ -418,9 +418,9 @@ build_info:
   output: "target/nextflow/bcl_convert"
   executable: "target/nextflow/bcl_convert/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf
index 2f52fa88..dcbe43d6 100644
--- a/target/nextflow/bcl_convert/main.nf
+++ b/target/nextflow/bcl_convert/main.nf
@@ -3329,9 +3329,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcl_convert",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index ce8677f3..e914cf4d 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -274,9 +274,9 @@ build_info:
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
index 8c3e098e..54331ce3 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
@@ -3146,9 +3146,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
index 4dc87c55..9d26d85e 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -1115,9 +1115,9 @@ build_info:
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf
index ab79f895..89f2fa26 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf
@@ -4193,9 +4193,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index 2cf1c33e..ca2eb1d3 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,9 +187,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bamtofastq"
   executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
index 3f523463..2f39872f 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
@@ -3050,9 +3050,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bamtofastq",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
index b70262e7..bf72eeb1 100644
--- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,9 +176,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bed12tobed6"
   executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf
index 58b2c59d..4b5b16d0 100644
--- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf
+++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf
@@ -3035,9 +3035,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bed12tobed6",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
index 95715359..b31a6555 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,9 +214,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bedtobam"
   executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
index 99793649..a0ede177 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf
+++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
@@ -3083,9 +3083,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bedtobam",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml
index 9ac9bd32..76de6d8a 100644
--- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -337,9 +337,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_genomecov"
   executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf
index 2793607d..b21a6beb 100644
--- a/target/nextflow/bedtools/bedtools_genomecov/main.nf
+++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf
@@ -3207,9 +3207,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_genomecov",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
index c88ec67b..a9619037 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,9 +232,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_getfasta"
   executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf
index fee09e76..40c0995e 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/main.nf
+++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf
@@ -3086,9 +3086,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_getfasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml
index bf426f45..4195bdb3 100644
--- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,9 +273,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_groupby"
   executable: "target/nextflow/bedtools/bedtools_groupby/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf
index 392facbd..55e57c50 100644
--- a/target/nextflow/bedtools/bedtools_groupby/main.nf
+++ b/target/nextflow/bedtools/bedtools_groupby/main.nf
@@ -3130,9 +3130,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_groupby",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
index fc062f82..f6bad6ab 100644
--- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,9 +410,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_intersect"
   executable: "target/nextflow/bedtools/bedtools_intersect/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf
index 4b971b25..35da9226 100644
--- a/target/nextflow/bedtools/bedtools_intersect/main.nf
+++ b/target/nextflow/bedtools/bedtools_intersect/main.nf
@@ -3282,9 +3282,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_intersect",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml
index 5ee6591d..0543e51c 100644
--- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,9 +210,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_links"
   executable: "target/nextflow/bedtools/bedtools_links/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf
index cad9b43b..4c1003e7 100644
--- a/target/nextflow/bedtools/bedtools_links/main.nf
+++ b/target/nextflow/bedtools/bedtools_links/main.nf
@@ -3073,9 +3073,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_links",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml
index 8d0842a2..e88e4115 100644
--- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,9 +279,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_merge"
   executable: "target/nextflow/bedtools/bedtools_merge/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf
index dbb62914..e746dcf1 100644
--- a/target/nextflow/bedtools/bedtools_merge/main.nf
+++ b/target/nextflow/bedtools/bedtools_merge/main.nf
@@ -3134,9 +3134,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_merge",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
index 9bef6637..c2ddabe6 100644
--- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_sort"
   executable: "target/nextflow/bedtools/bedtools_sort/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf
index 26dd26b5..97b9304e 100644
--- a/target/nextflow/bedtools/bedtools_sort/main.nf
+++ b/target/nextflow/bedtools/bedtools_sort/main.nf
@@ -3092,9 +3092,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_sort",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
index e2f291eb..590c158d 100644
--- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,9 +158,9 @@ build_info:
   output: "target/nextflow/busco/busco_download_datasets"
   executable: "target/nextflow/busco/busco_download_datasets/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf
index 0802def3..e3239b39 100644
--- a/target/nextflow/busco/busco_download_datasets/main.nf
+++ b/target/nextflow/busco/busco_download_datasets/main.nf
@@ -3011,9 +3011,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_download_datasets",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
index ef5e1762..2df647b2 100644
--- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,9 +145,9 @@ build_info:
   output: "target/nextflow/busco/busco_list_datasets"
   executable: "target/nextflow/busco/busco_list_datasets/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf
index da587152..d252e8f8 100644
--- a/target/nextflow/busco/busco_list_datasets/main.nf
+++ b/target/nextflow/busco/busco_list_datasets/main.nf
@@ -2997,9 +2997,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_list_datasets",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml
index a403970b..a9ae8837 100644
--- a/target/nextflow/busco/busco_run/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_run/.config.vsh.yaml
@@ -423,9 +423,9 @@ build_info:
   output: "target/nextflow/busco/busco_run"
   executable: "target/nextflow/busco/busco_run/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf
index de5910f7..3c10af5a 100644
--- a/target/nextflow/busco/busco_run/main.nf
+++ b/target/nextflow/busco/busco_run/main.nf
@@ -3309,9 +3309,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_run",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml
index 73a1715b..8788cb7e 100644
--- a/target/nextflow/cutadapt/.config.vsh.yaml
+++ b/target/nextflow/cutadapt/.config.vsh.yaml
@@ -740,9 +740,9 @@ build_info:
   output: "target/nextflow/cutadapt"
   executable: "target/nextflow/cutadapt/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf
index 3ede1273..c38f7055 100644
--- a/target/nextflow/cutadapt/main.nf
+++ b/target/nextflow/cutadapt/main.nf
@@ -3619,9 +3619,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/cutadapt",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml
index 96cf3b06..c01f5044 100644
--- a/target/nextflow/falco/.config.vsh.yaml
+++ b/target/nextflow/falco/.config.vsh.yaml
@@ -317,9 +317,9 @@ build_info:
   output: "target/nextflow/falco"
   executable: "target/nextflow/falco/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf
index 0c870987..e270c472 100644
--- a/target/nextflow/falco/main.nf
+++ b/target/nextflow/falco/main.nf
@@ -3170,9 +3170,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/falco",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml
index e2dd4bed..fa1eabc2 100644
--- a/target/nextflow/fastp/.config.vsh.yaml
+++ b/target/nextflow/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
   output: "target/nextflow/fastp"
   executable: "target/nextflow/fastp/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf
index bec74ffc..b635e7da 100644
--- a/target/nextflow/fastp/main.nf
+++ b/target/nextflow/fastp/main.nf
@@ -4023,9 +4023,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/fastp",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml
index 0a79d383..84103af1 100644
--- a/target/nextflow/fastqc/.config.vsh.yaml
+++ b/target/nextflow/fastqc/.config.vsh.yaml
@@ -340,9 +340,9 @@ build_info:
   output: "target/nextflow/fastqc"
   executable: "target/nextflow/fastqc/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf
index ae53d965..ff664c21 100644
--- a/target/nextflow/fastqc/main.nf
+++ b/target/nextflow/fastqc/main.nf
@@ -3182,9 +3182,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/fastqc",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml
index 371544e3..0dfc492a 100644
--- a/target/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/nextflow/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
   output: "target/nextflow/featurecounts"
   executable: "target/nextflow/featurecounts/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf
index 45b3bd2c..bf8a1f4c 100644
--- a/target/nextflow/featurecounts/main.nf
+++ b/target/nextflow/featurecounts/main.nf
@@ -3549,9 +3549,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/featurecounts",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml
index 24a39ac1..a8cd153b 100644
--- a/target/nextflow/fq_subsample/.config.vsh.yaml
+++ b/target/nextflow/fq_subsample/.config.vsh.yaml
@@ -190,9 +190,9 @@ build_info:
   output: "target/nextflow/fq_subsample"
   executable: "target/nextflow/fq_subsample/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf
index 4ffb71b8..a6f286fd 100644
--- a/target/nextflow/fq_subsample/main.nf
+++ b/target/nextflow/fq_subsample/main.nf
@@ -3032,9 +3032,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/fq_subsample",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml
index f7a99b73..6f92dc7e 100644
--- a/target/nextflow/gffread/.config.vsh.yaml
+++ b/target/nextflow/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
   output: "target/nextflow/gffread"
   executable: "target/nextflow/gffread/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf
index f8c89193..c755ff35 100644
--- a/target/nextflow/gffread/main.nf
+++ b/target/nextflow/gffread/main.nf
@@ -3606,9 +3606,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/gffread",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml
index 0eca68c0..6bfc974a 100644
--- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml
@@ -218,9 +218,9 @@ build_info:
   output: "target/nextflow/kallisto/kallisto_index"
   executable: "target/nextflow/kallisto/kallisto_index/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf
index 0f74c331..aea87359 100644
--- a/target/nextflow/kallisto/kallisto_index/main.nf
+++ b/target/nextflow/kallisto/kallisto_index/main.nf
@@ -3071,9 +3071,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/kallisto/kallisto_index",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml
index 1c54bba2..839799ca 100644
--- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml
@@ -234,9 +234,9 @@ build_info:
   output: "target/nextflow/kallisto/kallisto_quant"
   executable: "target/nextflow/kallisto/kallisto_quant/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf
index 177e1cdb..fd9ce0c1 100644
--- a/target/nextflow/kallisto/kallisto_quant/main.nf
+++ b/target/nextflow/kallisto/kallisto_quant/main.nf
@@ -3092,9 +3092,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/kallisto/kallisto_quant",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
index 90878229..ab1aa412 100644
--- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,9 +507,9 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_call"
   executable: "target/nextflow/lofreq/lofreq_call/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf
index 335ab6e1..c338dab8 100644
--- a/target/nextflow/lofreq/lofreq_call/main.nf
+++ b/target/nextflow/lofreq/lofreq_call/main.nf
@@ -3414,9 +3414,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_call",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
index 8e3affc7..51c27db0 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_indelqual"
   executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf
index 7ec2089f..0f675132 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/main.nf
+++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf
@@ -3077,9 +3077,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_indelqual",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml
index 41e3b198..bf23523e 100644
--- a/target/nextflow/multiqc/.config.vsh.yaml
+++ b/target/nextflow/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
   output: "target/nextflow/multiqc"
   executable: "target/nextflow/multiqc/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf
index afc91c43..a9054271 100644
--- a/target/nextflow/multiqc/main.nf
+++ b/target/nextflow/multiqc/main.nf
@@ -3366,9 +3366,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/multiqc",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml
index cd83f5cf..aba23d95 100644
--- a/target/nextflow/pear/.config.vsh.yaml
+++ b/target/nextflow/pear/.config.vsh.yaml
@@ -398,9 +398,9 @@ build_info:
   output: "target/nextflow/pear"
   executable: "target/nextflow/pear/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf
index 059b29da..6164f1a7 100644
--- a/target/nextflow/pear/main.nf
+++ b/target/nextflow/pear/main.nf
@@ -3259,9 +3259,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/pear",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
index e523b6e5..b8a36d54 100644
--- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -264,9 +264,9 @@ build_info:
   output: "target/nextflow/qualimap/qualimap_rnaseq"
   executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
index 2c3f9308..b7715bbe 100644
--- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf
+++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
@@ -3129,9 +3129,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/qualimap/qualimap_rnaseq",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml
index bc840c80..c48ca0fd 100644
--- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -852,9 +852,9 @@ build_info:
   output: "target/nextflow/rsem/rsem_calculate_expression"
   executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf
index 67dce4c4..da70dfa4 100644
--- a/target/nextflow/rsem/rsem_calculate_expression/main.nf
+++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf
@@ -3661,9 +3661,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/rsem/rsem_calculate_expression",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
index 89785127..654ff7d4 100644
--- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
   output: "target/nextflow/rsem/rsem_prepare_reference"
   executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf
index 99d768ee..eac4db68 100644
--- a/target/nextflow/rsem/rsem_prepare_reference/main.nf
+++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf
@@ -3245,9 +3245,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/rsem/rsem_prepare_reference",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
index 094f8156..a292ffd0 100644
--- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -277,9 +277,9 @@ build_info:
   output: "target/nextflow/salmon/salmon_index"
   executable: "target/nextflow/salmon/salmon_index/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf
index 4de67be5..460fc9ee 100644
--- a/target/nextflow/salmon/salmon_index/main.nf
+++ b/target/nextflow/salmon/salmon_index/main.nf
@@ -3129,9 +3129,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_index",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
index 70a0ffed..402f23a7 100644
--- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,9 +1173,9 @@ build_info:
   output: "target/nextflow/salmon/salmon_quant"
   executable: "target/nextflow/salmon/salmon_quant/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf
index 60f30b07..a31b55bc 100644
--- a/target/nextflow/salmon/salmon_quant/main.nf
+++ b/target/nextflow/salmon/salmon_quant/main.nf
@@ -3964,9 +3964,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_quant",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
index a2d2681a..882861ce 100644
--- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
@@ -264,9 +264,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_collate"
   executable: "target/nextflow/samtools/samtools_collate/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf
index d5b178eb..4cc53544 100644
--- a/target/nextflow/samtools/samtools_collate/main.nf
+++ b/target/nextflow/samtools/samtools_collate/main.nf
@@ -3140,9 +3140,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_collate",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
index cc67dc00..e17166c1 100644
--- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,9 +243,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_faidx"
   executable: "target/nextflow/samtools/samtools_faidx/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf
index 352f17f8..8ec4710b 100644
--- a/target/nextflow/samtools/samtools_faidx/main.nf
+++ b/target/nextflow/samtools/samtools_faidx/main.nf
@@ -3112,9 +3112,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_faidx",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
index c00734e6..72a5850f 100644
--- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,9 +433,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_fasta"
   executable: "target/nextflow/samtools/samtools_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf
index ae7d1b25..72023b00 100644
--- a/target/nextflow/samtools/samtools_fasta/main.nf
+++ b/target/nextflow/samtools/samtools_fasta/main.nf
@@ -3304,9 +3304,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
index 845bdc27..e854e46a 100644
--- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,9 +433,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_fastq"
   executable: "target/nextflow/samtools/samtools_fastq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf
index 17aecc9a..2e92324b 100644
--- a/target/nextflow/samtools/samtools_fastq/main.nf
+++ b/target/nextflow/samtools/samtools_fastq/main.nf
@@ -3304,9 +3304,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fastq",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
index 02e0e914..8479a4bb 100644
--- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,9 +173,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_flagstat"
   executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf
index 5b3de654..1ac4f606 100644
--- a/target/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/nextflow/samtools/samtools_flagstat/main.nf
@@ -3028,9 +3028,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_flagstat",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
index ec6145a0..15ba27df 100644
--- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_idxstats"
   executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf
index a463f520..b47f344d 100644
--- a/target/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/nextflow/samtools/samtools_idxstats/main.nf
@@ -3040,9 +3040,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_idxstats",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
index a2a1d11c..8aa94a39 100644
--- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -189,9 +189,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_index"
   executable: "target/nextflow/samtools/samtools_index/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf
index 1c1f9c44..f3446818 100644
--- a/target/nextflow/samtools/samtools_index/main.nf
+++ b/target/nextflow/samtools/samtools_index/main.nf
@@ -3053,9 +3053,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_index",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
index fd0a6c7a..10adadca 100644
--- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -332,9 +332,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_sort"
   executable: "target/nextflow/samtools/samtools_sort/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf
index e56ae685..07562f31 100644
--- a/target/nextflow/samtools/samtools_sort/main.nf
+++ b/target/nextflow/samtools/samtools_sort/main.nf
@@ -3225,9 +3225,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_sort",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
index 3f94667d..b4e83892 100644
--- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -401,9 +401,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_stats"
   executable: "target/nextflow/samtools/samtools_stats/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf
index df7de859..3d8db615 100644
--- a/target/nextflow/samtools/samtools_stats/main.nf
+++ b/target/nextflow/samtools/samtools_stats/main.nf
@@ -3295,9 +3295,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_stats",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
index 829b2ed3..211392a0 100644
--- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
@@ -665,9 +665,9 @@ build_info:
   output: "target/nextflow/samtools/samtools_view"
   executable: "target/nextflow/samtools/samtools_view/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf
index 6ea26375..e0f32bdc 100644
--- a/target/nextflow/samtools/samtools_view/main.nf
+++ b/target/nextflow/samtools/samtools_view/main.nf
@@ -3476,9 +3476,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_view",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
index 333a06b9..30a6103b 100644
--- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,9 +173,9 @@ build_info:
   output: "target/nextflow/seqtk/seqtk_sample"
   executable: "target/nextflow/seqtk/seqtk_sample/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf
index 37a181d7..822b4131 100644
--- a/target/nextflow/seqtk/seqtk_sample/main.nf
+++ b/target/nextflow/seqtk/seqtk_sample/main.nf
@@ -3030,9 +3030,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_sample",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
index fcadef42..d9196184 100644
--- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,9 +196,9 @@ build_info:
   output: "target/nextflow/seqtk/seqtk_subseq"
   executable: "target/nextflow/seqtk/seqtk_subseq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf
index 0a6bb83e..79f6377f 100644
--- a/target/nextflow/seqtk/seqtk_subseq/main.nf
+++ b/target/nextflow/seqtk/seqtk_subseq/main.nf
@@ -3060,9 +3060,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_subseq",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/.config.vsh.yaml
new file mode 100644
index 00000000..f66226cb
--- /dev/null
+++ b/target/nextflow/snpeff/.config.vsh.yaml
@@ -0,0 +1,655 @@
+name: "snpeff"
+version: "main"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input variants file."
+    info: null
+    example:
+    - "test.vcf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--genome_version"
+    description: "Reference genome version."
+    info: null
+    example:
+    - "GRCh37.75"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The output file."
+    info: null
+    example:
+    - "out.vcf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary"
+    description: "Summary file directory."
+    info: null
+    example:
+    - "summary_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genes"
+    description: "Txt file directory."
+    info: null
+    example:
+    - "genes_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "string"
+    name: "--chr"
+    description: "Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1').\
+      \ Only on TXT output.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--classic"
+    description: "Use old style annotations instead of Sequence Ontology and Hgvs."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--csv_stats"
+    description: "Create CSV summary file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--download"
+    description: "Download reference genome if not available."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--input_format"
+    alternatives:
+    - "-i"
+    description: "Input format [ vcf, bed ]. Default: VCF.\nexample: \"VCF\"\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--file_list"
+    description: "Input actually contains a list of files to process."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--output_format"
+    alternatives:
+    - "-o"
+    description: "Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n"
+    info: null
+    example:
+    - "VCF"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--stats"
+    alternatives:
+    - "-s"
+    - "--htmlStats"
+    description: "Create HTML summary file."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_stats"
+    description: "Do not create stats (summary) file."
+    info: null
+    direction: "input"
+- name: "Results filter options"
+  arguments:
+  - type: "file"
+    name: "--fi"
+    alternatives:
+    - "--filterInterval"
+    description: "Only analyze changes that intersect with the intervals \nspecified\
+      \ in this file. This option can be used several times.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_downstream"
+    description: "Do not show DOWNSTREAM changes"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_intergenic"
+    description: "Do not show INTERGENIC changes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_intron"
+    description: "Do not show INTRON changes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_upstream"
+    description: "Do not show UPSTREAM changes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_utr"
+    description: "Do not show 5_PRIME_UTR or 3_PRIME_UTR changes."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--no"
+    description: "Do not show 'EffectType'. This option can be used several times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Annotations options"
+  arguments:
+  - type: "boolean_true"
+    name: "--cancer"
+    description: "Perform 'cancer' comparisons (Somatic vs Germline)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--cancer_samples"
+    description: "Two column TXT file defining 'original \\t derived' samples."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastaprot"
+    description: "Create an output file containing the resulting protein sequences.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--format_eff"
+    description: "Use 'EFF' field compatible with older versions (instead of 'ANN').\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--gene_id"
+    description: "Use gene ID instead of gene name (VCF output)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs"
+    description: "Use HGVS annotations for amino acid sub-field."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs_old"
+    description: "Use old HGVS notation."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs1_letter_aa"
+    description: "Use one letter Amino acid codes in HGVS notation."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--hgvs_tr_id"
+    description: "Use transcript ID in HGVS notation."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--lof"
+    description: "Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "-no_hgvs"
+    description: "Do not add HGVS annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_lof"
+    description: "Do not add LOF and NMD annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_shift_hgvs"
+    description: "Do not shift variants according to HGVS notation (most 3prime end).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--oicr"
+    description: "Add OICR tag in VCF file."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sequence_ontology"
+    description: "Use Sequence Ontology terms."
+    info: null
+    direction: "input"
+- name: "Generic options"
+  arguments:
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Specify config file"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--config_option"
+    description: "Override a config file option (name=value)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--debug"
+    alternatives:
+    - "-d"
+    description: "Debug mode (very verbose)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--data_dir"
+    description: "Override data_dir parameter from config file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_download"
+    description: "Do not download a SnpEff database, if not available locally."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_log"
+    description: "Do not report usage statistics to server."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--quiet"
+    alternatives:
+    - "-q"
+    description: "Quiet mode (do not show any messages or errors)"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--verbose"
+    alternatives:
+    - "-v"
+    description: "Verbose mode."
+    info: null
+    direction: "input"
+- name: "Database options"
+  arguments:
+  - type: "boolean_true"
+    name: "--canon"
+    description: "Only use canonical transcripts."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--canon_list"
+    description: "Only use canonical transcripts, replace some transcripts using the\
+      \ 'gene_id         \ntranscript_id' entries in <file>.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--tag"
+    description: "Only use transcript having a tag 'tagName'. This option can be used\
+      \ multiple times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_tag"
+    description: "Filter out transcript having a tag 'tagName'. This option can be\
+      \ used multiple times.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--interaction"
+    description: "Annotate using interactions (requires interaction database)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--interval"
+    description: "Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use\
+      \ this option many times).\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_tsl"
+    description: "Only use transcripts having Transcript Support Level lower than\
+      \ <TSL_number>."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--motif"
+    description: "Annotate using motifs (requires Motif database)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nextprot"
+    description: "Annotate using NextProt (requires NextProt database)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_genome"
+    description: "Do not load any genomic database (e.g. annotate using custom files)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_expand_iub"
+    description: "Disable IUB code expansion in input variants."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_interaction"
+    description: "Disable inteaction annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_motif"
+    description: "Disable motif annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_nextprot"
+    description: "Disable NextProt annotations."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--only_reg"
+    description: "Only use regulation tracks."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--only_protein"
+    description: "Only use protein coding transcripts."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--only_tr"
+    description: "Only use the transcripts in this file. Format: One transcript ID\
+      \ per line.\n"
+    info: null
+    example:
+    - "file.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reg"
+    description: "Regulation track to use (this option can be used add several times)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--ss"
+    alternatives:
+    - "--spliceSiteSize"
+    description: "Set size for splice sites (donor and acceptor) in bases. Default:\
+      \ 2.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--splice_region_exon_size"
+    description: "Set size for splice site region within exons. Default: 3 bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--splice_region_intron_min"
+    description: "Set minimum number of bases for splice site region within intron.\
+      \ Default: 3 bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--splice_region_intron_max"
+    description: "Set maximum number of bases for splice site region within intron.\
+      \ Default: 8 bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--strict"
+    description: "Only use 'validated' transcripts (i.e. sequence has been checked)."
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--ud"
+    alternatives:
+    - "--upDownStreamLen"
+    description: "Set upstream downstream interval length (in bases)."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Genetic variant annotation, and functional effect prediction toolbox.\
+  \ \nIt annotates and predicts the effects of genetic variants on genes and \nproteins\
+  \ (such as amino acid changes).\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "annotation"
+- "effect prediction"
+- "snp"
+- "variant"
+- "vcf"
+license: "MIT"
+references:
+  doi:
+  - "10.3389/fgene.2012.00035"
+links:
+  repository: "https://github.com/pcingola/SnpEff"
+  homepage: "https://pcingola.github.io/SnpEff/"
+  documentation: "https://pcingola.github.io/SnpEff/"
+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: "quay.io/staphb/snpeff:5.2a"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "version=$(snpEff -version) && \\\nversion_trimmed=$(echo \"$version\" | awk\
+      \ '{print $1, $2}') && \\\necho \"$version_trimmed\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/snpeff/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/snpeff"
+  executable: "target/nextflow/snpeff/main.nf"
+  viash_version: "0.9.0"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
+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"
diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/main.nf
new file mode 100644
index 00000000..c8a7fb42
--- /dev/null
+++ b/target/nextflow/snpeff/main.nf
@@ -0,0 +1,4315 @@
+// snpeff main
+// 
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
+// 
+// The component may contain files which fall under a different license. The
+// authors of this component should specify the license in the header of such
+// files, or include a separate license file detailing the licenses of all included
+// files.
+
+////////////////////////////
+// VDSL3 helper functions //
+////////////////////////////
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_checkArgumentType.nf'
+class UnexpectedArgumentTypeException extends Exception {
+  String errorIdentifier
+  String stage
+  String plainName
+  String expectedClass
+  String foundClass
+  
+  // ${key ? " in module '$key'" : ""}${id ? " id '$id'" : ""}
+  UnexpectedArgumentTypeException(String errorIdentifier, String stage, String plainName, String expectedClass, String foundClass) {
+    super("Error${errorIdentifier ? " $errorIdentifier" : ""}:${stage ? " $stage" : "" } argument '${plainName}' has the wrong type. " +
+      "Expected type: ${expectedClass}. Found type: ${foundClass}")
+    this.errorIdentifier = errorIdentifier
+    this.stage = stage
+    this.plainName = plainName
+    this.expectedClass = expectedClass
+    this.foundClass = foundClass
+  }
+}
+
+/**
+  * Checks if the given value is of the expected type. If not, an exception is thrown.
+  *
+  * @param stage The stage of the argument (input or output)
+  * @param par The parameter definition
+  * @param value The value to check
+  * @param errorIdentifier The identifier to use in the error message
+  * @return The value, if it is of the expected type
+  * @throws UnexpectedArgumentTypeException If the value is not of the expected type
+*/
+def _checkArgumentType(String stage, Map par, Object value, String errorIdentifier) {
+  // expectedClass will only be != null if value is not of the expected type
+  def expectedClass = null
+  def foundClass = null
+  
+  // todo: split if need be
+  
+  if (!par.required && value == null) {
+    expectedClass = null
+  } else if (par.multiple) {
+    if (value !instanceof Collection) {
+      value = [value]
+    }
+    
+    // split strings
+    value = value.collectMany{ val ->
+      if (val instanceof String) {
+        // collect() to ensure that the result is a List and not simply an array
+        val.split(par.multiple_sep).collect()
+      } else {
+        [val]
+      }
+    }
+
+    // process globs
+    if (par.type == "file" && par.direction == "input") {
+      value = value.collect{ it instanceof String ? file(it, hidden: true) : it }.flatten()
+    }
+
+    // check types of elements in list
+    try {
+      value = value.collect { listVal ->
+        _checkArgumentType(stage, par + [multiple: false], listVal, errorIdentifier)
+      }
+    } catch (UnexpectedArgumentTypeException e) {
+      expectedClass = "List[${e.expectedClass}]"
+      foundClass = "List[${e.foundClass}]"
+    }
+  } else if (par.type == "string") {
+    // cast to string if need be
+    if (value instanceof GString) {
+      value = value.toString()
+    }
+    expectedClass = value instanceof String ? null : "String"
+  } else if (par.type == "integer") {
+    // cast to integer if need be
+    if (value instanceof String) {
+      try {
+        value = value.toInteger()
+      } catch (NumberFormatException e) {
+        // do nothing
+      }
+    }
+    if (value instanceof java.math.BigInteger) {
+      value = value.intValue()
+    }
+    expectedClass = value instanceof Integer ? null : "Integer"
+  } else if (par.type == "long") {
+    // cast to long if need be
+    if (value instanceof String) {
+      try {
+        value = value.toLong()
+      } catch (NumberFormatException e) {
+        // do nothing
+      }
+    }
+    if (value instanceof Integer) {
+      value = value.toLong()
+    }
+    expectedClass = value instanceof Long ? null : "Long"
+  } else if (par.type == "double") {
+    // cast to double if need be
+    if (value instanceof String) {
+      try {
+        value = value.toDouble()
+      } catch (NumberFormatException e) {
+        // do nothing
+      }
+    }
+    if (value instanceof java.math.BigDecimal) {
+      value = value.doubleValue()
+    }
+    if (value instanceof Float) {
+      value = value.toDouble()
+    }
+    expectedClass = value instanceof Double ? null : "Double"
+  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
+    // cast to boolean if need be
+    if (value instanceof String) {
+      def valueLower = value.toLowerCase()
+      if (valueLower == "true") {
+        value = true
+      } else if (valueLower == "false") {
+        value = false
+      }
+    }
+    expectedClass = value instanceof Boolean ? null : "Boolean"
+  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
+    // cast to path if need be
+    if (value instanceof String) {
+      value = file(value, hidden: true)
+    }
+    if (value instanceof File) {
+      value = value.toPath()
+    }
+    expectedClass = value instanceof Path ? null : "Path"
+  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
+    // cast to string if need be
+    if (value instanceof GString) {
+      value = value.toString()
+    }
+    expectedClass = value instanceof String ? null : "String"
+  } else {
+    // didn't find a match for par.type
+    expectedClass = par.type
+  }
+
+  if (expectedClass != null) {
+    if (foundClass == null) {
+      foundClass = value.getClass().getName()
+    }
+    throw new UnexpectedArgumentTypeException(errorIdentifier, stage, par.plainName, expectedClass, foundClass)
+  }
+  
+  return value
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processInputValues.nf'
+Map _processInputValues(Map inputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.required) {
+        assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
+      }
+    }
+
+    inputs = inputs.collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") }
+      assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument"
+
+      value = _checkArgumentType("input", par, value, "in module '$key' id '$id'")
+
+      [ name, value ]
+    }
+  }
+  return inputs
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
+Map _processOutputValues(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+
+    outputs = outputs.collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
+      assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
+      
+      value = _checkArgumentType("output", par, value, "in module '$key' id '$id'")
+      
+      [ name, value ]
+    }
+  }
+  return outputs
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
+class IDChecker {
+  final def items = [] as Set
+
+  @groovy.transform.WithWriteLock
+  boolean observe(String item) {
+    if (items.contains(item)) {
+      return false
+    } else {
+      items << item
+      return true
+    }
+  }
+
+  @groovy.transform.WithReadLock
+  boolean contains(String item) {
+    return items.contains(item)
+  }
+
+  @groovy.transform.WithReadLock
+  Set getItems() {
+    return items.clone()
+  }
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_checkUniqueIds.nf'
+
+/**
+ * Check if the ids are unique across parameter sets
+ *
+ * @param parameterSets a list of parameter sets.
+ */
+private void _checkUniqueIds(List<Tuple2<String, Map<String, Object>>> parameterSets) {
+  def ppIds = parameterSets.collect{it[0]}
+  assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds"
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_getChild.nf'
+
+// helper functions for reading params from file //
+def _getChild(parent, child) {
+  if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) {
+    child
+  } else {
+    def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString()
+    parentAbsolute.replaceAll('/[^/]*$', "/") + child
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_parseParamList.nf'
+/**
+  * Figure out the param list format based on the file extension
+  *
+  * @param param_list A String containing the path to the parameter list file.
+  *
+  * @return A String containing the format of the parameter list file.
+  */
+def _paramListGuessFormat(param_list) {
+  if (param_list !instanceof String) {
+    "asis"
+  } else if (param_list.endsWith(".csv")) {
+    "csv"
+  } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) {
+    "json"
+  } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) {
+    "yaml"
+  } else {
+    "yaml_blob"
+  }
+}
+
+
+/**
+  * Read the param list
+  * 
+  * @param param_list One of the following:
+  *   - A String containing the path to the parameter list file (csv, json or yaml),
+  *   - A yaml blob of a list of maps (yaml_blob),
+  *   - Or a groovy list of maps (asis).
+  * @param config A Map of the Viash configuration.
+  * 
+  * @return A List of Maps containing the parameters.
+  */
+def _parseParamList(param_list, Map config) {
+  // first determine format by extension
+  def paramListFormat = _paramListGuessFormat(param_list)
+
+  def paramListPath = (paramListFormat != "asis" && paramListFormat != "yaml_blob") ?
+    file(param_list, hidden: true) :
+    null
+
+  // get the correct parser function for the detected params_list format
+  def paramSets = []
+  if (paramListFormat == "asis") {
+    paramSets = param_list
+  } else if (paramListFormat == "yaml_blob") {
+    paramSets = readYamlBlob(param_list)
+  } else if (paramListFormat == "yaml") {
+    paramSets = readYaml(paramListPath)
+  } else if (paramListFormat == "json") {
+    paramSets = readJson(paramListPath)
+  } else if (paramListFormat == "csv") {
+    paramSets = readCsv(paramListPath)
+  } else {
+    error "Format of provided --param_list not recognised.\n" +
+    "Found: '$paramListFormat'.\n" +
+    "Expected: a csv file, a json file, a yaml file,\n" +
+    "a yaml blob or a groovy list of maps."
+  }
+
+  // data checks
+  assert paramSets instanceof List: "--param_list should contain a list of maps"
+  for (value in paramSets) {
+    assert value instanceof Map: "--param_list should contain a list of maps"
+  }
+
+  // id is argument
+  def idIsArgument = config.allArguments.any{it.plainName == "id"}
+
+  // Reformat from List<Map> to List<Tuple2<String, Map>> by adding the ID as first element of a Tuple2
+  paramSets = paramSets.collect({ data ->
+    def id = data.id
+    if (!idIsArgument) {
+      data = data.findAll{k, v -> k != "id"}
+    }
+    [id, data]
+  })
+
+  // Split parameters with 'multiple: true'
+  paramSets = paramSets.collect({ id, data ->
+    data = _splitParams(data, config)
+    [id, data]
+  })
+  
+  // The paths of input files inside a param_list file may have been specified relatively to the
+  // location of the param_list file. These paths must be made absolute.
+  if (paramListPath) {
+    paramSets = paramSets.collect({ id, data ->
+      def new_data = data.collectEntries{ parName, parValue ->
+        def par = config.allArguments.find{it.plainName == parName}
+        if (par && par.type == "file" && par.direction == "input") {
+          if (parValue instanceof Collection) {
+            parValue = parValue.collectMany{path -> 
+              def x = _resolveSiblingIfNotAbsolute(path, paramListPath)
+              x instanceof Collection ? x : [x]
+            }
+          } else {
+            parValue = _resolveSiblingIfNotAbsolute(parValue, paramListPath) 
+          }
+        }
+        [parName, parValue]
+      }
+      [id, new_data]
+    })
+  }
+
+  return paramSets
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_splitParams.nf'
+/**
+ * Split parameters for arguments that accept multiple values using their separator
+ *
+ * @param paramList A Map containing parameters to split.
+ * @param config A Map of the Viash configuration. This Map can be generated from the config file
+ *               using the readConfig() function.
+ *
+ * @return A Map of parameters where the parameter values have been split into a list using
+ *         their seperator.
+ */
+Map<String, Object> _splitParams(Map<String, Object> parValues, Map config){
+  def parsedParamValues = parValues.collectEntries { parName, parValue ->
+    def parameterSettings = config.allArguments.find({it.plainName == parName})
+
+    if (!parameterSettings) {
+      // if argument is not found, do not alter 
+      return [parName, parValue]
+    }
+    if (parameterSettings.multiple) { // Check if parameter can accept multiple values
+      if (parValue instanceof Collection) {
+        parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it }
+      } else if (parValue instanceof String) {
+        parValue = parValue.split(parameterSettings.multiple_sep)
+      } else if (parValue == null) {
+        parValue = []
+      } else {
+        parValue = [ parValue ]
+      }
+      parValue = parValue.flatten()
+    }
+    // For all parameters check if multiple values are only passed for
+    // arguments that allow it. Quietly simplify lists of length 1.
+    if (!parameterSettings.multiple && parValue instanceof Collection) {
+      assert parValue.size() == 1 : 
+      "Error: argument ${parName} has too many values.\n" +
+      "  Expected amount: 1. Found: ${parValue.size()}"
+      parValue = parValue[0]
+    }
+    [parName, parValue]
+  }
+  return parsedParamValues
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf'
+/**
+ * Parse nextflow parameters based on settings defined in a viash config.
+ * Return a list of parameter sets, each parameter set corresponding to 
+ * an event in a nextflow channel. The output from this function can be used
+ * with Channel.fromList to create a nextflow channel with Vdsl3 formatted 
+ * events.
+ *
+ * This function performs:
+ *   - A filtering of the params which can be found in the config file.
+ *   - Process the params_list argument which allows a user to to initialise 
+ *     a Vsdl3 channel with multiple parameter sets. Possible formats are 
+ *     csv, json, yaml, or simply a yaml_blob. A csv should have column names 
+ *     which correspond to the different arguments of this pipeline. A json or a yaml
+ *     file should be a list of maps, each of which has keys corresponding to the
+ *     arguments of the pipeline. A yaml blob can also be passed directly as a parameter.
+ *     When passing a csv, json or yaml, relative path names are relativized to the
+ *     location of the parameter file.
+ *   - Combine the parameter sets into a vdsl3 Channel.
+ *
+ * @param params Input parameters. Can optionaly contain a 'param_list' key that
+ *               provides a list of arguments that can be split up into multiple events
+ *               in the output channel possible formats of param_lists are: a csv file, 
+ *               json file, a yaml file or a yaml blob. Each parameters set (event) must
+ *               have a unique ID.
+ * @param config A Map of the Viash configuration. This Map can be generated from the config file
+ *               using the readConfig() function.
+ * 
+ * @return A list of parameters with the first element of the event being
+ *         the event ID and the second element containing a map of the parsed parameters.
+ */
+ 
+private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params, Map config){
+  // todo: fetch key from run args
+  def key_ = config.name
+  
+  /* parse regular parameters (not in param_list)  */
+  /*************************************************/
+  def globalParams = config.allArguments
+    .findAll { params.containsKey(it.plainName) }
+    .collectEntries { [ it.plainName, params[it.plainName] ] }
+  def globalID = params.get("id", null)
+
+  /* process params_list arguments */
+  /*********************************/
+  def paramList = params.containsKey("param_list") && params.param_list != null ?
+    params.param_list : []
+  // if (paramList instanceof String) {
+  //   paramList = [paramList]
+  // }
+  // def paramSets = paramList.collectMany{ _parseParamList(it, config) }
+  // TODO: be able to process param_list when it is a list of strings
+  def paramSets = _parseParamList(paramList, config)
+  if (paramSets.isEmpty()) {
+    paramSets = [[null, [:]]]
+  }
+
+  /* combine arguments into channel */
+  /**********************************/
+  def processedParams = paramSets.indexed().collect{ index, tup ->
+    // Process ID
+    def id = tup[0] ?: globalID
+  
+    if (workflow.stubRun && !id) {
+      // if stub run, explicitly add an id if missing
+      id = "stub${index}"
+    }
+    assert id != null: "Each parameter set should have at least an 'id'"
+
+    // Process params
+    def parValues = globalParams + tup[1]
+    // // Remove parameters which are null, if the default is also null
+    // parValues = parValues.collectEntries{paramName, paramValue ->
+    //   parameterSettings = config.functionality.allArguments.find({it.plainName == paramName})
+    //   if ( paramValue != null || parameterSettings.get("default", null) != null ) {
+    //     [paramName, paramValue]
+    //   }
+    // }
+    parValues = parValues.collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") }
+      assert par != null : "Error in module '${key_}' id '${id}': '${name}' is not a valid input argument"
+
+      if (par == null) {
+        return [:]
+      }
+      value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'")
+
+      [ name, value ]
+    }
+
+    [id, parValues]
+  }
+
+  // Check if ids (first element of each list) is unique
+  _checkUniqueIds(processedParams)
+  return processedParams
+}
+
+/**
+ * Parse nextflow parameters based on settings defined in a viash config 
+ * and return a nextflow channel.
+ * 
+ * @param params Input parameters. Can optionaly contain a 'param_list' key that
+ *               provides a list of arguments that can be split up into multiple events
+ *               in the output channel possible formats of param_lists are: a csv file, 
+ *               json file, a yaml file or a yaml blob. Each parameters set (event) must
+ *               have a unique ID.
+ * @param config A Map of the Viash configuration. This Map can be generated from the config file
+ *               using the readConfig() function.
+ * 
+ * @return A nextflow Channel with events. Events are formatted as a tuple that contains 
+ *         first contains the ID of the event and as second element holds a parameter map.
+ *       
+ *
+ */
+def channelFromParams(Map params, Map config) {
+  def processedParams = _paramsToParamSets(params, config)
+  return Channel.fromList(processedParams)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/checkUniqueIds.nf'
+def checkUniqueIds(Map args) {
+  def stopOnError = args.stopOnError == null ? args.stopOnError : true
+
+  def idChecker = new IDChecker()
+
+  return filter { tup ->
+    if (!idChecker.observe(tup[0])) {
+      if (stopOnError) {
+        error "Duplicate id: ${tup[0]}"
+      } else {
+        log.warn "Duplicate id: ${tup[0]}, removing duplicate entry"
+        return false
+      }
+    }
+    return true
+  }
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/preprocessInputs.nf'
+// This helper file will be deprecated soon
+preprocessInputsDeprecationWarningPrinted = false
+
+def preprocessInputsDeprecationWarning() {
+  if (!preprocessInputsDeprecationWarningPrinted) {
+    preprocessInputsDeprecationWarningPrinted = true
+    System.err.println("Warning: preprocessInputs() is deprecated and will be removed in Viash 0.9.0.")
+  }
+}
+
+/**
+ * Generate a nextflow Workflow that allows processing a channel of 
+ * Vdsl3 formatted events and apply a Viash config to them:
+ *    - Gather default parameters from the Viash config and make 
+ *      sure that they are correctly formatted (see applyConfig method).
+ *    - Format the input parameters (also using the applyConfig method).
+ *    - Apply the default parameter to the input parameters.
+ *    - Do some assertions:
+ *        ~ Check if the event IDs in the channel are unique.
+ * 
+ * The events in the channel are formatted as tuples, with the 
+ * first element of the tuples being a unique id of the parameter set, 
+ * and the second element containg the the parameters themselves.
+ * Optional extra elements of the tuples will be passed to the output as is.
+ *
+ * @param args A map that must contain a 'config' key that points
+ *              to a parsed config (see readConfig()). Optionally, a
+ *              'key' key can be provided which can be used to create a unique
+ *              name for the workflow process.
+ *
+ * @return A workflow that allows processing a channel of Vdsl3 formatted events
+ * and apply a Viash config to them.
+ */
+def preprocessInputs(Map args) {
+  preprocessInputsDeprecationWarning()
+
+  def config = args.config
+  assert config instanceof Map : 
+    "Error in preprocessInputs: config must be a map. " +
+    "Expected class: Map. Found: config.getClass() is ${config.getClass()}"
+  def key_ = args.key ?: config.name
+
+  // Get different parameter types (used throughout this function)
+  def defaultArgs = config.allArguments
+    .findAll { it.containsKey("default") }
+    .collectEntries { [ it.plainName, it.default ] }
+
+  map { tup ->
+    def id = tup[0]
+    def data = tup[1]
+    def passthrough = tup.drop(2)
+
+    def new_data = (defaultArgs + data).collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") }
+      
+      if (par != null) {
+        value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'")
+      }
+
+      [ name, value ]
+    }
+
+    [ id, new_data ] + passthrough
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runComponents.nf'
+/**
+ * Run a list of components on a stream of data.
+ * 
+ * @param components: list of Viash VDSL3 modules to run
+ * @param fromState: a closure, a map or a list of keys to extract from the input data.
+ *   If a closure, it will be called with the id, the data and the component config.
+ * @param toState: a closure, a map or a list of keys to extract from the output data
+ *   If a closure, it will be called with the id, the output data, the old state and the component config.
+ * @param filter: filter function to apply to the input.
+ *   It will be called with the id, the data and the component config.
+ * @param id: id to use for the output data
+ *   If a closure, it will be called with the id, the data and the component config.
+ * @param auto: auto options to pass to the components
+ *
+ * @return: a workflow that runs the components
+ **/
+def runComponents(Map args) {
+  log.warn("runComponents is deprecated, use runEach instead")
+  assert args.components: "runComponents should be passed a list of components to run"
+
+  def components_ = args.components
+  if (components_ !instanceof List) {
+    components_ = [ components_ ]
+  }
+  assert components_.size() > 0: "pass at least one component to runComponents"
+
+  def fromState_ = args.fromState
+  def toState_ = args.toState
+  def filter_ = args.filter
+  def id_ = args.id
+
+  workflow runComponentsWf {
+    take: input_ch
+    main:
+
+    // generate one channel per method
+    out_chs = components_.collect{ comp_ ->
+      def comp_config = comp_.config
+
+      def filter_ch = filter_
+        ? input_ch | filter{tup ->
+          filter_(tup[0], tup[1], comp_config)
+        }
+        : input_ch
+      def id_ch = id_
+        ? filter_ch | map{tup ->
+          // def new_id = id_(tup[0], tup[1], comp_config)
+          def new_id = tup[0]
+          if (id_ instanceof String) {
+            new_id = id_
+          } else if (id_ instanceof Closure) {
+            new_id = id_(new_id, tup[1], comp_config)
+          }
+          [new_id] + tup.drop(1)
+        }
+        : filter_ch
+      def data_ch = id_ch | map{tup ->
+          def new_data = tup[1]
+          if (fromState_ instanceof Map) {
+            new_data = fromState_.collectEntries{ key0, key1 ->
+              [key0, new_data[key1]]
+            }
+          } else if (fromState_ instanceof List) {
+            new_data = fromState_.collectEntries{ key ->
+              [key, new_data[key]]
+            }
+          } else if (fromState_ instanceof Closure) {
+            new_data = fromState_(tup[0], new_data, comp_config)
+          }
+          tup.take(1) + [new_data] + tup.drop(1)
+        }
+      def out_ch = data_ch
+        | comp_.run(
+          auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false]
+        )
+      def post_ch = toState_
+        ? out_ch | map{tup ->
+          def output = tup[1]
+          def old_state = tup[2]
+          def new_state = null
+          if (toState_ instanceof Map) {
+            new_state = old_state + toState_.collectEntries{ key0, key1 ->
+              [key0, output[key1]]
+            }
+          } else if (toState_ instanceof List) {
+            new_state = old_state + toState_.collectEntries{ key ->
+              [key, output[key]]
+            }
+          } else if (toState_ instanceof Closure) {
+            new_state = toState_(tup[0], output, old_state, comp_config)
+          }
+          [tup[0], new_state] + tup.drop(3)
+        }
+        : out_ch
+      
+      post_ch
+    }
+
+    // mix all results
+    output_ch =
+      (out_chs.size == 1)
+        ? out_chs[0]
+        : out_chs[0].mix(*out_chs.drop(1))
+
+    emit: output_ch
+  }
+
+  return runComponentsWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runEach.nf'
+/**
+ * Run a list of components on a stream of data.
+ * 
+ * @param components: list of Viash VDSL3 modules to run
+ * @param fromState: a closure, a map or a list of keys to extract from the input data.
+ *   If a closure, it will be called with the id, the data and the component itself.
+ * @param toState: a closure, a map or a list of keys to extract from the output data
+ *   If a closure, it will be called with the id, the output data, the old state and the component itself.
+ * @param filter: filter function to apply to the input.
+ *   It will be called with the id, the data and the component itself.
+ * @param id: id to use for the output data
+ *   If a closure, it will be called with the id, the data and the component itself.
+ * @param auto: auto options to pass to the components
+ *
+ * @return: a workflow that runs the components
+ **/
+def runEach(Map args) {
+  assert args.components: "runEach should be passed a list of components to run"
+
+  def components_ = args.components
+  if (components_ !instanceof List) {
+    components_ = [ components_ ]
+  }
+  assert components_.size() > 0: "pass at least one component to runEach"
+
+  def fromState_ = args.fromState
+  def toState_ = args.toState
+  def filter_ = args.filter
+  def runIf_ = args.runIf
+  def id_ = args.id
+
+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
+  workflow runEachWf {
+    take: input_ch
+    main:
+
+    // generate one channel per method
+    out_chs = components_.collect{ comp_ ->
+      def filter_ch = filter_
+        ? input_ch | filter{tup ->
+          filter_(tup[0], tup[1], comp_)
+        }
+        : input_ch
+      def id_ch = id_
+        ? filter_ch | map{tup ->
+          def new_id = id_
+          if (new_id instanceof Closure) {
+            new_id = new_id(tup[0], tup[1], comp_)
+          }
+          assert new_id instanceof String : "Error in runEach: id should be a String or a Closure that returns a String. Expected: id instanceof String. Found: ${new_id.getClass()}"
+          [new_id] + tup.drop(1)
+        }
+        : filter_ch
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
+          def new_data = tup[1]
+          if (fromState_ instanceof Map) {
+            new_data = fromState_.collectEntries{ key0, key1 ->
+              [key0, new_data[key1]]
+            }
+          } else if (fromState_ instanceof List) {
+            new_data = fromState_.collectEntries{ key ->
+              [key, new_data[key]]
+            }
+          } else if (fromState_ instanceof Closure) {
+            new_data = fromState_(tup[0], new_data, comp_)
+          }
+          tup.take(1) + [new_data] + tup.drop(1)
+        }
+      def out_ch = data_ch
+        | comp_.run(
+          auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false]
+        )
+      def post_ch = toState_
+        ? out_ch | map{tup ->
+          def output = tup[1]
+          def old_state = tup[2]
+          def new_state = null
+          if (toState_ instanceof Map) {
+            new_state = old_state + toState_.collectEntries{ key0, key1 ->
+              [key0, output[key1]]
+            }
+          } else if (toState_ instanceof List) {
+            new_state = old_state + toState_.collectEntries{ key ->
+              [key, output[key]]
+            }
+          } else if (toState_ instanceof Closure) {
+            new_state = toState_(tup[0], output, old_state, comp_)
+          }
+          [tup[0], new_state] + tup.drop(3)
+        }
+        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      return_ch
+    }
+
+    // mix all results
+    output_ch =
+      (out_chs.size == 1)
+        ? out_chs[0]
+        : out_chs[0].mix(*out_chs.drop(1))
+
+    emit: output_ch
+  }
+
+  return runEachWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/safeJoin.nf'
+/**
+ * Join sourceChannel to targetChannel
+ * 
+ * This function joins the sourceChannel to the targetChannel. 
+ * However, each id in the targetChannel must be present in the
+ * sourceChannel. If _meta.join_id exists in the targetChannel, that is 
+ * used as an id instead. If the id doesn't match any id in the sourceChannel,
+ * an error is thrown.
+ */
+
+def safeJoin(targetChannel, sourceChannel, key) {
+  def sourceIDs = new IDChecker()
+
+  def sourceCheck = sourceChannel
+    | map { tup ->
+      sourceIDs.observe(tup[0])
+      tup
+    }
+  def targetCheck = targetChannel
+    | map { tup ->
+      def id = tup[0]
+      
+      if (!sourceIDs.contains(id)) {
+        error (
+          "Error in module '${key}' when merging output with original state.\n" +
+          "  Reason: output with id '${id}' could not be joined with source channel.\n" +
+          "    If the IDs in the output channel differ from the input channel,\n" + 
+          "    please set `tup[1]._meta.join_id to the original ID.\n" +
+          "  Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + 
+          "  Unexpected ID in the output channel: '${id}'.\n" +
+          "  Example input event: [\"id\", [input: file(...)]],\n" +
+          "  Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]"
+        )
+      }
+      // TODO: add link to our documentation on how to fix this
+
+      tup
+    }
+  
+  sourceCheck.cross(targetChannel)
+    | map{ left, right ->
+      right + left.drop(1)
+    }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/_processArgument.nf'
+def _processArgument(arg) {
+  arg.multiple = arg.multiple != null ? arg.multiple : false
+  arg.required = arg.required != null ? arg.required : false
+  arg.direction = arg.direction != null ? arg.direction : "input"
+  arg.multiple_sep = arg.multiple_sep != null ? arg.multiple_sep : ";"
+  arg.plainName = arg.name.replaceAll("^-*", "")
+
+  if (arg.type == "file") {
+    arg.must_exist = arg.must_exist != null ? arg.must_exist : true
+    arg.create_parent = arg.create_parent != null ? arg.create_parent : true
+  }
+
+  // add default values to output files which haven't already got a default
+  if (arg.type == "file" && arg.direction == "output" && arg.default == null) {
+    def mult = arg.multiple ? "_*" : ""
+    def extSearch = ""
+    if (arg.default != null) {
+      extSearch = arg.default
+    } else if (arg.example != null) {
+      extSearch = arg.example
+    }
+    if (extSearch instanceof List) {
+      extSearch = extSearch[0]
+    }
+    def extSearchResult = extSearch.find("\\.[^\\.]+\$")
+    def ext = extSearchResult != null ? extSearchResult : ""
+    arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}"
+    if (arg.multiple) {
+      arg.default = [arg.default]
+    }
+  }
+
+  if (!arg.multiple) {
+    if (arg.default != null && arg.default instanceof List) {
+      arg.default = arg.default[0]
+    }
+    if (arg.example != null && arg.example instanceof List) {
+      arg.example = arg.example[0]
+    }
+  }
+
+  if (arg.type == "boolean_true") {
+    arg.default = false
+  }
+  if (arg.type == "boolean_false") {
+    arg.default = true
+  }
+
+  arg
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/addGlobalParams.nf'
+def addGlobalArguments(config) {
+  def localConfig = [
+    "argument_groups": [
+      [
+        "name": "Nextflow input-output arguments",
+        "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+        "arguments" : [
+          [
+            'name': '--publish_dir',
+            'required': true,
+            'type': 'string',
+            'description': 'Path to an output directory.',
+            'example': 'output/',
+            'multiple': false
+          ],
+          [
+            'name': '--param_list',
+            'required': false,
+            'type': 'string',
+            'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.
+            |
+            |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`.
+            |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.
+            |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`.
+            |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`.
+            |
+            |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(),
+            'example': 'my_params.yaml',
+            'multiple': false,
+            'hidden': true
+          ]
+          // TODO: allow multiple: true in param_list?
+          // TODO: allow to specify a --param_list_regex to filter the param_list?
+          // TODO: allow to specify a --param_list_from_state to remap entries in the param_list?
+        ]
+      ]
+    ]
+  ]
+
+  return processConfig(_mergeMap(config, localConfig))
+}
+
+def _mergeMap(Map lhs, Map rhs) {
+  return rhs.inject(lhs.clone()) { map, entry ->
+    if (map[entry.key] instanceof Map && entry.value instanceof Map) {
+      map[entry.key] = _mergeMap(map[entry.key], entry.value)
+    } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) {
+      map[entry.key] += entry.value
+    } else {
+      map[entry.key] = entry.value
+    }
+    return map
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/generateHelp.nf'
+def _generateArgumentHelp(param) {
+  // alternatives are not supported
+  // def names = param.alternatives ::: List(param.name)
+
+  def unnamedProps = [
+    ["required parameter", param.required],
+    ["multiple values allowed", param.multiple],
+    ["output", param.direction.toLowerCase() == "output"],
+    ["file must exist", param.type == "file" && param.must_exist]
+  ].findAll{it[1]}.collect{it[0]}
+  
+  def dflt = null
+  if (param.default != null) {
+    if (param.default instanceof List) {
+      dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ")
+    } else {
+      dflt = param.default.toString()
+    }
+  }
+  def example = null
+  if (param.example != null) {
+    if (param.example instanceof List) {
+      example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ")
+    } else {
+      example = param.example.toString()
+    }
+  }
+  def min = param.min?.toString()
+  def max = param.max?.toString()
+
+  def escapeChoice = { choice ->
+    def s1 = choice.replaceAll("\\n", "\\\\n")
+    def s2 = s1.replaceAll("\"", """\\\"""")
+    s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2
+  }
+  def choices = param.choices == null ? 
+    null : 
+    "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]"
+
+  def namedPropsStr = [
+    ["type", ([param.type] + unnamedProps).join(", ")],
+    ["default", dflt],
+    ["example", example],
+    ["choices", choices],
+    ["min", min],
+    ["max", max]
+  ]
+    .findAll{it[1]}
+    .collect{"\n        " + it[0] + ": " + it[1].replaceAll("\n", "\\n")}
+    .join("")
+  
+  def descStr = param.description == null ?
+    "" :
+    _paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n        ")
+  
+  "\n    --" + param.plainName +
+    namedPropsStr +
+    descStr
+}
+
+// Based on Helper.generateHelp() in Helper.scala
+def _generateHelp(config) {
+  def fun = config
+
+  // PART 1: NAME AND VERSION
+  def nameStr = fun.name + 
+    (fun.version == null ? "" : " " + fun.version)
+
+  // PART 2: DESCRIPTION
+  def descrStr = fun.description == null ? 
+    "" :
+    "\n\n" + _paragraphWrap(fun.description.trim(), 80).join("\n")
+
+  // PART 3: Usage
+  def usageStr = fun.usage == null ? 
+    "" :
+    "\n\nUsage:\n" + fun.usage.trim()
+
+  // PART 4: Options
+  def argGroupStrs = fun.allArgumentGroups.collect{argGroup ->
+    def name = argGroup.name
+    def descriptionStr = argGroup.description == null ?
+      "" :
+      "\n    " + _paragraphWrap(argGroup.description.trim(), 80-4).join("\n    ") + "\n"
+    def arguments = argGroup.arguments.collect{arg -> 
+      arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg
+    }.findAll{it != null}
+    def argumentStrs = arguments.collect{param -> _generateArgumentHelp(param)}
+    
+    "\n\n$name:" +
+      descriptionStr +
+      argumentStrs.join("\n")
+  }
+
+  // FINAL: combine
+  def out = nameStr + 
+    descrStr +
+    usageStr + 
+    argGroupStrs.join("")
+
+  return out
+}
+
+// based on Format._paragraphWrap
+def _paragraphWrap(str, maxLength) {
+  def outLines = []
+  str.split("\n").each{par ->
+    def words = par.split("\\s").toList()
+
+    def word = null
+    def line = words.pop()
+    while(!words.isEmpty()) {
+      word = words.pop()
+      if (line.length() + word.length() + 1 <= maxLength) {
+        line = line + " " + word
+      } else {
+        outLines.add(line)
+        line = word
+      }
+    }
+    if (words.isEmpty()) {
+      outLines.add(line)
+    }
+  }
+  return outLines
+}
+
+def helpMessage(config) {
+  if (params.containsKey("help") && params.help) {
+    def mergedConfig = addGlobalArguments(config)
+    def helpStr = _generateHelp(mergedConfig)
+    println(helpStr)
+    exit 0
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/processConfig.nf'
+def processConfig(config) {
+  // set defaults for arguments
+  config.arguments = 
+    (config.arguments ?: []).collect{_processArgument(it)}
+
+  // set defaults for argument_group arguments
+  config.argument_groups =
+    (config.argument_groups ?: []).collect{grp ->
+      grp.arguments = (grp.arguments ?: []).collect{_processArgument(it)}
+      grp
+    }
+
+  // create combined arguments list
+  config.allArguments = 
+    config.arguments +
+    config.argument_groups.collectMany{it.arguments}
+
+  // add missing argument groups (based on Functionality::allArgumentGroups())
+  def argGroups = config.argument_groups
+  if (argGroups.any{it.name.toLowerCase() == "arguments"}) {
+    argGroups = argGroups.collect{ grp ->
+      if (grp.name.toLowerCase() == "arguments") {
+        grp = grp + [
+          arguments: grp.arguments + config.arguments
+        ]
+      }
+      grp
+    }
+  } else {
+    argGroups = argGroups + [
+      name: "Arguments",
+      arguments: config.arguments
+    ]
+  }
+  config.allArgumentGroups = argGroups
+
+  config
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/readConfig.nf'
+
+def readConfig(file) {
+  def config = readYaml(file ?: moduleDir.resolve("config.vsh.yaml"))
+  processConfig(config)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_resolveSiblingIfNotAbsolute.nf'
+/**
+  * Resolve a path relative to the current file.
+  * 
+  * @param str The path to resolve, as a String.
+  * @param parentPath The path to resolve relative to, as a Path.
+  *
+  * @return The path that may have been resovled, as a Path.
+  */
+def _resolveSiblingIfNotAbsolute(str, parentPath) {
+  if (str !instanceof String) {
+    return str
+  }
+  if (!_stringIsAbsolutePath(str)) {
+    return parentPath.resolveSibling(str)
+  } else {
+    return file(str, hidden: true)
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_stringIsAbsolutePath.nf'
+/**
+  * Check whether a path as a string is absolute.
+  *
+  * In the past, we tried using `file(., relative: true).isAbsolute()`,
+  * but the 'relative' option was added in 22.10.0.
+  *
+  * @param path The path to check, as a String.
+  *
+  * @return Whether the path is absolute, as a boolean.
+  */
+def _stringIsAbsolutePath(path) {
+  def _resolve_URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*:)?\\/.+/
+
+  assert path instanceof String
+  return _resolve_URL_PROTOCOL.matcher(path).matches()
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/collectTraces.nf'
+class CustomTraceObserver implements nextflow.trace.TraceObserver {
+  List traces
+
+  CustomTraceObserver(List traces) {
+    this.traces = traces
+  }
+
+  @Override
+  void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) {
+    def trace2 = trace.store.clone()
+    trace2.script = null
+    traces.add(trace2)
+  }
+
+  @Override
+  void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) {
+    def trace2 = trace.store.clone()
+    trace2.script = null
+    traces.add(trace2)
+  }
+}
+
+def collectTraces() {
+  def traces = Collections.synchronizedList([])
+
+  // add custom trace observer which stores traces in the traces object
+  session.observers.add(new CustomTraceObserver(traces))
+
+  traces
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/deepClone.nf'
+/**
+  * Performs a deep clone of the given object.
+  * @param x an object
+  */
+def deepClone(x) {
+  iterateMap(x, {it instanceof Cloneable ? it.clone() : it})
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getPublishDir.nf'
+def getPublishDir() {
+  return params.containsKey("publish_dir") ? params.publish_dir : 
+    params.containsKey("publishDir") ? params.publishDir : 
+    null
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getRootDir.nf'
+
+// Recurse upwards until we find a '.build.yaml' file
+def _findBuildYamlFile(pathPossiblySymlink) {
+  def path = pathPossiblySymlink.toRealPath()
+  def child = path.resolve(".build.yaml")
+  if (java.nio.file.Files.isDirectory(path) && java.nio.file.Files.exists(child)) {
+    return child
+  } else {
+    def parent = path.getParent()
+    if (parent == null) {
+      return null
+    } else {
+      return _findBuildYamlFile(parent)
+    }
+  }
+}
+
+// get the root of the target folder
+def getRootDir() {
+  def dir = _findBuildYamlFile(meta.resources_dir)
+  assert dir != null: "Could not find .build.yaml in the folder structure"
+  dir.getParent()
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/iterateMap.nf'
+/**
+  * Recursively apply a function over the leaves of an object.
+  * @param obj The object to iterate over.
+  * @param fun The function to apply to each value.
+  * @return The object with the function applied to each value.
+  */
+def iterateMap(obj, fun) {
+  if (obj instanceof List && obj !instanceof String) {
+    return obj.collect{item ->
+      iterateMap(item, fun)
+    }
+  } else if (obj instanceof Map) {
+    return obj.collectEntries{key, item ->
+      [key.toString(), iterateMap(item, fun)]
+    }
+  } else {
+    return fun(obj)
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/niceView.nf'
+/**
+  * A view for printing the event of each channel as a YAML blob.
+  * This is useful for debugging.
+  */
+def niceView() {
+  workflow niceViewWf {
+    take: input
+    main:
+      output = input
+        | view{toYamlBlob(it)}
+    emit: output
+  }
+  return niceViewWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readCsv.nf'
+
+def readCsv(file_path) {
+  def output = []
+  def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path
+
+  // todo: allow escaped quotes in string
+  // todo: allow single quotes?
+  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
+  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')
+
+  def br = java.nio.file.Files.newBufferedReader(inputFile)
+
+  def row = -1
+  def header = null
+  while (br.ready() && header == null) {
+    def line = br.readLine()
+    row++
+    if (!line.startsWith("#")) {
+      header = splitRegex.split(line, -1).collect{field ->
+        m = removeQuote.matcher(field)
+        m.find() ? m.replaceFirst('$1') : field
+      }
+    }
+  }
+  assert header != null: "CSV file should contain a header"
+
+  while (br.ready()) {
+    def line = br.readLine()
+    row++
+    if (line == null) {
+      br.close()
+      break
+    }
+
+    if (!line.startsWith("#")) {
+      def predata = splitRegex.split(line, -1)
+      def data = predata.collect{field ->
+        if (field == "") {
+          return null
+        }
+        def m = removeQuote.matcher(field)
+        if (m.find()) {
+          return m.replaceFirst('$1')
+        } else {
+          return field
+        }
+      }
+      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      
+      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+      output.add(dataMap)
+    }
+  }
+
+  output
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJson.nf'
+def readJson(file_path) {
+  def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path
+  def jsonSlurper = new groovy.json.JsonSlurper()
+  jsonSlurper.parse(inputFile)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJsonBlob.nf'
+def readJsonBlob(str) {
+  def jsonSlurper = new groovy.json.JsonSlurper()
+  jsonSlurper.parseText(str)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readTaggedYaml.nf'
+// Custom constructor to modify how certain objects are parsed from YAML
+class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor {
+  Path root
+
+  class ConstructPath extends org.yaml.snakeyaml.constructor.AbstractConstruct {
+    public Object construct(org.yaml.snakeyaml.nodes.Node node) {
+      String filename = (String) constructScalar(node);
+      if (root != null) {
+        return root.resolve(filename);
+      }
+      return java.nio.file.Paths.get(filename);
+    }
+  }
+
+  CustomConstructor(org.yaml.snakeyaml.LoaderOptions options, Path root) {
+    super(options)
+    this.root = root
+    // Handling !file tag and parse it back to a File type
+    this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructPath())
+  }
+}
+
+def readTaggedYaml(Path path) {
+  def options = new org.yaml.snakeyaml.LoaderOptions()
+  def constructor = new CustomConstructor(options, path.getParent())
+  def yaml = new org.yaml.snakeyaml.Yaml(constructor)
+  return yaml.load(path.text)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYaml.nf'
+def readYaml(file_path) {
+  def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path
+  def yamlSlurper = new org.yaml.snakeyaml.Yaml()
+  yamlSlurper.load(inputFile)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYamlBlob.nf'
+def readYamlBlob(str) {
+  def yamlSlurper = new org.yaml.snakeyaml.Yaml()
+  yamlSlurper.load(str)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toJsonBlob.nf'
+String toJsonBlob(data) {
+  return groovy.json.JsonOutput.toJson(data)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toTaggedYamlBlob.nf'
+// Custom representer to modify how certain objects are represented in YAML
+class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer {
+  Path relativizer
+
+  class RepresentPath implements org.yaml.snakeyaml.representer.Represent {
+    public String getFileName(Object obj) {
+      if (obj instanceof File) {
+        obj = ((File) obj).toPath();
+      }
+      if (obj !instanceof Path) {
+        throw new IllegalArgumentException("Object: " + obj + " is not a Path or File");
+      }
+      def path = (Path) obj;
+
+      if (relativizer != null) {
+        return relativizer.relativize(path).toString()
+      } else {
+        return path.toString()
+      }
+    }
+
+    public org.yaml.snakeyaml.nodes.Node representData(Object data) {
+      String filename = getFileName(data);
+      def tag = new org.yaml.snakeyaml.nodes.Tag("!file");
+      return representScalar(tag, filename);
+    }
+  }
+  CustomRepresenter(org.yaml.snakeyaml.DumperOptions options, Path relativizer) {
+    super(options)
+    this.relativizer = relativizer
+    this.representers.put(sun.nio.fs.UnixPath, new RepresentPath())
+    this.representers.put(Path, new RepresentPath())
+    this.representers.put(File, new RepresentPath())
+  }
+}
+
+String toTaggedYamlBlob(data) {
+  return toRelativeTaggedYamlBlob(data, null)
+}
+String toRelativeTaggedYamlBlob(data, Path relativizer) {
+  def options = new org.yaml.snakeyaml.DumperOptions()
+  options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK)
+  def representer = new CustomRepresenter(options, relativizer)
+  def yaml = new org.yaml.snakeyaml.Yaml(representer, options)
+  return yaml.dump(data)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toYamlBlob.nf'
+String toYamlBlob(data) {
+  def options = new org.yaml.snakeyaml.DumperOptions()
+  options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK)
+  options.setPrettyFlow(true)
+  def yaml = new org.yaml.snakeyaml.Yaml(options)
+  def cleanData = iterateMap(data, { it instanceof Path ? it.toString() : it })
+  return yaml.dump(cleanData)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeJson.nf'
+void writeJson(data, file) {
+  assert data: "writeJson: data should not be null"
+  assert file: "writeJson: file should not be null"
+  file.write(toJsonBlob(data))
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeYaml.nf'
+void writeYaml(data, file) {
+  assert data: "writeYaml: data should not be null"
+  assert file: "writeYaml: file should not be null"
+  file.write(toYamlBlob(data))
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/findStates.nf'
+def findStates(Map params, Map config) {
+  def auto_config = deepClone(config)
+  def auto_params = deepClone(params)
+
+  auto_config = auto_config.clone()
+  // override arguments
+  auto_config.argument_groups = []
+  auto_config.arguments = [
+    [
+      type: "string",
+      name: "--id",
+      description: "A dummy identifier",
+      required: false
+    ],
+    [
+      type: "file",
+      name: "--input_states",
+      example: "/path/to/input/directory/**/state.yaml",
+      description: "Path to input directory containing the datasets to be integrated.",
+      required: true,
+      multiple: true,
+      multiple_sep: ";"
+    ],
+    [
+      type: "string",
+      name: "--filter",
+      example: "foo/.*/state.yaml",
+      description: "Regex to filter state files by path.",
+      required: false
+    ],
+    // to do: make this a yaml blob?
+    [
+      type: "string",
+      name: "--rename_keys",
+      example: ["newKey1:oldKey1", "newKey2:oldKey2"],
+      description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.",
+      required: false,
+      multiple: true,
+      multiple_sep: ";"
+    ],
+    [
+      type: "string",
+      name: "--settings",
+      example: '{"output_dataset": "dataset.h5ad", "k": 10}',
+      description: "Global arguments as a JSON glob to be passed to all components.",
+      required: false
+    ]
+  ]
+  if (!(auto_params.containsKey("id"))) {
+    auto_params["id"] = "auto"
+  }
+
+  // run auto config through processConfig once more
+  auto_config = processConfig(auto_config)
+
+  workflow findStatesWf {
+    helpMessage(auto_config)
+
+    output_ch = 
+      channelFromParams(auto_params, auto_config)
+        | flatMap { autoId, args ->
+
+          def globalSettings = args.settings ? readYamlBlob(args.settings) : [:]
+
+          // look for state files in input dir
+          def stateFiles = args.input_states
+
+          // filter state files by regex
+          if (args.filter) {
+            stateFiles = stateFiles.findAll{ stateFile ->
+              def stateFileStr = stateFile.toString()
+              def matcher = stateFileStr =~ args.filter
+              matcher.matches()}
+          }
+
+          // read in states
+          def states = stateFiles.collect { stateFile ->
+            def state_ = readTaggedYaml(stateFile)
+            [state_.id, state_]
+          }
+
+          // construct renameMap
+          if (args.rename_keys) {
+            def renameMap = args.rename_keys.collectEntries{renameString ->
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
+              split
+            }
+
+            // rename keys in state, only let states through which have all keys
+            // also add global settings
+            states = states.collectMany{id, state ->
+              def newState = [:]
+
+              for (key in renameMap.keySet()) {
+                def origKey = renameMap[key]
+                if (!(state.containsKey(origKey))) {
+                  return []
+                }
+                newState[key] = state[origKey]
+              }
+
+              [[id, globalSettings + newState]]
+            }
+          }
+
+          states
+        }
+    emit:
+    output_ch
+  }
+
+  return findStatesWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/joinStates.nf'
+def joinStates(Closure apply_) {
+  workflow joinStatesWf {
+    take: input_ch
+    main:
+    output_ch = input_ch
+      | toSortedList
+      | filter{ it.size() > 0 }
+      | map{ tups ->
+        def ids = tups.collect{it[0]}
+        def states = tups.collect{it[1]}
+        apply_(ids, states)
+      }
+
+    emit: output_ch
+  }
+  return joinStatesWf
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
+def collectFiles(obj) {
+  if (obj instanceof java.io.File || obj instanceof Path)  {
+    return [obj]
+  } else if (obj instanceof List && obj !instanceof String) {
+    return obj.collectMany{item ->
+      collectFiles(item)
+    }
+  } else if (obj instanceof Map) {
+    return obj.collectMany{key, item ->
+      collectFiles(item)
+    }
+  } else {
+    return []
+  }
+}
+
+/**
+ * Recurse through a state and collect all input files and their target output filenames.
+ * @param obj The state to recurse through.
+ * @param prefix The prefix to prepend to the output filenames.
+ */
+def collectInputOutputPaths(obj, prefix) {
+  if (obj instanceof File || obj instanceof Path)  {
+    def path = obj instanceof Path ? obj : obj.toPath()
+    def ext = path.getFileName().toString().find("\\.[^\\.]+\$") ?: ""
+    def newFilename = prefix + ext
+    return [[obj, newFilename]]
+  } else if (obj instanceof List && obj !instanceof String) {
+    return obj.withIndex().collectMany{item, ix ->
+      collectInputOutputPaths(item, prefix + "_" + ix)
+    }
+  } else if (obj instanceof Map) {
+    return obj.collectMany{key, item ->
+      collectInputOutputPaths(item, prefix + "." + key)
+    }
+  } else {
+    return []
+  }
+}
+
+def publishStates(Map args) {
+  def key_ = args.get("key")
+  def yamlTemplate_ = args.get("output_state", args.get("outputState", '$id.$key.state.yaml'))
+
+  assert key_ != null : "publishStates: key must be specified"
+  
+  workflow publishStatesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          def yamlFilename = yamlTemplate_
+            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
+            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
+
+            // TODO: do the pathnames in state_ match up with the outputFilenames_?
+
+          // convert state to yaml blob
+          def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
+
+          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+        }
+        | publishStatesProc
+    emit: input_ch
+  }
+  return publishStatesWf
+}
+process publishStatesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{[yamlFile] + outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+mkdir -p "\$(dirname '${yamlFile}')"
+echo "Storing state as yaml"
+echo '${yamlBlob}' > '${yamlFile}'
+echo "Copying output files to destination folder"
+${copyCommands.join("\n  ")}
+"""
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishStatesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishStatesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishStatesByConfig: key must be specified"
+  
+  workflow publishStatesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+          // TODO: allow overriding the state.yaml template
+          // TODO TODO: if auto.publish == "state", add output_state as an argument
+          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
+          def yamlFilename = yamlTemplate
+            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
+            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
+          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (key, value) are the tuples that will be saved to the state.yaml file
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def value_ = java.nio.file.Paths.get(filename_ix)
+                    // if id contains a slash
+                    if (yamlDir != null) {
+                      value_ = yamlDir.relativize(value_)
+                    }
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  // if id contains a slash
+                  if (yamlDir != null) {
+                    value_ = yamlDir.relativize(value_)
+                  }
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def updatedState_ = processedState.collectEntries{[it.key, it.value]}
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+          // convert state to yaml blob
+          def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
+
+          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+        }
+        | publishStatesProc
+    emit: input_ch
+  }
+  return publishStatesSimpleWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/setState.nf'
+def setState(fun) {
+  assert fun instanceof Closure || fun instanceof Map || fun instanceof List :
+    "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}"
+
+  // if fun is a List, convert to map
+  if (fun instanceof List) {
+    // check whether fun is a list[string]
+    assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings"
+    fun = fun.collectEntries{[it, it]}
+  }
+
+  // if fun is a map, convert to closure
+  if (fun instanceof Map) {
+    // check whether fun is a map[string, string]
+    assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings"
+    assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings"
+    def funMap = fun.clone()
+    // turn the map into a closure to be used later on
+    fun = { id_, state_ ->
+      assert state_ instanceof Map : "Error in setState: the state is not a Map"
+      funMap.collectMany{newkey, origkey ->
+        if (state_.containsKey(origkey)) {
+          [[newkey, state_[origkey]]]
+        } else {
+          []
+        }
+      }.collectEntries()
+    }
+  }
+
+  map { tup ->
+    def id = tup[0]
+    def state = tup[1]
+    def unfilteredState = fun(id, state)
+    def newState = unfilteredState.findAll{key, val -> val != null}
+    [id, newState] + tup.drop(2)
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processAuto.nf'
+// TODO: unit test processAuto
+def processAuto(Map auto) {
+  // remove null values
+  auto = auto.findAll{k, v -> v != null}
+
+  // check for unexpected keys
+  def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"]
+  def unexpectedKeys = auto.keySet() - expectedKeys
+  assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'"
+
+  // check auto.simplifyInput
+  assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean"
+
+  // check auto.simplifyOutput
+  assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean"
+
+  // check auto.transcript
+  assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean"
+
+  // check auto.publish
+  assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'"
+
+  return auto.subMap(expectedKeys)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processDirectives.nf'
+def assertMapKeys(map, expectedKeys, requiredKeys, mapName) {
+  assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}"
+  map.forEach { key, val -> 
+    assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map"
+  }
+  requiredKeys.forEach { requiredKey -> 
+    assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map"
+  }
+}
+
+// TODO: unit test processDirectives
+def processDirectives(Map drctv) {
+  // remove null values
+  drctv = drctv.findAll{k, v -> v != null}
+
+  // check for unexpected keys
+  def expectedKeys = [
+    "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time"
+  ]
+  def unexpectedKeys = drctv.keySet() - expectedKeys
+  assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'"
+
+  /* DIRECTIVE accelerator
+    accepted examples:
+    - [ limit: 4, type: "nvidia-tesla-k80" ]
+  */
+  if (drctv.containsKey("accelerator")) {
+    assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator")
+  }
+
+  /* DIRECTIVE afterScript
+    accepted examples:
+    - "source /cluster/bin/cleanup"
+  */
+  if (drctv.containsKey("afterScript")) {
+    assert drctv["afterScript"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE beforeScript
+    accepted examples:
+    - "source /cluster/bin/setup"
+  */
+  if (drctv.containsKey("beforeScript")) {
+    assert drctv["beforeScript"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE cache
+    accepted examples:
+    - true
+    - false
+    - "deep"
+    - "lenient"
+  */
+  if (drctv.containsKey("cache")) {
+    assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean
+    if (drctv["cache"] instanceof CharSequence) {
+      assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache"
+    }
+  }
+
+  /* DIRECTIVE conda
+    accepted examples:
+    - "bwa=0.7.15"
+    - "bwa=0.7.15 fastqc=0.11.5"
+    - ["bwa=0.7.15", "fastqc=0.11.5"]
+  */
+  if (drctv.containsKey("conda")) {
+    if (drctv["conda"] instanceof List) {
+      drctv["conda"] = drctv["conda"].join(" ")
+    }
+    assert drctv["conda"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE container
+    accepted examples:
+    - "foo/bar:tag"
+    - [ registry: "reg", image: "im", tag: "ta" ]
+      is transformed to "reg/im:ta"
+    - [ image: "im" ] 
+      is transformed to "im:latest"
+  */
+  if (drctv.containsKey("container")) {
+    assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence
+    if (drctv["container"] instanceof Map) {
+      def m = drctv["container"]
+      assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container")
+      def part1 = 
+        System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : 
+        params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove?
+        m.registry ? m.registry + "/" : 
+        ""
+      def part2 = m.image
+      def part3 = m.tag ? ":" + m.tag : ":latest"
+      drctv["container"] = part1 + part2 + part3
+    }
+  }
+
+  /* DIRECTIVE containerOptions
+    accepted examples:
+    - "--foo bar"
+    - ["--foo bar", "-f b"]
+  */
+  if (drctv.containsKey("containerOptions")) {
+    if (drctv["containerOptions"] instanceof List) {
+      drctv["containerOptions"] = drctv["containerOptions"].join(" ")
+    }
+    assert drctv["containerOptions"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE cpus
+    accepted examples:
+    - 1
+    - 10
+  */
+  if (drctv.containsKey("cpus")) {
+    assert drctv["cpus"] instanceof Integer
+  }
+
+  /* DIRECTIVE disk
+    accepted examples:
+    - "1 GB"
+    - "2TB"
+    - "3.2KB"
+    - "10.B"
+  */
+  if (drctv.containsKey("disk")) {
+    assert drctv["disk"] instanceof CharSequence
+    // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B")
+    // ^ does not allow closures
+  }
+
+  /* DIRECTIVE echo
+    accepted examples:
+    - true
+    - false
+  */
+  if (drctv.containsKey("echo")) {
+    assert drctv["echo"] instanceof Boolean
+  }
+
+  /* DIRECTIVE errorStrategy
+    accepted examples:
+    - "terminate"
+    - "finish"
+  */
+  if (drctv.containsKey("errorStrategy")) {
+    assert drctv["errorStrategy"] instanceof CharSequence
+    assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy"
+  }
+
+  /* DIRECTIVE executor
+    accepted examples:
+    - "local"
+    - "sge"
+  */
+  if (drctv.containsKey("executor")) {
+    assert drctv["executor"] instanceof CharSequence
+    assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor"
+  }
+
+  /* DIRECTIVE machineType
+    accepted examples:
+    - "n1-highmem-8"
+  */
+  if (drctv.containsKey("machineType")) {
+    assert drctv["machineType"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE maxErrors
+    accepted examples:
+    - 1
+    - 3
+  */
+  if (drctv.containsKey("maxErrors")) {
+    assert drctv["maxErrors"] instanceof Integer
+  }
+
+  /* DIRECTIVE maxForks
+    accepted examples:
+    - 1
+    - 3
+  */
+  if (drctv.containsKey("maxForks")) {
+    assert drctv["maxForks"] instanceof Integer
+  }
+
+  /* DIRECTIVE maxRetries
+    accepted examples:
+    - 1
+    - 3
+  */
+  if (drctv.containsKey("maxRetries")) {
+    assert drctv["maxRetries"] instanceof Integer
+  }
+
+  /* DIRECTIVE memory
+    accepted examples:
+    - "1 GB"
+    - "2TB"
+    - "3.2KB"
+    - "10.B"
+  */
+  if (drctv.containsKey("memory")) {
+    assert drctv["memory"] instanceof CharSequence
+    // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B")
+    // ^ does not allow closures
+  }
+
+  /* DIRECTIVE module
+    accepted examples:
+    - "ncbi-blast/2.2.27"
+    - "ncbi-blast/2.2.27:t_coffee/10.0"
+    - ["ncbi-blast/2.2.27", "t_coffee/10.0"]
+  */
+  if (drctv.containsKey("module")) {
+    if (drctv["module"] instanceof List) {
+      drctv["module"] = drctv["module"].join(":")
+    }
+    assert drctv["module"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE penv
+    accepted examples:
+    - "smp"
+  */
+  if (drctv.containsKey("penv")) {
+    assert drctv["penv"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE pod
+    accepted examples:
+    - [ label: "key", value: "val" ]
+    - [ annotation: "key", value: "val" ]
+    - [ env: "key", value: "val" ]
+    - [ [label: "l", value: "v"], [env: "e", value: "v"]]
+  */
+  if (drctv.containsKey("pod")) {
+    if (drctv["pod"] instanceof Map) {
+      drctv["pod"] = [ drctv["pod"] ]
+    }
+    assert drctv["pod"] instanceof List
+    drctv["pod"].forEach { pod ->
+      assert pod instanceof Map
+      // TODO: should more checks be added?
+      // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod
+      // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...?
+    }
+  }
+
+  /* DIRECTIVE publishDir
+    accepted examples:
+    - []
+    - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ]
+    - "/path/to/dir" 
+      is transformed to [[ path: "/path/to/dir" ]]
+    - [ path: "/path/to/dir", mode: "cache" ]
+      is transformed to [[ path: "/path/to/dir", mode: "cache" ]]
+  */
+  // TODO: should we also look at params["publishDir"]?
+  if (drctv.containsKey("publishDir")) {
+    def pblsh = drctv["publishDir"]
+    
+    // check different options
+    assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence
+    
+    // turn into list if not already so
+    // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work.
+    pblsh = pblsh instanceof List ? pblsh : [ pblsh ]
+
+    // check elements of publishDir
+    pblsh = pblsh.collect{ elem ->
+      // turn into map if not already so
+      elem = elem instanceof CharSequence ? [ path: elem ] : elem
+
+      // check types and keys
+      assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}"
+      assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir")
+
+      // check elements in map
+      assert elem.containsKey("path")
+      assert elem["path"] instanceof CharSequence
+      if (elem.containsKey("mode")) {
+        assert elem["mode"] instanceof CharSequence
+        assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ]
+      }
+      if (elem.containsKey("overwrite")) {
+        assert elem["overwrite"] instanceof Boolean
+      }
+      if (elem.containsKey("pattern")) {
+        assert elem["pattern"] instanceof CharSequence
+      }
+      if (elem.containsKey("saveAs")) {
+        assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'"
+      }
+      if (elem.containsKey("enabled")) {
+        assert elem["enabled"] instanceof Boolean
+      }
+
+      // return final result
+      elem
+    }
+    // store final directive
+    drctv["publishDir"] = pblsh
+  }
+
+  /* DIRECTIVE queue
+    accepted examples:
+    - "long"
+    - "short,long"
+    - ["short", "long"]
+  */
+  if (drctv.containsKey("queue")) {
+    if (drctv["queue"] instanceof List) {
+      drctv["queue"] = drctv["queue"].join(",")
+    }
+    assert drctv["queue"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE label
+    accepted examples:
+    - "big_mem"
+    - "big_cpu"
+    - ["big_mem", "big_cpu"]
+  */
+  if (drctv.containsKey("label")) {
+    if (drctv["label"] instanceof CharSequence) {
+      drctv["label"] = [ drctv["label"] ]
+    }
+    assert drctv["label"] instanceof List
+    drctv["label"].forEach { label ->
+      assert label instanceof CharSequence
+      // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?")
+      // ^ does not allow closures
+    }
+  }
+
+  /* DIRECTIVE scratch
+    accepted examples:
+    - true
+    - "/path/to/scratch"
+    - '$MY_PATH_TO_SCRATCH'
+    - "ram-disk"
+  */
+  if (drctv.containsKey("scratch")) {
+    assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE storeDir
+    accepted examples:
+    - "/path/to/storeDir"
+  */
+  if (drctv.containsKey("storeDir")) {
+    assert drctv["storeDir"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE stageInMode
+    accepted examples:
+    - "copy"
+    - "link"
+  */
+  if (drctv.containsKey("stageInMode")) {
+    assert drctv["stageInMode"] instanceof CharSequence
+    assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"]
+  }
+
+  /* DIRECTIVE stageOutMode
+    accepted examples:
+    - "copy"
+    - "link"
+  */
+  if (drctv.containsKey("stageOutMode")) {
+    assert drctv["stageOutMode"] instanceof CharSequence
+    assert drctv["stageOutMode"] in ["copy", "move", "rsync"]
+  }
+
+  /* DIRECTIVE tag
+    accepted examples:
+    - "foo"
+    - '$id'
+  */
+  if (drctv.containsKey("tag")) {
+    assert drctv["tag"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE time
+    accepted examples:
+    - "1h"
+    - "2days"
+    - "1day 6hours 3minutes 30seconds"
+  */
+  if (drctv.containsKey("time")) {
+    assert drctv["time"] instanceof CharSequence
+    // todo: validation regex?
+  }
+
+  return drctv
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processWorkflowArgs.nf'
+def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) {
+  // override defaults with args
+  def workflowArgs = defaultWfArgs + args
+
+  // check whether 'key' exists
+  assert workflowArgs.containsKey("key") : "Error in module '${meta.config.name}': key is a required argument"
+
+  // if 'key' is a closure, apply it to the original key
+  if (workflowArgs["key"] instanceof Closure) {
+    workflowArgs["key"] = workflowArgs["key"](meta.config.name)
+  }
+  def key = workflowArgs["key"]
+  assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}"
+  assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}"
+
+  // check for any unexpected keys
+  def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"]
+  def unexpectedKeys = workflowArgs.keySet() - expectedKeys
+  assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'"
+
+  // check whether directives exists and apply defaults
+  assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument"
+  assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}"
+  workflowArgs["directives"] = processDirectives(defaultWfArgs.directives + workflowArgs["directives"])
+
+  // check whether directives exists and apply defaults
+  assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument"
+  assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}"
+  workflowArgs["auto"] = processAuto(defaultWfArgs.auto + workflowArgs["auto"])
+
+  // auto define publish, if so desired
+  if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) {
+    // can't assert at this level thanks to the no_publish profile
+    // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : 
+    //   "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" +
+    //   "  Example: params.publish_dir = \"./output/\""
+    def publishDir = getPublishDir()
+    
+    if (publishDir != null) {
+      workflowArgs.directives.publishDir = [[ 
+        path: publishDir, 
+        saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default
+        mode: "copy"
+      ]]
+    }
+  }
+
+  // auto define transcript, if so desired
+  if (workflowArgs.auto.transcript == true) {
+    // can't assert at this level thanks to the no_publish profile
+    // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : 
+    //   "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" +
+    //   "  Example: params.transcripts_dir = \"./transcripts/\""
+    def transcriptsDir = 
+      params.containsKey("transcripts_dir") ? params.transcripts_dir : 
+      params.containsKey("transcriptsDir") ? params.transcriptsDir : 
+      params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" :
+      params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : 
+      null
+    if (transcriptsDir != null) {
+      def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss')
+      def transcriptsPublishDir = [ 
+        path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/",
+        saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", 
+        mode: "copy"
+      ]
+      def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : []
+      workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir
+    }
+  }
+
+  // if this is a stubrun, remove certain directives?
+  if (workflow.stubRun) {
+    workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"])
+  }
+
+  for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter", "runIf"]) {
+    if (workflowArgs.containsKey(nam) && workflowArgs[nam]) {
+      assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}"
+    }
+  }
+
+  // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well?
+  for (nam in ["map", "mapData", "mapPassthrough", "renameKeys"]) {
+    if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) {
+      log.warn "module '$key': workflow argument '$nam' is deprecated and will be removed in Viash 0.9.0. Please use 'fromState' and 'toState' instead."
+    }
+  }
+
+  // check fromState
+  workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, meta.config)
+
+  // check toState
+  workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, meta.config)
+
+  // return output
+  return workflowArgs
+}
+
+def _processFromState(fromState, key_, config_) {
+  assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List :
+    "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}"
+  if (fromState == null) {
+    return null
+  }
+  
+  // if fromState is a List, convert to map
+  if (fromState instanceof List) {
+    // check whether fromstate is a list[string]
+    assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings"
+    fromState = fromState.collectEntries{[it, it]}
+  }
+
+  // if fromState is a map, convert to closure
+  if (fromState instanceof Map) {
+    // check whether fromstate is a map[string, string]
+    assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings"
+    assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings"
+    def fromStateMap = fromState.clone()
+    def requiredInputNames = meta.config.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName}
+    // turn the map into a closure to be used later on
+    fromState = { it ->
+      def state = it[1]
+      assert state instanceof Map : "Error in module '$key_': the state is not a Map"
+      def data = fromStateMap.collectMany{newkey, origkey ->
+        // check whether newkey corresponds to a required argument
+        if (state.containsKey(origkey)) {
+          [[newkey, state[origkey]]]
+        } else if (!requiredInputNames.contains(origkey)) {
+          []
+        } else {
+          throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state")
+        }
+      }.collectEntries()
+      data
+    }
+  }
+  
+  return fromState
+}
+
+def _processToState(toState, key_, config_) {
+  if (toState == null) {
+    toState = { tup -> tup[1] }
+  }
+
+  // toState should be a closure, map[string, string], or list[string]
+  assert toState instanceof Closure || toState instanceof Map || toState instanceof List :
+    "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}"
+
+  // if toState is a List, convert to map
+  if (toState instanceof List) {
+    // check whether toState is a list[string]
+    assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings"
+    toState = toState.collectEntries{[it, it]}
+  }
+
+  // if toState is a map, convert to closure
+  if (toState instanceof Map) {
+    // check whether toState is a map[string, string]
+    assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings"
+    assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings"
+    def toStateMap = toState.clone()
+    def requiredOutputNames = config_.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName}
+    // turn the map into a closure to be used later on
+    toState = { it ->
+      def output = it[1]
+      def state = it[2]
+      assert output instanceof Map : "Error in module '$key_': the output is not a Map"
+      assert state instanceof Map : "Error in module '$key_': the state is not a Map"
+      def extraEntries = toStateMap.collectMany{newkey, origkey ->
+        // check whether newkey corresponds to a required argument
+        if (output.containsKey(origkey)) {
+          [[newkey, output[origkey]]]
+        } else if (!requiredOutputNames.contains(origkey)) {
+          []
+        } else {
+          throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output")
+        }
+      }.collectEntries()
+      state + extraEntries
+    }
+  }
+
+  return toState
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/workflowFactory.nf'
+def _debug(workflowArgs, debugKey) {
+  if (workflowArgs.debug) {
+    view { "process '${workflowArgs.key}' $debugKey tuple: $it"  }
+  } else {
+    map { it }
+  }
+}
+
+// depends on: innerWorkflowFactory
+def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
+  def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
+  def key_ = workflowArgs["key"]
+  
+  workflow workflowInstance {
+    take: input_
+
+    main:
+    def chModified = input_
+      | checkUniqueIds([:])
+      | _debug(workflowArgs, "input")
+      | map { tuple ->
+        tuple = deepClone(tuple)
+        
+        if (workflowArgs.map) {
+          tuple = workflowArgs.map(tuple)
+        }
+        if (workflowArgs.mapId) {
+          tuple[0] = workflowArgs.mapId(tuple[0])
+        }
+        if (workflowArgs.mapData) {
+          tuple[1] = workflowArgs.mapData(tuple[1])
+        }
+        if (workflowArgs.mapPassthrough) {
+          tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2))
+        }
+
+        // check tuple
+        assert tuple instanceof List : 
+          "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        assert tuple.size() >= 2 : 
+          "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Found: tuple.size() == ${tuple.size()}"
+        
+        // check id field
+        if (tuple[0] instanceof GString) {
+          tuple[0] = tuple[0].toString()
+        }
+        assert tuple[0] instanceof CharSequence : 
+          "Error in module '${key_}': first element of tuple in channel should be a String\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Found: ${tuple[0]}"
+        
+        // match file to input file
+        if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) {
+          def inputFiles = meta.config.allArguments
+            .findAll { it.type == "file" && it.direction == "input" }
+          
+          assert inputFiles.size() == 1 : 
+              "Error in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Anonymous file inputs are only allowed when the process has exactly one file input.\n" +
+              "  Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}"
+
+          tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries()
+        }
+
+        // check data field
+        assert tuple[1] instanceof Map : 
+          "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}"
+
+        // rename keys of data field in tuple
+        if (workflowArgs.renameKeys) {
+          assert workflowArgs.renameKeys instanceof Map : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Example: renameKeys: ['new_key': 'old_key'].\n" +
+              "  Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}"
+          assert tuple[1] instanceof Map : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}"
+
+          // TODO: allow renameKeys to be a function?
+          workflowArgs.renameKeys.each { newKey, oldKey ->
+            assert newKey instanceof CharSequence : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Example: renameKeys: ['new_key': 'old_key'].\n" +
+              "  Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}"
+            assert oldKey instanceof CharSequence : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Example: renameKeys: ['new_key': 'old_key'].\n" +
+              "  Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}"
+            assert tuple[1].containsKey(oldKey) : 
+              "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" +
+              "  Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'"
+            tuple[1].put(newKey, tuple[1][oldKey])
+          }
+          tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey })
+        }
+        tuple
+      }
+
+
+    def chRun = null
+    def chPassthrough = null
+    if (workflowArgs.runIf) {
+      def runIfBranch = chModified.branch{ tup ->
+        run: workflowArgs.runIf(tup[0], tup[1])
+        passthrough: true
+      }
+      chRun = runIfBranch.run
+      chPassthrough = runIfBranch.passthrough
+    } else {
+      chRun = chModified
+      chPassthrough = Channel.empty()
+    }
+
+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
+    def chArgs = workflowArgs.fromState ? 
+      chRunFiltered | map{
+        def new_data = workflowArgs.fromState(it.take(2))
+        [it[0], new_data]
+      } :
+      chRunFiltered | map {tup -> tup.take(2)}
+
+    // fill in defaults
+    def chArgsWithDefaults = chArgs
+      | map { tuple ->
+        def id_ = tuple[0]
+        def data_ = tuple[1]
+
+        // TODO: could move fromState to here
+
+        // fetch default params from functionality
+        def defaultArgs = meta.config.allArguments
+          .findAll { it.containsKey("default") }
+          .collectEntries { [ it.plainName, it.default ] }
+
+        // fetch overrides in params
+        def paramArgs = meta.config.allArguments
+          .findAll { par ->
+            def argKey = key_ + "__" + par.plainName
+            params.containsKey(argKey)
+          }
+          .collectEntries { [ it.plainName, params[key_ + "__" + it.plainName] ] }
+        
+        // fetch overrides in data
+        def dataArgs = meta.config.allArguments
+          .findAll { data_.containsKey(it.plainName) }
+          .collectEntries { [ it.plainName, data_[it.plainName] ] }
+        
+        // combine params
+        def combinedArgs = defaultArgs + paramArgs + workflowArgs.args + dataArgs
+
+        // remove arguments with explicit null values
+        combinedArgs
+          .removeAll{_, val -> val == null || val == "viash_no_value" || val == "force_null"}
+
+        combinedArgs = _processInputValues(combinedArgs, meta.config, id_, key_)
+
+        [id_, combinedArgs] + tuple.drop(2)
+      }
+
+    // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
+    def chInitialOutput = chArgsWithDefaults
+      | _debug(workflowArgs, "processed")
+      // run workflow
+      | innerWorkflowFactory(workflowArgs)
+      // check output tuple
+      | map { id_, output_ ->
+
+        // see if output map contains metadata
+        def meta_ =
+          output_ instanceof Map && output_.containsKey("_meta") ? 
+          output_["_meta"] :
+          [:]
+        def join_id = meta_.join_id ?: id_
+        
+        // remove metadata
+        output_ = output_.findAll{k, v -> k != "_meta"}
+
+        // check value types
+        output_ = _processOutputValues(output_, meta.config, id_, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
+          output_ = output_.values()[0]
+        }
+
+        [join_id, id_, output_]
+      }
+      // | view{"chInitialOutput: ${it.take(3)}"}
+
+    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+      // input tuple format: [join_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(1).take(3))
+        tup.take(2) + [new_state] + tup.drop(4)
+      }
+
+    if (workflowArgs.auto.publish == "state") {
+      def chPublish = chNewState
+        // input tuple format: [join_id, id, new_state, ...]
+        // output tuple format: [join_id, id, new_state]
+        | map{ tup ->
+          tup.take(3)
+        }
+
+      safeJoin(chPublish, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(1).take(3)
+      }
+        | publishStatesByConfig(key: key_, config: meta.config)
+    }
+
+    // remove join_id and meta
+    chReturn = chNewState
+      | map { tup ->
+        // input tuple format: [join_id, id, new_state, ...]
+        // output tuple format: [id, new_state, ...]
+        tup.drop(1)
+      }
+      | _debug(workflowArgs, "output")
+      | concat(chPassthrough)
+
+    emit: chReturn
+  }
+
+  def wf = workflowInstance.cloneWithName(key_)
+
+  // add factory function
+  wf.metaClass.run = { runArgs ->
+    workflowFactory(runArgs, workflowArgs, meta)
+  }
+  // add config to module for later introspection
+  wf.metaClass.config = meta.config
+
+  return wf
+}
+
+nextflow.enable.dsl=2
+
+// START COMPONENT-SPECIFIC CODE
+
+// create meta object
+meta = [
+  "resources_dir": moduleDir.toRealPath().normalize(),
+  "config": processConfig(readJsonBlob('''{
+  "name" : "snpeff",
+  "version" : "main",
+  "argument_groups" : [
+    {
+      "name" : "Inputs",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--input",
+          "description" : "Input variants file.",
+          "example" : [
+            "test.vcf"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--genome_version",
+          "description" : "Reference genome version.",
+          "example" : [
+            "GRCh37.75"
+          ],
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    },
+    {
+      "name" : "Outputs",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--output",
+          "description" : "The output file.",
+          "example" : [
+            "out.vcf"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--summary",
+          "description" : "Summary file directory.",
+          "example" : [
+            "summary_dir"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--genes",
+          "description" : "Txt file directory.",
+          "example" : [
+            "genes_dir"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    },
+    {
+      "name" : "Options",
+      "arguments" : [
+        {
+          "type" : "string",
+          "name" : "--chr",
+          "description" : "Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--classic",
+          "description" : "Use old style annotations instead of Sequence Ontology and Hgvs.",
+          "direction" : "input"
+        },
+        {
+          "type" : "file",
+          "name" : "--csv_stats",
+          "description" : "Create CSV summary file.",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--download",
+          "description" : "Download reference genome if not available.",
+          "direction" : "input"
+        },
+        {
+          "type" : "string",
+          "name" : "--input_format",
+          "alternatives" : [
+            "-i"
+          ],
+          "description" : "Input format [ vcf, bed ]. Default: VCF.\nexample: \\"VCF\\"\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--file_list",
+          "description" : "Input actually contains a list of files to process.",
+          "direction" : "input"
+        },
+        {
+          "type" : "string",
+          "name" : "--output_format",
+          "alternatives" : [
+            "-o"
+          ],
+          "description" : "Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n",
+          "example" : [
+            "VCF"
+          ],
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--stats",
+          "alternatives" : [
+            "-s",
+            "--htmlStats"
+          ],
+          "description" : "Create HTML summary file.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_stats",
+          "description" : "Do not create stats (summary) file.",
+          "direction" : "input"
+        }
+      ]
+    },
+    {
+      "name" : "Results filter options",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--fi",
+          "alternatives" : [
+            "--filterInterval"
+          ],
+          "description" : "Only analyze changes that intersect with the intervals \nspecified in this file. This option can be used several times.\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_downstream",
+          "description" : "Do not show DOWNSTREAM changes",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_intergenic",
+          "description" : "Do not show INTERGENIC changes.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_intron",
+          "description" : "Do not show INTRON changes.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_upstream",
+          "description" : "Do not show UPSTREAM changes.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_utr",
+          "description" : "Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.",
+          "direction" : "input"
+        },
+        {
+          "type" : "string",
+          "name" : "--no",
+          "description" : "Do not show 'EffectType'. This option can be used several times.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    },
+    {
+      "name" : "Annotations options",
+      "arguments" : [
+        {
+          "type" : "boolean_true",
+          "name" : "--cancer",
+          "description" : "Perform 'cancer' comparisons (Somatic vs Germline).",
+          "direction" : "input"
+        },
+        {
+          "type" : "file",
+          "name" : "--cancer_samples",
+          "description" : "Two column TXT file defining 'original \\\\t derived' samples.",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--fastaprot",
+          "description" : "Create an output file containing the resulting protein sequences.\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--format_eff",
+          "description" : "Use 'EFF' field compatible with older versions (instead of 'ANN').\n",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--gene_id",
+          "description" : "Use gene ID instead of gene name (VCF output).",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--hgvs",
+          "description" : "Use HGVS annotations for amino acid sub-field.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--hgvs_old",
+          "description" : "Use old HGVS notation.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--hgvs1_letter_aa",
+          "description" : "Use one letter Amino acid codes in HGVS notation.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--hgvs_tr_id",
+          "description" : "Use transcript ID in HGVS notation.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--lof",
+          "description" : "Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "-no_hgvs",
+          "description" : "Do not add HGVS annotations.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_lof",
+          "description" : "Do not add LOF and NMD annotations.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_shift_hgvs",
+          "description" : "Do not shift variants according to HGVS notation (most 3prime end).\n",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--oicr",
+          "description" : "Add OICR tag in VCF file.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--sequence_ontology",
+          "description" : "Use Sequence Ontology terms.",
+          "direction" : "input"
+        }
+      ]
+    },
+    {
+      "name" : "Generic options",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--config",
+          "alternatives" : [
+            "-c"
+          ],
+          "description" : "Specify config file",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--config_option",
+          "description" : "Override a config file option (name=value).",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--debug",
+          "alternatives" : [
+            "-d"
+          ],
+          "description" : "Debug mode (very verbose).",
+          "direction" : "input"
+        },
+        {
+          "type" : "file",
+          "name" : "--data_dir",
+          "description" : "Override data_dir parameter from config file.",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_download",
+          "description" : "Do not download a SnpEff database, if not available locally.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_log",
+          "description" : "Do not report usage statistics to server.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--quiet",
+          "alternatives" : [
+            "-q"
+          ],
+          "description" : "Quiet mode (do not show any messages or errors)",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--verbose",
+          "alternatives" : [
+            "-v"
+          ],
+          "description" : "Verbose mode.",
+          "direction" : "input"
+        }
+      ]
+    },
+    {
+      "name" : "Database options",
+      "arguments" : [
+        {
+          "type" : "boolean_true",
+          "name" : "--canon",
+          "description" : "Only use canonical transcripts.",
+          "direction" : "input"
+        },
+        {
+          "type" : "file",
+          "name" : "--canon_list",
+          "description" : "Only use canonical transcripts, replace some transcripts using the 'gene_id         \ntranscript_id' entries in <file>.\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--tag",
+          "description" : "Only use transcript having a tag 'tagName'. This option can be used multiple times.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_tag",
+          "description" : "Filter out transcript having a tag 'tagName'. This option can be used multiple times.\n",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--interaction",
+          "description" : "Annotate using interactions (requires interaction database).",
+          "direction" : "input"
+        },
+        {
+          "type" : "file",
+          "name" : "--interval",
+          "description" : "Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).\n",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--max_tsl",
+          "description" : "Only use transcripts having Transcript Support Level lower than <TSL_number>.",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--motif",
+          "description" : "Annotate using motifs (requires Motif database).",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--nextprot",
+          "description" : "Annotate using NextProt (requires NextProt database).",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_genome",
+          "description" : "Do not load any genomic database (e.g. annotate using custom files).",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_expand_iub",
+          "description" : "Disable IUB code expansion in input variants.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_interaction",
+          "description" : "Disable inteaction annotations.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_motif",
+          "description" : "Disable motif annotations.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--no_nextprot",
+          "description" : "Disable NextProt annotations.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--only_reg",
+          "description" : "Only use regulation tracks.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--only_protein",
+          "description" : "Only use protein coding transcripts.",
+          "direction" : "input"
+        },
+        {
+          "type" : "file",
+          "name" : "--only_tr",
+          "description" : "Only use the transcripts in this file. Format: One transcript ID per line.\n",
+          "example" : [
+            "file.txt"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--reg",
+          "description" : "Regulation track to use (this option can be used add several times).",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--ss",
+          "alternatives" : [
+            "--spliceSiteSize"
+          ],
+          "description" : "Set size for splice sites (donor and acceptor) in bases. Default: 2.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--splice_region_exon_size",
+          "description" : "Set size for splice site region within exons. Default: 3 bases.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--splice_region_intron_min",
+          "description" : "Set minimum number of bases for splice site region within intron. Default: 3 bases.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--splice_region_intron_max",
+          "description" : "Set maximum number of bases for splice site region within intron. Default: 8 bases.\n",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--strict",
+          "description" : "Only use 'validated' transcripts (i.e. sequence has been checked).",
+          "direction" : "input"
+        },
+        {
+          "type" : "integer",
+          "name" : "--ud",
+          "alternatives" : [
+            "--upDownStreamLen"
+          ],
+          "description" : "Set upstream downstream interval length (in bases).",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    }
+  ],
+  "resources" : [
+    {
+      "type" : "bash_script",
+      "path" : "script.sh",
+      "is_executable" : true
+    }
+  ],
+  "description" : "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n",
+  "test_resources" : [
+    {
+      "type" : "bash_script",
+      "path" : "test.sh",
+      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "test_data"
+    }
+  ],
+  "status" : "enabled",
+  "requirements" : {
+    "commands" : [
+      "ps"
+    ]
+  },
+  "keywords" : [
+    "annotation",
+    "effect prediction",
+    "snp",
+    "variant",
+    "vcf"
+  ],
+  "license" : "MIT",
+  "references" : {
+    "doi" : [
+      "10.3389/fgene.2012.00035"
+    ]
+  },
+  "links" : {
+    "repository" : "https://github.com/pcingola/SnpEff",
+    "homepage" : "https://pcingola.github.io/SnpEff/",
+    "documentation" : "https://pcingola.github.io/SnpEff/"
+  },
+  "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" : "quay.io/staphb/snpeff:5.2a",
+      "target_registry" : "images.viash-hub.com",
+      "target_tag" : "main",
+      "namespace_separator" : "/",
+      "setup" : [
+        {
+          "type" : "docker",
+          "run" : [
+            "version=$(snpEff -version) && \\\\\nversion_trimmed=$(echo \\"$version\\" | awk '{print $1, $2}') && \\\\\necho \\"$version_trimmed\\" > /var/software_versions.txt\n"
+          ]
+        }
+      ]
+    },
+    {
+      "type" : "native",
+      "id" : "native"
+    }
+  ],
+  "build_info" : {
+    "config" : "/workdir/root/repo/src/snpeff/config.vsh.yaml",
+    "runner" : "nextflow",
+    "engine" : "docker|native",
+    "output" : "target/nextflow/snpeff",
+    "viash_version" : "0.9.0",
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
+  },
+  "package_config" : {
+    "name" : "biobox",
+    "version" : "main",
+    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
+    "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"
+    }
+  }
+}'''))
+]
+
+// resolve dependencies dependencies (if any)
+
+
+// inner workflow
+// inner workflow hook
+def innerWorkflowFactory(args) {
+  def rawScript = '''set -e
+tempscript=".viash_script.sh"
+cat > "$tempscript" << VIASHMAIN
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+# The following code has been auto-generated by Viash.
+$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
+$( if [ ! -z ${VIASH_PAR_GENOME_VERSION+x} ]; then echo "${VIASH_PAR_GENOME_VERSION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_genome_version='&'#" ; else echo "# par_genome_version="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
+$( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
+$( if [ ! -z ${VIASH_PAR_GENES+x} ]; then echo "${VIASH_PAR_GENES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_genes='&'#" ; else echo "# par_genes="; fi )
+$( if [ ! -z ${VIASH_PAR_CHR+x} ]; then echo "${VIASH_PAR_CHR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_chr='&'#" ; else echo "# par_chr="; fi )
+$( if [ ! -z ${VIASH_PAR_CLASSIC+x} ]; then echo "${VIASH_PAR_CLASSIC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_classic='&'#" ; else echo "# par_classic="; fi )
+$( if [ ! -z ${VIASH_PAR_CSV_STATS+x} ]; then echo "${VIASH_PAR_CSV_STATS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_csv_stats='&'#" ; else echo "# par_csv_stats="; fi )
+$( if [ ! -z ${VIASH_PAR_DOWNLOAD+x} ]; then echo "${VIASH_PAR_DOWNLOAD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_download='&'#" ; else echo "# par_download="; fi )
+$( if [ ! -z ${VIASH_PAR_INPUT_FORMAT+x} ]; then echo "${VIASH_PAR_INPUT_FORMAT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_format='&'#" ; else echo "# par_input_format="; fi )
+$( if [ ! -z ${VIASH_PAR_FILE_LIST+x} ]; then echo "${VIASH_PAR_FILE_LIST}" | sed "s#'#'\\"'\\"'#g;s#.*#par_file_list='&'#" ; else echo "# par_file_list="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT_FORMAT+x} ]; then echo "${VIASH_PAR_OUTPUT_FORMAT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_format='&'#" ; else echo "# par_output_format="; fi )
+$( if [ ! -z ${VIASH_PAR_STATS+x} ]; then echo "${VIASH_PAR_STATS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_stats='&'#" ; else echo "# par_stats="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_STATS+x} ]; then echo "${VIASH_PAR_NO_STATS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_stats='&'#" ; else echo "# par_no_stats="; fi )
+$( if [ ! -z ${VIASH_PAR_FI+x} ]; then echo "${VIASH_PAR_FI}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fi='&'#" ; else echo "# par_fi="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_DOWNSTREAM+x} ]; then echo "${VIASH_PAR_NO_DOWNSTREAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_downstream='&'#" ; else echo "# par_no_downstream="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_INTERGENIC+x} ]; then echo "${VIASH_PAR_NO_INTERGENIC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_intergenic='&'#" ; else echo "# par_no_intergenic="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_INTRON+x} ]; then echo "${VIASH_PAR_NO_INTRON}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_intron='&'#" ; else echo "# par_no_intron="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_UPSTREAM+x} ]; then echo "${VIASH_PAR_NO_UPSTREAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_upstream='&'#" ; else echo "# par_no_upstream="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_UTR+x} ]; then echo "${VIASH_PAR_NO_UTR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_utr='&'#" ; else echo "# par_no_utr="; fi )
+$( if [ ! -z ${VIASH_PAR_NO+x} ]; then echo "${VIASH_PAR_NO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no='&'#" ; else echo "# par_no="; fi )
+$( if [ ! -z ${VIASH_PAR_CANCER+x} ]; then echo "${VIASH_PAR_CANCER}" | sed "s#'#'\\"'\\"'#g;s#.*#par_cancer='&'#" ; else echo "# par_cancer="; fi )
+$( if [ ! -z ${VIASH_PAR_CANCER_SAMPLES+x} ]; then echo "${VIASH_PAR_CANCER_SAMPLES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_cancer_samples='&'#" ; else echo "# par_cancer_samples="; fi )
+$( if [ ! -z ${VIASH_PAR_FASTAPROT+x} ]; then echo "${VIASH_PAR_FASTAPROT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fastaprot='&'#" ; else echo "# par_fastaprot="; fi )
+$( if [ ! -z ${VIASH_PAR_FORMAT_EFF+x} ]; then echo "${VIASH_PAR_FORMAT_EFF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_format_eff='&'#" ; else echo "# par_format_eff="; fi )
+$( if [ ! -z ${VIASH_PAR_GENE_ID+x} ]; then echo "${VIASH_PAR_GENE_ID}" | sed "s#'#'\\"'\\"'#g;s#.*#par_gene_id='&'#" ; else echo "# par_gene_id="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS+x} ]; then echo "${VIASH_PAR_HGVS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_hgvs='&'#" ; else echo "# par_hgvs="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS_OLD+x} ]; then echo "${VIASH_PAR_HGVS_OLD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_hgvs_old='&'#" ; else echo "# par_hgvs_old="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS1_LETTER_AA+x} ]; then echo "${VIASH_PAR_HGVS1_LETTER_AA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_hgvs1_letter_aa='&'#" ; else echo "# par_hgvs1_letter_aa="; fi )
+$( if [ ! -z ${VIASH_PAR_HGVS_TR_ID+x} ]; then echo "${VIASH_PAR_HGVS_TR_ID}" | sed "s#'#'\\"'\\"'#g;s#.*#par_hgvs_tr_id='&'#" ; else echo "# par_hgvs_tr_id="; fi )
+$( if [ ! -z ${VIASH_PAR_LOF+x} ]; then echo "${VIASH_PAR_LOF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_lof='&'#" ; else echo "# par_lof="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_HGVS+x} ]; then echo "${VIASH_PAR_NO_HGVS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_hgvs='&'#" ; else echo "# par_no_hgvs="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_LOF+x} ]; then echo "${VIASH_PAR_NO_LOF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_lof='&'#" ; else echo "# par_no_lof="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_SHIFT_HGVS+x} ]; then echo "${VIASH_PAR_NO_SHIFT_HGVS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_shift_hgvs='&'#" ; else echo "# par_no_shift_hgvs="; fi )
+$( if [ ! -z ${VIASH_PAR_OICR+x} ]; then echo "${VIASH_PAR_OICR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_oicr='&'#" ; else echo "# par_oicr="; fi )
+$( if [ ! -z ${VIASH_PAR_SEQUENCE_ONTOLOGY+x} ]; then echo "${VIASH_PAR_SEQUENCE_ONTOLOGY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_sequence_ontology='&'#" ; else echo "# par_sequence_ontology="; fi )
+$( if [ ! -z ${VIASH_PAR_CONFIG+x} ]; then echo "${VIASH_PAR_CONFIG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_config='&'#" ; else echo "# par_config="; fi )
+$( if [ ! -z ${VIASH_PAR_CONFIG_OPTION+x} ]; then echo "${VIASH_PAR_CONFIG_OPTION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_config_option='&'#" ; else echo "# par_config_option="; fi )
+$( if [ ! -z ${VIASH_PAR_DEBUG+x} ]; then echo "${VIASH_PAR_DEBUG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_debug='&'#" ; else echo "# par_debug="; fi )
+$( if [ ! -z ${VIASH_PAR_DATA_DIR+x} ]; then echo "${VIASH_PAR_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_data_dir='&'#" ; else echo "# par_data_dir="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_DOWNLOAD+x} ]; then echo "${VIASH_PAR_NO_DOWNLOAD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_download='&'#" ; else echo "# par_no_download="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_LOG+x} ]; then echo "${VIASH_PAR_NO_LOG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_log='&'#" ; else echo "# par_no_log="; fi )
+$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\\"'\\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
+$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
+$( if [ ! -z ${VIASH_PAR_CANON+x} ]; then echo "${VIASH_PAR_CANON}" | sed "s#'#'\\"'\\"'#g;s#.*#par_canon='&'#" ; else echo "# par_canon="; fi )
+$( if [ ! -z ${VIASH_PAR_CANON_LIST+x} ]; then echo "${VIASH_PAR_CANON_LIST}" | sed "s#'#'\\"'\\"'#g;s#.*#par_canon_list='&'#" ; else echo "# par_canon_list="; fi )
+$( if [ ! -z ${VIASH_PAR_TAG+x} ]; then echo "${VIASH_PAR_TAG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_tag='&'#" ; else echo "# par_tag="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_TAG+x} ]; then echo "${VIASH_PAR_NO_TAG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_tag='&'#" ; else echo "# par_no_tag="; fi )
+$( if [ ! -z ${VIASH_PAR_INTERACTION+x} ]; then echo "${VIASH_PAR_INTERACTION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_interaction='&'#" ; else echo "# par_interaction="; fi )
+$( if [ ! -z ${VIASH_PAR_INTERVAL+x} ]; then echo "${VIASH_PAR_INTERVAL}" | sed "s#'#'\\"'\\"'#g;s#.*#par_interval='&'#" ; else echo "# par_interval="; fi )
+$( if [ ! -z ${VIASH_PAR_MAX_TSL+x} ]; then echo "${VIASH_PAR_MAX_TSL}" | sed "s#'#'\\"'\\"'#g;s#.*#par_max_tsl='&'#" ; else echo "# par_max_tsl="; fi )
+$( if [ ! -z ${VIASH_PAR_MOTIF+x} ]; then echo "${VIASH_PAR_MOTIF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_motif='&'#" ; else echo "# par_motif="; fi )
+$( if [ ! -z ${VIASH_PAR_NEXTPROT+x} ]; then echo "${VIASH_PAR_NEXTPROT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nextprot='&'#" ; else echo "# par_nextprot="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_GENOME+x} ]; then echo "${VIASH_PAR_NO_GENOME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_genome='&'#" ; else echo "# par_no_genome="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_EXPAND_IUB+x} ]; then echo "${VIASH_PAR_NO_EXPAND_IUB}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_expand_iub='&'#" ; else echo "# par_no_expand_iub="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_INTERACTION+x} ]; then echo "${VIASH_PAR_NO_INTERACTION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_interaction='&'#" ; else echo "# par_no_interaction="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_MOTIF+x} ]; then echo "${VIASH_PAR_NO_MOTIF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_motif='&'#" ; else echo "# par_no_motif="; fi )
+$( if [ ! -z ${VIASH_PAR_NO_NEXTPROT+x} ]; then echo "${VIASH_PAR_NO_NEXTPROT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_nextprot='&'#" ; else echo "# par_no_nextprot="; fi )
+$( if [ ! -z ${VIASH_PAR_ONLY_REG+x} ]; then echo "${VIASH_PAR_ONLY_REG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_only_reg='&'#" ; else echo "# par_only_reg="; fi )
+$( if [ ! -z ${VIASH_PAR_ONLY_PROTEIN+x} ]; then echo "${VIASH_PAR_ONLY_PROTEIN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_only_protein='&'#" ; else echo "# par_only_protein="; fi )
+$( if [ ! -z ${VIASH_PAR_ONLY_TR+x} ]; then echo "${VIASH_PAR_ONLY_TR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_only_tr='&'#" ; else echo "# par_only_tr="; fi )
+$( if [ ! -z ${VIASH_PAR_REG+x} ]; then echo "${VIASH_PAR_REG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_reg='&'#" ; else echo "# par_reg="; fi )
+$( if [ ! -z ${VIASH_PAR_SS+x} ]; then echo "${VIASH_PAR_SS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ss='&'#" ; else echo "# par_ss="; fi )
+$( if [ ! -z ${VIASH_PAR_SPLICE_REGION_EXON_SIZE+x} ]; then echo "${VIASH_PAR_SPLICE_REGION_EXON_SIZE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_splice_region_exon_size='&'#" ; else echo "# par_splice_region_exon_size="; fi )
+$( if [ ! -z ${VIASH_PAR_SPLICE_REGION_INTRON_MIN+x} ]; then echo "${VIASH_PAR_SPLICE_REGION_INTRON_MIN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_splice_region_intron_min='&'#" ; else echo "# par_splice_region_intron_min="; fi )
+$( if [ ! -z ${VIASH_PAR_SPLICE_REGION_INTRON_MAX+x} ]; then echo "${VIASH_PAR_SPLICE_REGION_INTRON_MAX}" | sed "s#'#'\\"'\\"'#g;s#.*#par_splice_region_intron_max='&'#" ; else echo "# par_splice_region_intron_max="; fi )
+$( if [ ! -z ${VIASH_PAR_STRICT+x} ]; then echo "${VIASH_PAR_STRICT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_strict='&'#" ; else echo "# par_strict="; fi )
+$( if [ ! -z ${VIASH_PAR_UD+x} ]; then echo "${VIASH_PAR_UD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ud='&'#" ; else echo "# par_ud="; fi )
+$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
+$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
+$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
+$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
+$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
+$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
+$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
+
+## VIASH END
+
+# Unset flags if 'false'
+unset_if_false=(
+    par_classic
+    par_download
+    par_file_list
+    par_stats
+    par_cancer
+    par_format_eff
+    par_gene_id
+    par_hgvs
+    par_hgvs_old
+    par_hgvs1_letter_aa
+    par_hgvs_tr_id
+    par_lof
+    par_oicr
+    par_sequence_ontology
+    par_debug
+    par_quiet
+    par_verbose
+    par_canon
+    par_interaction
+    par_motif
+    par_nextprot
+    par_only_reg
+    par_only_protein
+    par_strict
+    par_no_stats
+    par_no_downstream
+    par_no_intergenic
+    par_no_intron
+    par_no_upstream
+    par_no_utr
+    par_no_hgvs
+    par_no_lof
+    par_no_shift_hgvs
+    par_no_download
+    par_no_log
+    par_no_tag
+    par_no_genome
+    par_no_expand_iub
+    par_no_interaction
+    par_no_motif
+    par_no_nextprot
+)
+for par in \\${unset_if_false[@]}; do
+    test_val="\\${!par}" # contains the value of the 'par'
+    [[ "\\$test_val" == "false" ]] && unset \\$par
+done
+
+
+# Run SnpEff
+snpEff \\\\
+    \\${par_chr:+-chr "\\$par_chr"} \\\\
+    \\${par_classic:+-classic} \\\\
+    \\${par_csv_stats:+-csvStats "\\$par_csv_stats"} \\\\
+    \\${par_download:+-download} \\\\
+    \\${par_input_format:+-i "\\$par_input_format"} \\\\
+    \\${par_file_list:+-fileList} \\\\
+    \\${par_output_format:+-o "\\$par_output_format"} \\\\
+    \\${par_stats:+-stats} \\\\
+    \\${par_no_stats:+-noStats} \\\\
+    \\${par_fi:+-fi "\\$par_fi"} \\\\
+    \\${par_no_downstream:+-no-downstream} \\\\
+    \\${par_no_intergenic:+-no-intergenic} \\\\
+    \\${par_no_intron:+-no-intron} \\\\
+    \\${par_no_upstream:+-no-upstream} \\\\
+    \\${par_no_utr:+-no-utr} \\\\
+    \\${par_no:+-no "\\$par_no"} \\\\
+    \\${par_cancer:+-cancer} \\\\
+    \\${par_cancer_samples:+-cancerSamples "\\$par_cancer_samples]"} \\\\
+    \\${par_fastaprot:+-fastaProt "\\$par_fastaprot]"} \\\\
+    \\${par_format_eff:+-formatEff} \\\\
+    \\${par_gene_id:+-geneId} \\\\
+    \\${par_hgvs:+-hgvs} \\\\
+    \\${par_hgvs_old:+-hgvsOld} \\\\
+    \\${par_hgvs1_letter_aa:+-hgvs1LetterAa} \\\\
+    \\${par_hgvs_tr_id:+-hgvsTrId} \\\\
+    \\${par_lof:+-lof} \\\\
+    \\${par_no_hgvs:+-noHgvs} \\\\
+    \\${par_no_lof:+-noLof} \\\\
+    \\${par_no_shift_hgvs:+-noShiftHgvs} \\\\
+    \\${par_oicr:+-oicr} \\\\
+    \\${par_sequence_ontology:+-sequenceOntology} \\\\
+    \\${par_config:+-config "\\$par_config"} \\\\
+    \\${par_config_option:+-configOption "\\$par_config_option"} \\\\
+    \\${par_debug:+-debug} \\\\
+    \\${par_data_dir:+-dataDir "\\$par_data_dir"} \\\\
+    \\${par_no_download:+-nodownload} \\\\
+    \\${par_no_log:+-noLog} \\\\
+    \\${par_quiet:+-quiet} \\\\
+    \\${par_verbose:+-verbose} \\\\
+    \\${par_canon:+-canon} \\\\
+    \\${par_canon_list:+-canonList "\\$par_canon_list"} \\\\
+    \\${par_tag:+-tag "\\$par_tag"} \\\\
+    \\${par_no_tag:+-notag} \\\\
+    \\${par_interaction:+-interaction} \\\\
+    \\${par_interval:+-interval "\\$par_interval"} \\\\
+    \\${par_max_tsl:+-maxTSL "\\$par_max_tsl"} \\\\
+    \\${par_motif:+-motif} \\\\
+    \\${par_nextprot:+-nextProt} \\\\
+    \\${par_no_genome:+-noGenome} \\\\
+    \\${par_no_expand_iub:+-noExpandIUB} \\\\
+    \\${par_no_interaction:+-noInteraction} \\\\
+    \\${par_no_motif:+-noMotif} \\\\
+    \\${par_no_nextprot:+-noNextProt} \\\\
+    \\${par_only_reg:+-onlyReg} \\\\
+    \\${par_only_protein:+-onlyProtein} \\\\
+    \\${par_only_tr:+-onlyTr "\\$par_onlyTr"} \\\\
+    \\${par_reg:+-reg "\\$par_reg"} \\\\
+    \\${par_ss:+-ss "\\$par_ss"} \\\\
+    \\${par_splice_region_exon_size:+-spliceRegionExonSize "\\$par_splice_region_exon_size"} \\\\
+    \\${par_splice_region_intron_min:+-spliceRegionIntronMin "\\$par_splice_region_intron_min"} \\\\
+    \\${par_splice_region_intron_max:+-spliceRegionIntronMax "\\$par_splice_region_intron_max"} \\\\
+    \\${par_strict:+-strict} \\\\
+    \\${par_ud:+-ud "\\$par_ud"} \\\\
+    "\\$par_genome_version" \\\\
+    "\\$par_input" \\\\
+    > "\\$par_output"
+
+# Path of the output file (par_output)
+absolute_path=\\$(realpath "\\$par_output")
+directory_path=\\$(dirname "\\$absolute_path")
+
+# Move the automatically generated outputs to their locations
+if [ -z "\\$par_no_stats" ]; then
+    if [ ! -z "\\$par_summary" ]; then
+        mv -n snpEff_summary.html "\\$par_summary"
+    else
+        mv -n snpEff_summary.html "\\$directory_path"
+    fi
+fi 
+
+if [ -z "\\$par_no_stats" ]; then
+    if [ ! -z "\\$par_genes" ]; then
+        mv -n snpEff_genes.txt "\\$par_genes"
+    else
+        mv -n snpEff_genes.txt "\\$directory_path"
+    fi
+fi
+
+exit 0
+VIASHMAIN
+bash "$tempscript"
+'''
+  
+  return vdsl3WorkflowFactory(args, meta, rawScript)
+}
+
+
+
+/**
+  * Generate a workflow for VDSL3 modules.
+  * 
+  * This function is called by the workflowFactory() function.
+  * 
+  * Input channel: [id, input_map]
+  * Output channel: [id, output_map]
+  * 
+  * Internally, this workflow will convert the input channel
+  * to a format which the Nextflow module will be able to handle.
+  */
+def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
+  def key = args["key"]
+  def processObj = null
+
+  workflow processWf {
+    take: input_
+    main:
+
+    if (processObj == null) {
+      processObj = _vdsl3ProcessFactory(args, meta, rawScript)
+    }
+    
+    output_ = input_
+      | map { tuple ->
+        def id = tuple[0]
+        def data_ = tuple[1]
+
+        if (workflow.stubRun) {
+          // add id if missing
+          data_ = [id: 'stub'] + data_
+        }
+
+        // process input files separately
+        def inputPaths = meta.config.allArguments
+          .findAll { it.type == "file" && it.direction == "input" }
+          .collect { par ->
+            def val = data_.containsKey(par.plainName) ? data_[par.plainName] : []
+            def inputFiles = []
+            if (val == null) {
+              inputFiles = []
+            } else if (val instanceof List) {
+              inputFiles = val
+            } else if (val instanceof Path) {
+              inputFiles = [ val ]
+            } else {
+              inputFiles = []
+            }
+            if (!workflow.stubRun) {
+              // throw error when an input file doesn't exist
+              inputFiles.each{ file -> 
+                assert file.exists() :
+                  "Error in module '${key}' id '${id}' argument '${par.plainName}'.\n" +
+                  "  Required input file does not exist.\n" +
+                  "  Path: '$file'.\n" +
+                  "  Expected input file to exist"
+              }
+            }
+            inputFiles 
+          } 
+
+        // remove input files
+        def argsExclInputFiles = meta.config.allArguments
+          .findAll { (it.type != "file" || it.direction != "input") && data_.containsKey(it.plainName) }
+          .collectEntries { par ->
+            def parName = par.plainName
+            def val = data_[parName]
+            if (par.multiple && val instanceof Collection) {
+              val = val.join(par.multiple_sep)
+            }
+            if (par.direction == "output" && par.type == "file") {
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
+            }
+            [parName, val]
+          }
+
+        [ id ] + inputPaths + [ argsExclInputFiles, meta.resources_dir ]
+      }
+      | processObj
+      | map { output ->
+        def outputFiles = meta.config.allArguments
+          .findAll { it.type == "file" && it.direction == "output" }
+          .indexed()
+          .collectEntries{ index, par ->
+            def out = output[index + 1]
+            // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678)
+            if (!out instanceof List || out.size() <= 1) {
+              if (par.multiple) {
+                out = []
+              } else {
+                assert !par.required :
+                    "Error in module '${key}' id '${output[0]}' argument '${par.plainName}'.\n" +
+                    "  Required output file is missing"
+                out = null
+              }
+            } else if (out.size() == 2 && !par.multiple) {
+              out = out[1]
+            } else {
+              out = out.drop(1)
+            }
+            [ par.plainName, out ]
+          }
+        
+        // drop null outputs
+        outputFiles.removeAll{it.value == null}
+
+        [ output[0], outputFiles ]
+      }
+    emit: output_
+  }
+
+  return processWf
+}
+
+// depends on: session?
+def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
+  // autodetect process key
+  def wfKey = workflowArgs["key"]
+  def procKeyPrefix = "${wfKey}_process"
+  def scriptMeta = nextflow.script.ScriptMeta.current()
+  def existing = scriptMeta.getProcessNames().findAll{it.startsWith(procKeyPrefix)}
+  def numbers = existing.collect{it.replace(procKeyPrefix, "0").toInteger()}
+  def newNumber = (numbers + [-1]).max() + 1
+
+  def procKey = newNumber == 0 ? procKeyPrefix : "$procKeyPrefix$newNumber"
+
+  if (newNumber > 0) {
+    log.warn "Key for module '${wfKey}' is duplicated.\n",
+      "If you run a component multiple times in the same workflow,\n" +
+      "it's recommended you set a unique key for every call,\n" +
+      "for example: ${wfKey}.run(key: \"foo\")."
+  }
+
+  // subset directives and convert to list of tuples
+  def drctv = workflowArgs.directives
+
+  // TODO: unit test the two commands below
+  // convert publish array into tags
+  def valueToStr = { val ->
+    // ignore closures
+    if (val instanceof CharSequence) {
+      if (!val.matches('^[{].*[}]$')) {
+        '"' + val + '"'
+      } else {
+        val
+      }
+    } else if (val instanceof List) {
+      "[" + val.collect{valueToStr(it)}.join(", ") + "]"
+    } else if (val instanceof Map) {
+      "[" + val.collect{k, v -> k + ": " + valueToStr(v)}.join(", ") + "]"
+    } else {
+      val.inspect()
+    }
+  }
+
+  // multiple entries allowed: label, publishdir
+  def drctvStrs = drctv.collect { key, value ->
+    if (key in ["label", "publishDir"]) {
+      value.collect{ val ->
+        if (val instanceof Map) {
+          "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ")
+        } else if (val == null) {
+          ""
+        } else {
+          "\n$key " + valueToStr(val)
+        }
+      }.join()
+    } else if (value instanceof Map) {
+      "\n$key " + value.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ")
+    } else {
+      "\n$key " + valueToStr(value)
+    }
+  }.join()
+
+  def inputPaths = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "input" }
+    .collect { ', path(viash_par_' + it.plainName + ', stageAs: "_viash_par/' + it.plainName + '_?/*")' }
+    .join()
+
+  def outputPaths = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "output" }
+    .collect { par ->
+      // insert dummy into every output (see nextflow-io/nextflow#2678)
+      if (!par.multiple) {
+        ', path{[".exitcode", args.' + par.plainName + ']}'
+      } else {
+        ', path{[".exitcode"] + args.' + par.plainName + '}'
+      }
+    }
+    .join()
+
+  // TODO: move this functionality somewhere else?
+  if (workflowArgs.auto.transcript) {
+    outputPaths = outputPaths + ', path{[".exitcode", ".command*"]}'
+  } else {
+    outputPaths = outputPaths + ', path{[".exitcode"]}'
+  }
+
+  // create dirs for output files (based on BashWrapper.createParentFiles)
+  def createParentStr = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
+    .collect { par -> 
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
+    }
+    .join("\n")
+
+  // construct inputFileExports
+  def inputFileExports = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
+    .collect { par ->
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
+    }
+
+  // NOTE: if using docker, use /tmp instead of tmpDir!
+  def tmpDir = java.nio.file.Paths.get(
+    System.getenv('NXF_TEMP') ?: 
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('VIASH_TMPDIR') ?: 
+    System.getenv('VIASH_TEMPDIR') ?: 
+    System.getenv('VIASH_TMP') ?: 
+    System.getenv('TEMP') ?: 
+    System.getenv('TMPDIR') ?: 
+    System.getenv('TEMPDIR') ?:
+    System.getenv('TMP') ?: 
+    '/tmp'
+  ).toAbsolutePath()
+
+  // construct stub
+  def stub = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "output" }
+    .collect { par -> 
+      "\${ args.containsKey(\"${par.plainName}\") ? \"touch2 \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"].replace(\"_*\", \"_0\") : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+    }
+    .join("\n")
+
+  // escape script
+  def escapedScript = rawScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"')
+
+  // publishdir assert
+  def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? 
+    """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n  Example: --publish_dir './output/'" """ :
+    ""
+
+  // generate process string
+  def procStr = 
+  """nextflow.enable.dsl=2
+  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
+  |process $procKey {$drctvStrs
+  |input:
+  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
+  |output:
+  |  tuple val("\$id")$outputPaths, optional: true
+  |stub:
+  |\"\"\"
+  |touch2() { mkdir -p "\\\$(dirname "\\\$1")" && touch "\\\$1" ; }
+  |$stub
+  |\"\"\"
+  |script:$assertStr
+  |def parInject = args
+  |  .findAll{key, value -> value != null}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
+  |  .join("\\n")
+  |\"\"\"
+  |# meta exports
+  |export VIASH_META_RESOURCES_DIR="\${resourcesDir}"
+  |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}"
+  |export VIASH_META_NAME="${meta.config.name}"
+  |# export VIASH_META_EXECUTABLE="\\\$VIASH_META_RESOURCES_DIR/\\\$VIASH_META_NAME"
+  |export VIASH_META_CONFIG="\\\$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
+  |\${task.cpus ? "export VIASH_META_CPUS=\$task.cpus" : "" }
+  |\${task.memory?.bytes != null ? "export VIASH_META_MEMORY_B=\$task.memory.bytes" : "" }
+  |if [ ! -z \\\${VIASH_META_MEMORY_B+x} ]; then
+  |  export VIASH_META_MEMORY_KB=\\\$(( (\\\$VIASH_META_MEMORY_B+999) / 1000 ))
+  |  export VIASH_META_MEMORY_MB=\\\$(( (\\\$VIASH_META_MEMORY_KB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_GB=\\\$(( (\\\$VIASH_META_MEMORY_MB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_TB=\\\$(( (\\\$VIASH_META_MEMORY_GB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_PB=\\\$(( (\\\$VIASH_META_MEMORY_TB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_KIB=\\\$(( (\\\$VIASH_META_MEMORY_B+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_MIB=\\\$(( (\\\$VIASH_META_MEMORY_KIB+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_GIB=\\\$(( (\\\$VIASH_META_MEMORY_MIB+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_TIB=\\\$(( (\\\$VIASH_META_MEMORY_GIB+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_PIB=\\\$(( (\\\$VIASH_META_MEMORY_TIB+1023) / 1024 ))
+  |fi
+  |
+  |# meta synonyms
+  |export VIASH_TEMP="\\\$VIASH_META_TEMP_DIR"
+  |export TEMP_DIR="\\\$VIASH_META_TEMP_DIR"
+  |
+  |# create output dirs if need be
+  |function mkdir_parent {
+  |  for file in "\\\$@"; do 
+  |    mkdir -p "\\\$(dirname "\\\$file")"
+  |  done
+  |}
+  |$createParentStr
+  |
+  |# argument exports${inputFileExports.join()}
+  |\$parInject
+  |
+  |# process script
+  |${escapedScript}
+  |\"\"\"
+  |}
+  |""".stripMargin()
+
+  // TODO: print on debug
+  // if (workflowArgs.debug == true) {
+  //   println("######################\n$procStr\n######################")
+  // }
+
+  // write process to temp file
+  def tempFile = java.nio.file.Files.createTempFile("viash-process-${procKey}-", ".nf")
+  addShutdownHook { java.nio.file.Files.deleteIfExists(tempFile) }
+  tempFile.text = procStr
+
+  // create process from temp file
+  def binding = new nextflow.script.ScriptBinding([:])
+  def session = nextflow.Nextflow.getSession()
+  def parser = new nextflow.script.ScriptParser(session)
+    .setModule(true)
+    .setBinding(binding)
+  def moduleScript = parser.runScript(tempFile)
+    .getScript()
+
+  // register module in meta
+  def module = new nextflow.script.IncludeDef.Module(name: procKey)
+  scriptMeta.addModule(moduleScript, module.name, module.alias)
+
+  // retrieve and return process from meta
+  return scriptMeta.getProcess(procKey)
+}
+
+// defaults
+meta["defaults"] = [
+  // key to be used to trace the process and determine output names
+  key: null,
+
+  // fixed arguments to be passed to script
+  args: [:],
+
+  // default directives
+  directives: readJsonBlob('''{
+  "container" : {
+    "registry" : "images.viash-hub.com",
+    "image" : "vsh/biobox/snpeff",
+    "tag" : "main"
+  },
+  "tag" : "$id"
+}'''),
+
+  // auto settings
+  auto: readJsonBlob('''{
+  "simplifyInput" : true,
+  "simplifyOutput" : false,
+  "transcript" : false,
+  "publish" : false
+}'''),
+
+  // Apply a map over the incoming tuple
+  // Example: `{ tup -> [ tup[0], [input: tup[1].output] ] + tup.drop(2) }`
+  map: null,
+
+  // Apply a map over the ID element of a tuple (i.e. the first element)
+  // Example: `{ id -> id + "_foo" }`
+  mapId: null,
+
+  // Apply a map over the data element of a tuple (i.e. the second element)
+  // Example: `{ data -> [ input: data.output ] }`
+  mapData: null,
+
+  // Apply a map over the passthrough elements of a tuple (i.e. the tuple excl. the first two elements)
+  // Example: `{ pt -> pt.drop(1) }`
+  mapPassthrough: null,
+
+  // Filter the channel
+  // Example: `{ tup -> tup[0] == "foo" }`
+  filter: null,
+
+  // Choose whether or not to run the component on the tuple if the condition is true.
+  // Otherwise, the tuple will be passed through.
+  // Example: `{ tup -> tup[0] != "skip_this" }`
+  runIf: null,
+
+  // Rename keys in the data field of the tuple (i.e. the second element)
+  // Will likely be deprecated in favour of `fromState`.
+  // Example: `[ "new_key": "old_key" ]`
+  renameKeys: null,
+
+  // Fetch data from the state and pass it to the module without altering the current state.
+  // 
+  // `fromState` should be `null`, `List[String]`, `Map[String, String]` or a function. 
+  // 
+  // - If it is `null`, the state will be passed to the module as is.
+  // - If it is a `List[String]`, the data will be the values of the state at the given keys.
+  // - If it is a `Map[String, String]`, the data will be the values of the state at the given keys, with the keys renamed according to the map.
+  // - If it is a function, the tuple (`[id, state]`) in the channel will be passed to the function, and the result will be used as the data.
+  // 
+  // Example: `{ id, state -> [input: state.fastq_file] }`
+  // Default: `null`
+  fromState: null,
+
+  // Determine how the state should be updated after the module has been run.
+  // 
+  // `toState` should be `null`, `List[String]`, `Map[String, String]` or a function.
+  // 
+  // - If it is `null`, the state will be replaced with the output of the module.
+  // - If it is a `List[String]`, the state will be updated with the values of the data at the given keys.
+  // - If it is a `Map[String, String]`, the state will be updated with the values of the data at the given keys, with the keys renamed according to the map.
+  // - If it is a function, a tuple (`[id, output, state]`) will be passed to the function, and the result will be used as the new state.
+  //
+  // Example: `{ id, output, state -> state + [counts: state.output] }`
+  // Default: `{ id, output, state -> output }`
+  toState: null,
+
+  // Whether or not to print debug messages
+  // Default: `false`
+  debug: false
+]
+
+// initialise default workflow
+meta["workflow"] = workflowFactory([key: meta.config.name], meta.defaults, meta)
+
+// add workflow to environment
+nextflow.script.ScriptMeta.current().addDefinition(meta.workflow)
+
+// anonymous workflow for running this module as a standalone
+workflow {
+  // add id argument if it's not already in the config
+  // TODO: deep copy
+  def newConfig = deepClone(meta.config)
+  def newParams = deepClone(params)
+
+  def argsContainsId = newConfig.allArguments.any{it.plainName == "id"}
+  if (!argsContainsId) {
+    def idArg = [
+      'name': '--id',
+      'required': false,
+      'type': 'string',
+      'description': 'A unique id for every entry.',
+      'multiple': false
+    ]
+    newConfig.arguments.add(0, idArg)
+    newConfig = processConfig(newConfig)
+  }
+  if (!newParams.containsKey("id")) {
+    newParams.id = "run"
+  }
+
+  helpMessage(newConfig)
+
+  channelFromParams(newParams, newConfig)
+    // make sure id is not in the state if id is not in the args
+    | map {id, state ->
+      if (!argsContainsId) {
+        [id, state.findAll{k, v -> k != "id"}]
+      } else {
+        [id, state]
+      }
+    }
+    | meta.workflow.run(
+      auto: [ publish: "state" ]
+    )
+}
+
+// END COMPONENT-SPECIFIC CODE
diff --git a/target/nextflow/snpeff/nextflow.config b/target/nextflow/snpeff/nextflow.config
new file mode 100644
index 00000000..fdb4e533
--- /dev/null
+++ b/target/nextflow/snpeff/nextflow.config
@@ -0,0 +1,125 @@
+manifest {
+  name = 'snpeff'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+
diff --git a/target/nextflow/snpeff/nextflow_schema.json b/target/nextflow/snpeff/nextflow_schema.json
new file mode 100644
index 00000000..d86a4de3
--- /dev/null
+++ b/target/nextflow/snpeff/nextflow_schema.json
@@ -0,0 +1,868 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "snpeff",
+"description": "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "inputs" : {
+    "title": "Inputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `test.vcf`. Input variants file",
+                "help_text": "Type: `file`, required, example: `test.vcf`. Input variants file."
+            
+            }
+    
+
+        ,
+                "genome_version": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `GRCh37.75`. Reference genome version",
+                "help_text": "Type: `string`, required, example: `GRCh37.75`. Reference genome version."
+            
+            }
+    
+
+}
+},
+    
+    
+    "outputs" : {
+    "title": "Outputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output.vcf`, example: `out.vcf`. The output file",
+                "help_text": "Type: `file`, required, default: `$id.$key.output.vcf`, example: `out.vcf`. The output file."
+            ,
+                "default": "$id.$key.output.vcf"
+            }
+    
+
+        ,
+                "summary": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory",
+                "help_text": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory."
+            ,
+                "default": "$id.$key.summary.summary"
+            }
+    
+
+        ,
+                "genes": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory",
+                "help_text": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory."
+            ,
+                "default": "$id.$key.genes.genes"
+            }
+    
+
+}
+},
+    
+    
+    "options" : {
+    "title": "Options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "chr": {
+                "type":
+                "string",
+                "description": "Type: `string`. Prepend \u0027string\u0027 to chromosome name (e",
+                "help_text": "Type: `string`. Prepend \u0027string\u0027 to chromosome name (e.g. \u0027chr1\u0027 instead of \u00271\u0027). Only on TXT output.\n"
+            
+            }
+    
+
+        ,
+                "classic": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use old style annotations instead of Sequence Ontology and Hgvs",
+                "help_text": "Type: `boolean_true`, default: `false`. Use old style annotations instead of Sequence Ontology and Hgvs."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "csv_stats": {
+                "type":
+                "string",
+                "description": "Type: `file`. Create CSV summary file",
+                "help_text": "Type: `file`. Create CSV summary file."
+            
+            }
+    
+
+        ,
+                "download": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Download reference genome if not available",
+                "help_text": "Type: `boolean_true`, default: `false`. Download reference genome if not available."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "input_format": {
+                "type":
+                "string",
+                "description": "Type: `string`. Input format [ vcf, bed ]",
+                "help_text": "Type: `string`. Input format [ vcf, bed ]. Default: VCF.\nexample: \"VCF\"\n"
+            
+            }
+    
+
+        ,
+                "file_list": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Input actually contains a list of files to process",
+                "help_text": "Type: `boolean_true`, default: `false`. Input actually contains a list of files to process."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "output_format": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `VCF`. Output format [ vcf, gatk, bed, bedAnn ]",
+                "help_text": "Type: `string`, example: `VCF`. Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n"
+            
+            }
+    
+
+        ,
+                "stats": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Create HTML summary file",
+                "help_text": "Type: `boolean_true`, default: `false`. Create HTML summary file."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_stats": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not create stats (summary) file",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not create stats (summary) file."
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "results filter options" : {
+    "title": "Results filter options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "fi": {
+                "type":
+                "string",
+                "description": "Type: `file`. Only analyze changes that intersect with the intervals \nspecified in this file",
+                "help_text": "Type: `file`. Only analyze changes that intersect with the intervals \nspecified in this file. This option can be used several times.\n"
+            
+            }
+    
+
+        ,
+                "no_downstream": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not show DOWNSTREAM changes",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not show DOWNSTREAM changes"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_intergenic": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not show INTERGENIC changes",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not show INTERGENIC changes."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_intron": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not show INTRON changes",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not show INTRON changes."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_upstream": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not show UPSTREAM changes",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not show UPSTREAM changes."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_utr": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not show 5_PRIME_UTR or 3_PRIME_UTR changes",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not show 5_PRIME_UTR or 3_PRIME_UTR changes."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no": {
+                "type":
+                "string",
+                "description": "Type: `string`. Do not show \u0027EffectType\u0027",
+                "help_text": "Type: `string`. Do not show \u0027EffectType\u0027. This option can be used several times.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "annotations options" : {
+    "title": "Annotations options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "cancer": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Perform \u0027cancer\u0027 comparisons (Somatic vs Germline)",
+                "help_text": "Type: `boolean_true`, default: `false`. Perform \u0027cancer\u0027 comparisons (Somatic vs Germline)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "cancer_samples": {
+                "type":
+                "string",
+                "description": "Type: `file`. Two column TXT file defining \u0027original \\t derived\u0027 samples",
+                "help_text": "Type: `file`. Two column TXT file defining \u0027original \\t derived\u0027 samples."
+            
+            }
+    
+
+        ,
+                "fastaprot": {
+                "type":
+                "string",
+                "description": "Type: `file`. Create an output file containing the resulting protein sequences",
+                "help_text": "Type: `file`. Create an output file containing the resulting protein sequences.\n"
+            
+            }
+    
+
+        ,
+                "format_eff": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use \u0027EFF\u0027 field compatible with older versions (instead of \u0027ANN\u0027)",
+                "help_text": "Type: `boolean_true`, default: `false`. Use \u0027EFF\u0027 field compatible with older versions (instead of \u0027ANN\u0027).\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "gene_id": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use gene ID instead of gene name (VCF output)",
+                "help_text": "Type: `boolean_true`, default: `false`. Use gene ID instead of gene name (VCF output)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "hgvs": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use HGVS annotations for amino acid sub-field",
+                "help_text": "Type: `boolean_true`, default: `false`. Use HGVS annotations for amino acid sub-field."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "hgvs_old": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use old HGVS notation",
+                "help_text": "Type: `boolean_true`, default: `false`. Use old HGVS notation."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "hgvs1_letter_aa": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use one letter Amino acid codes in HGVS notation",
+                "help_text": "Type: `boolean_true`, default: `false`. Use one letter Amino acid codes in HGVS notation."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "hgvs_tr_id": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use transcript ID in HGVS notation",
+                "help_text": "Type: `boolean_true`, default: `false`. Use transcript ID in HGVS notation."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "lof": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Add loss of function (LOF) and Nonsense mediated decay (NMD) tags",
+                "help_text": "Type: `boolean_true`, default: `false`. Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "-no_hgvs": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not add HGVS annotations",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not add HGVS annotations."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_lof": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not add LOF and NMD annotations",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not add LOF and NMD annotations."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_shift_hgvs": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not shift variants according to HGVS notation (most 3prime end)",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not shift variants according to HGVS notation (most 3prime end).\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "oicr": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Add OICR tag in VCF file",
+                "help_text": "Type: `boolean_true`, default: `false`. Add OICR tag in VCF file."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "sequence_ontology": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms",
+                "help_text": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms."
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "generic options" : {
+    "title": "Generic options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "config": {
+                "type":
+                "string",
+                "description": "Type: `file`. Specify config file",
+                "help_text": "Type: `file`. Specify config file"
+            
+            }
+    
+
+        ,
+                "config_option": {
+                "type":
+                "string",
+                "description": "Type: `string`. Override a config file option (name=value)",
+                "help_text": "Type: `string`. Override a config file option (name=value)."
+            
+            }
+    
+
+        ,
+                "debug": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)",
+                "help_text": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "data_dir": {
+                "type":
+                "string",
+                "description": "Type: `file`. Override data_dir parameter from config file",
+                "help_text": "Type: `file`. Override data_dir parameter from config file."
+            
+            }
+    
+
+        ,
+                "no_download": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not download a SnpEff database, if not available locally",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not download a SnpEff database, if not available locally."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_log": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not report usage statistics to server",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not report usage statistics to server."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "quiet": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Quiet mode (do not show any messages or errors)",
+                "help_text": "Type: `boolean_true`, default: `false`. Quiet mode (do not show any messages or errors)"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "verbose": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Verbose mode",
+                "help_text": "Type: `boolean_true`, default: `false`. Verbose mode."
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "database options" : {
+    "title": "Database options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "canon": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Only use canonical transcripts",
+                "help_text": "Type: `boolean_true`, default: `false`. Only use canonical transcripts."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "canon_list": {
+                "type":
+                "string",
+                "description": "Type: `file`. Only use canonical transcripts, replace some transcripts using the \u0027gene_id         \ntranscript_id\u0027 entries in \u003cfile\u003e",
+                "help_text": "Type: `file`. Only use canonical transcripts, replace some transcripts using the \u0027gene_id         \ntranscript_id\u0027 entries in \u003cfile\u003e.\n"
+            
+            }
+    
+
+        ,
+                "tag": {
+                "type":
+                "string",
+                "description": "Type: `string`. Only use transcript having a tag \u0027tagName\u0027",
+                "help_text": "Type: `string`. Only use transcript having a tag \u0027tagName\u0027. This option can be used multiple times.\n"
+            
+            }
+    
+
+        ,
+                "no_tag": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Filter out transcript having a tag \u0027tagName\u0027",
+                "help_text": "Type: `boolean_true`, default: `false`. Filter out transcript having a tag \u0027tagName\u0027. This option can be used multiple times.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "interaction": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Annotate using interactions (requires interaction database)",
+                "help_text": "Type: `boolean_true`, default: `false`. Annotate using interactions (requires interaction database)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "interval": {
+                "type":
+                "string",
+                "description": "Type: `file`. Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)",
+                "help_text": "Type: `file`. Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).\n"
+            
+            }
+    
+
+        ,
+                "max_tsl": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Only use transcripts having Transcript Support Level lower than \u003cTSL_number\u003e",
+                "help_text": "Type: `integer`. Only use transcripts having Transcript Support Level lower than \u003cTSL_number\u003e."
+            
+            }
+    
+
+        ,
+                "motif": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Annotate using motifs (requires Motif database)",
+                "help_text": "Type: `boolean_true`, default: `false`. Annotate using motifs (requires Motif database)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "nextprot": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Annotate using NextProt (requires NextProt database)",
+                "help_text": "Type: `boolean_true`, default: `false`. Annotate using NextProt (requires NextProt database)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_genome": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not load any genomic database (e",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not load any genomic database (e.g. annotate using custom files)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_expand_iub": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable IUB code expansion in input variants",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable IUB code expansion in input variants."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_interaction": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable inteaction annotations",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable inteaction annotations."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_motif": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable motif annotations",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable motif annotations."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_nextprot": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable NextProt annotations",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable NextProt annotations."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "only_reg": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Only use regulation tracks",
+                "help_text": "Type: `boolean_true`, default: `false`. Only use regulation tracks."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "only_protein": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Only use protein coding transcripts",
+                "help_text": "Type: `boolean_true`, default: `false`. Only use protein coding transcripts."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "only_tr": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `file.txt`. Only use the transcripts in this file",
+                "help_text": "Type: `file`, example: `file.txt`. Only use the transcripts in this file. Format: One transcript ID per line.\n"
+            
+            }
+    
+
+        ,
+                "reg": {
+                "type":
+                "string",
+                "description": "Type: `string`. Regulation track to use (this option can be used add several times)",
+                "help_text": "Type: `string`. Regulation track to use (this option can be used add several times)."
+            
+            }
+    
+
+        ,
+                "ss": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Set size for splice sites (donor and acceptor) in bases",
+                "help_text": "Type: `integer`. Set size for splice sites (donor and acceptor) in bases. Default: 2.\n"
+            
+            }
+    
+
+        ,
+                "splice_region_exon_size": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Set size for splice site region within exons",
+                "help_text": "Type: `integer`. Set size for splice site region within exons. Default: 3 bases.\n"
+            
+            }
+    
+
+        ,
+                "splice_region_intron_min": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Set minimum number of bases for splice site region within intron",
+                "help_text": "Type: `integer`. Set minimum number of bases for splice site region within intron. Default: 3 bases.\n"
+            
+            }
+    
+
+        ,
+                "splice_region_intron_max": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Set maximum number of bases for splice site region within intron",
+                "help_text": "Type: `integer`. Set maximum number of bases for splice site region within intron. Default: 8 bases.\n"
+            
+            }
+    
+
+        ,
+                "strict": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Only use \u0027validated\u0027 transcripts (i",
+                "help_text": "Type: `boolean_true`, default: `false`. Only use \u0027validated\u0027 transcripts (i.e. sequence has been checked)."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "ud": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Set upstream downstream interval length (in bases)",
+                "help_text": "Type: `integer`. Set upstream downstream interval length (in bases)."
+            
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/inputs"
+    },
+
+    {
+    "$ref": "#/definitions/outputs"
+    },
+
+    {
+    "$ref": "#/definitions/options"
+    },
+
+    {
+    "$ref": "#/definitions/results filter options"
+    },
+
+    {
+    "$ref": "#/definitions/annotations options"
+    },
+
+    {
+    "$ref": "#/definitions/generic options"
+    },
+
+    {
+    "$ref": "#/definitions/database options"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}
diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml
index 06e9635f..cb8f61c3 100644
--- a/target/nextflow/sortmerna/.config.vsh.yaml
+++ b/target/nextflow/sortmerna/.config.vsh.yaml
@@ -591,9 +591,9 @@ build_info:
   output: "target/nextflow/sortmerna"
   executable: "target/nextflow/sortmerna/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf
index a0a2642a..33809318 100644
--- a/target/nextflow/sortmerna/main.nf
+++ b/target/nextflow/sortmerna/main.nf
@@ -3456,9 +3456,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/sortmerna",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml
index 1b672bba..76e1411f 100644
--- a/target/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2663,9 +2663,9 @@ build_info:
   output: "target/nextflow/star/star_align_reads"
   executable: "target/nextflow/star/star_align_reads/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf
index 62ec1abd..7b80abea 100644
--- a/target/nextflow/star/star_align_reads/main.nf
+++ b/target/nextflow/star/star_align_reads/main.nf
@@ -5943,9 +5943,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_align_reads",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
index 89e955a2..5047fd80 100644
--- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -333,9 +333,9 @@ build_info:
   output: "target/nextflow/star/star_genome_generate"
   executable: "target/nextflow/star/star_genome_generate/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf
index 9026a955..313240c2 100644
--- a/target/nextflow/star/star_genome_generate/main.nf
+++ b/target/nextflow/star/star_genome_generate/main.nf
@@ -3195,9 +3195,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_genome_generate",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml
index bad1ade5..3183912e 100644
--- a/target/nextflow/trimgalore/.config.vsh.yaml
+++ b/target/nextflow/trimgalore/.config.vsh.yaml
@@ -770,9 +770,9 @@ build_info:
   output: "target/nextflow/trimgalore"
   executable: "target/nextflow/trimgalore/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf
index 4c5894de..a05d22e2 100644
--- a/target/nextflow/trimgalore/main.nf
+++ b/target/nextflow/trimgalore/main.nf
@@ -3560,9 +3560,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/trimgalore",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
index 61e17f1d..4941dc3f 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,9 +611,9 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_dedup"
   executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
index af804da3..2ca61a0b 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
@@ -3487,9 +3487,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_dedup",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
index 6e9775fc..4a4a6397 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,9 +449,9 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_extract"
   executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf
index 09daa36e..2cccd244 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf
@@ -3316,9 +3316,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_extract",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",
diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
index a2961fc7..e86d7b36 100644
--- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
@@ -256,9 +256,9 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_prepareforrsem"
   executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf"
   viash_version: "0.9.0"
-  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
-  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-9-gadd1252"
+  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
+  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-10-g86333c1"
 package_config:
   name: "biobox"
   version: "main"
diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf
index 0035b6ae..58d48b70 100644
--- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf
@@ -3121,9 +3121,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem",
     "viash_version" : "0.9.0",
-    "git_commit" : "add125261c6fa0ed7c9906fc85e7368d2072c4a3",
-    "git_remote" : "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-9-gadd1252"
+    "git_commit" : "86333c1a465db45facd936695f1f33b186ccf0fc",
+    "git_remote" : "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-10-g86333c1"
   },
   "package_config" : {
     "name" : "biobox",