Build branch main with version main (38f635a)

Build pipeline: viash-hub.biobox.main-dz9k8 Source commit: 38f635ad57 Source message: Add agat convert genscan2gff (#100) * add config * add help * add test data and expected output adn the script to obtain them * add running script * add test script * update changelog * cleanup * fix tests * format description * remove unused argument --inflate-off * update --config description * add requirements * create temporary directory and clean up on exit * add GENSCAN in keywords * add set -e to test * fix create temporary directory * add set -eo pipefail to test * add set -eo pipefail to script * fix create temporary directory * update --config description * cleanup changelog * cleanup changelog * Update deprecated variable --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
2024-09-17 07:19:20 +00:00
parent 4b61e09a56
commit f47054953e
255 changed files with 8531 additions and 1561 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,14 @@
+# biobox x.x.x
+
+## NEW FUNCTIONALITY
+
+* `agat`:
+  - `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
+
+## MINOR CHANGES
+
+* Upgrade to Viash 0.9.0.
+
 # biobox 0.2.0

 ## BREAKING CHANGES
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -7,7 +7,7 @@ links:
  issue_tracker: https://github.com/viash-hub/biobox/issues
  repository: https://github.com/viash-hub/biobox

-viash_version: 0.9.0-RC7
+viash_version: 0.9.0

 config_mods: |
  .requirements.commands := ['ps']
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -0,0 +1,95 @@
+name: agat_convert_genscan2gff
+namespace: agat
+description: |
+  The script takes a GENSCAN file as input, and will translate it in gff
+  format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).
+  
+  **Known problem** 
+
+  You must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA
+  sequences and does not crash/warn if an header is submited along the
+  sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
+  nucleotides of the sequence. Then all prediction location are shifted
+  accordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). 
+  I don't know if there is the same problem elsewhere.)
+keywords: [gene annotations, GFF conversion, GENSCAN]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+requirements:
+  - commands: [agat]
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --genscan
+        alternatives: [-g]
+        description: Input genscan bed file that will be converted.
+        type: file
+        required: true
+        direction: input
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gff]
+        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --source
+        description: |
+          The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
+        type: string
+        required: false
+        example: Stringtie
+      - name: --primary_tag
+        description: |
+          The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
+        type: string
+        required: false
+        example: gene
+      - name: --inflate_type
+        description: |
+          Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
+        type: string
+        required: false
+        example: exon
+      - name: --verbose
+        description: add verbosity
+        type: boolean_true
+      - name: --config
+        alternatives: [-c]
+        description: |
+          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+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/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/agat/agat_convert_genscan2gff/help.txt
+++ b/src/agat/agat_convert_genscan2gff/help.txt
@@ -0,0 +1,94 @@
+```sh
+agat_convert_genscan2gff.pl --help
+```
+ ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+Name:
+    agat_convert_genscan2gff.pl
+
+Description:
+    The script takes a genscan file as input, and will translate it in gff
+    format. The genscan format is described here:
+    http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
+    can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
+    sequence, wihtout any header!! Indeed the tool expects only DNA
+    sequences and does not crash/warn if an header is submited along the
+    sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
+    nucleotides of the sequence. Then all prediction location are shifted
+    accordingly. (checked only on the online version
+    http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
+    pronlem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\
+
+Usage:
+        agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ]
+        agat_convert_genscan2gff.pl -h
+
+Options:
+    --genscan or -g
+            Input genscan bed file that will be convert.
+
+    --source
+            The source informs about the tool used to produce the data and
+            is stored in 2nd field of a gff file. Example:
+            Stringtie,Maker,Augustus,etc. [default: data]
+
+    --primary_tag
+            The primary_tag corresponf to the data type and is stored in 3rd
+            field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]
+
+    --inflate_off
+            By default we inflate the block fields (blockCount, blockSizes,
+            blockStarts) to create subfeatures of the main feature
+            (primary_tag). Type of subfeature created based on the
+            inflate_type parameter. If you don't want this inflating
+            behaviour you can deactivate it by using the option
+            --inflate_off.
+
+    --inflate_type
+            Feature type (3rd column in gff) created when inflate parameter
+            activated [default: exon].
+
+    --verbose
+            add verbosity
+
+    -o , --output , --out , --outfile or --gff
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    -h or --help
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
--- a/src/agat/agat_convert_genscan2gff/script.sh
+++ b/src/agat/agat_convert_genscan2gff/script.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# run agat_convert_genscan2gff
+agat_convert_genscan2gff.pl \
+  --genscan "$par_genscan" \
+  --output "$par_output" \
+  ${par_source:+--source "${par_source}"} \
+  ${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
+  ${par_inflate_off:+--inflate_off} \
+  ${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
+  ${par_verbose:+--verbose} \
+  ${par_config:+--config "${par_config}"}
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --genscan "$test_dir/test.genscan" \
+  --output "$TMPDIR/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$TMPDIR/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"
--- a/src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
+++ b/src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
@@ -0,0 +1,25 @@
+##gff-version 3
+unknown	genscan	gene	2223	4605	75.25	+	.	ID=gene_1
+unknown	genscan	mRNA	2223	4605	75.25	+	.	ID=mrna_1;Parent=gene_1
+unknown	genscan	exon	2223	3020	75.25	+	.	ID=exon_1;Parent=mrna_1
+unknown	genscan	exon	4249	4605	13.03	+	.	ID=exon_2;Parent=mrna_1
+unknown	genscan	CDS	2223	3020	75.25	+	0	ID=cds_1;Parent=mrna_1
+unknown	genscan	CDS	4249	4605	13.03	+	0	ID=cds_2;Parent=mrna_1
+unknown	genscan	gene	6829	8789	20.06	-	.	ID=gene_2
+unknown	genscan	mRNA	6829	8789	20.06	-	.	ID=mrna_2;Parent=gene_2
+unknown	genscan	exon	6829	7297	20.06	-	.	ID=exon_3;Parent=mrna_2
+unknown	genscan	exon	7730	7888	12.78	-	.	ID=exon_4;Parent=mrna_2
+unknown	genscan	exon	8029	8185	7.45	-	.	ID=exon_5;Parent=mrna_2
+unknown	genscan	exon	8278	8546	17.45	-	.	ID=exon_6;Parent=mrna_2
+unknown	genscan	exon	8647	8789	18.65	-	.	ID=exon_7;Parent=mrna_2
+unknown	genscan	CDS	6829	7297	20.06	-	1	ID=cds_3;Parent=mrna_2
+unknown	genscan	CDS	7730	7888	12.78	-	1	ID=cds_4;Parent=mrna_2
+unknown	genscan	CDS	8029	8185	7.45	-	2	ID=cds_5;Parent=mrna_2
+unknown	genscan	CDS	8278	8546	17.45	-	1	ID=cds_6;Parent=mrna_2
+unknown	genscan	CDS	8647	8789	18.65	-	0	ID=cds_7;Parent=mrna_2
+unknown	genscan	gene	10209	11924	16.18	+	.	ID=gene_3
+unknown	genscan	mRNA	10209	11924	16.18	+	.	ID=mrna_3;Parent=gene_3
+unknown	genscan	exon	10209	11313	16.18	+	.	ID=exon_8;Parent=mrna_3
+unknown	genscan	exon	11850	11924	3.27	+	.	ID=exon_9;Parent=mrna_3
+unknown	genscan	CDS	10209	11313	16.18	+	0	ID=cds_8;Parent=mrna_3
+unknown	genscan	CDS	11850	11924	3.27	+	2	ID=cds_9;Parent=mrna_3
--- a/src/agat/agat_convert_genscan2gff/test_data/script.sh
+++ b/src/agat/agat_convert_genscan2gff/test_data/script.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/in/test.genscan src/agat/agat_convert_genscan2gff/test_data/test.genscan
+cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_genscan2gff_1.gff src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
+
--- a/src/agat/agat_convert_genscan2gff/test_data/test.genscan
+++ b/src/agat/agat_convert_genscan2gff/test_data/test.genscan
@@ -0,0 +1,127 @@
+GENSCAN 1.0	Date run:  7-Mar-120	Time: 14:46:49
+
+
+
+Sequence /tmp/03_07_20-14:46:49.fasta : 12217 bp : 42.83% C+G : Isochore 1 ( 0 - 43 C+G%)
+
+
+
+Parameter matrix: HumanIso.smat
+
+
+
+Predicted genes/exons:
+
+
+
+Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
+
+----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
+
+
+
+ 1.01 Init +   2223   3020  798  2  0   55    2   924 0.940  75.25
+
+ 1.02 Term +   4249   4605  357  0  0   26   38   307 0.976  13.03
+
+ 1.03 PlyA +   4711   4716    6                              -0.45
+
+
+
+ 2.06 PlyA -   4852   4847    6                              -0.45
+
+ 2.05 Term -   7297   6829  469  0  1   13   42   387 0.281  20.06
+
+ 2.04 Intr -   7888   7730  159  0  0   85   93   144 0.998  12.78
+
+ 2.03 Intr -   8185   8029  157  2  1   65   60   144 0.787   7.45
+
+ 2.02 Intr -   8546   8278  269  1  2   36   65   287 0.946  17.45
+
+ 2.01 Init -   8789   8647  143  2  2   94   96   176 0.550  18.65
+
+ 2.00 Prom -   9720   9681   40                              -6.55
+
+
+
+ 3.00 Prom +  10160  10199   40                             -11.84
+
+ 3.01 Init +  10209  11313 1105  2  1   66   57   269 0.512  16.18
+
+ 3.02 Intr +  11850  11924   75  1  0   80   86    57 0.507   3.27
+
+
+
+Suboptimal exons with probability > 1.000
+
+
+
+Exnum Type S .Begin ...End .Len Fr Ph B/Ac Do/T CodRg P.... Tscr..
+
+----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
+
+
+
+NO EXONS FOUND AT GIVEN PROBABILITY CUTOFF
+
+
+
+
+
+Predicted peptide sequence(s):
+
+
+
+
+
+>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_1|384_aa
+
+MSSKNKVSKQDIDSIVESLMKKQKSYFEPRLAQIQQVGMENVQKLSAIHAELALLTASIS
+
+TVKSDVDKLKCKVENNFSAIDGHDQAFGELELKMADMEDRSRRCNIRVIGLKERLEGFNA
+
+IQYLTHSLPKWFPALADVPVEVMSAHRIYSDAKRGDNRTLIFNVLRYTTRQAILRAAKKD
+
+PLSVDDRKVRFSPDYSNFTVKRCQAFHQAKDAARNKCLDFFLLYPATLKIKEGAQYRSFT
+
+SPKEAEDYVNSAASNHAATPASPRQHGTILTIYRRIHSLYDGERARKIQLLEQAASVALT
+
+GDNWTSVRNDNYLGVTAHFIDNVWKLRCFALEVKKKKKHSRHTAEDCAEEFIDVSNRWEI
+
+NGKLTTLGTDSALIMLAAARLLPF
+
+
+
+>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_2|398_aa
+
+MASTMPSSSSTEDEENTPECLNKDHYHFHHYTMEYIQDKPTNVARVGGFTDKKSIAKVER
+
+CLARERQEATEDHEAIPSTSGATSLTKKLRSRSGLPIAGSGLVLPALCIICQKKEKFINR
+
+AGKRQRDPLSKAETLTVGQLQKAAELKDDQSILLHIKDKDCVALEVQYHKGCYNQYTRFM
+
+TRPEKPEKEQNEPTFDVGYKILCERIIRQRLLVNQEVLRMGQLRMAFIELVKANEGLDAS
+
+NYSIKNLERSRRADAGSQRIQIFDPDQRTPTQWKKFLSEGTKKEALAEFLYVAWKNADLT
+
+IVGKNLCLYIAHTNQCHCVTVKEGVQSVRVVEDLLLFLHAQHAAREHKAVIIKSSDTDVA
+
+VIAVSVQTDLPCSLYVFTGTGNRTRIIDITKVSSANKI
+
+
+
+>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_3|394_aa
+
+MQRGRAAGINGIPPEFYVAFWEQLSPFFLHMINFSIEKGGFLRDVNTALISLLMKKDKNP
+
+TDCSSYRPLSLLNSDVKIFAKLLPLRLEPHMPELVSSDQTGFIKSRTAADNIRRLLHIIA
+
+AAPGCETPMSVLSLDAMKAFDRLEWSFLWSVLEAMGFISTFIGMVKVLYSNPSARVLTGQ
+
+TFSSLFPVSRSSRQGCPLSPALFVLSLEPLAQAVRLSNLVLPICICDTQHKLSLFADDVI
+
+VFLEHPTQSLPHFLSICEEFRKLSGFKMNWSKSALMHLNDNARKSVTPVNIPLVGQLKYL
+
+GIEVFPSLNQIVKHNYSLAFTNVLKDMDRWISLPMSIQARISIIKMNGLPRIHFVSSMVP
+
+LPPPSDYWIKISAQGVRCPLAKPFTHSPYSKTKX
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -234,15 +234,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/agat/agat_convert_bed2gff"
  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -2,9 +2,9 @@

 # agat_convert_bed2gff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:16Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:34Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -224,15 +224,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/agat/agat_convert_embl2gff"
  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -2,9 +2,9 @@

 # agat_convert_embl2gff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:16Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:33Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -0,0 +1,257 @@
+name: "agat_convert_genscan2gff"
+namespace: "agat"
+version: "main"
+authors:
+- name: "Leïla Paquay"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "leila@data-intuitive.com"
+      github: "Leila011"
+      linkedin: "leilapaquay"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Software Developer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--genscan"
+    alternatives:
+    - "-g"
+    description: "Input genscan bed file that will be converted."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gff"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--source"
+    description: "The source informs about the tool used to produce the data and is\
+      \ stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc.\
+      \ [default: data]\n"
+    info: null
+    example:
+    - "Stringtie"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--primary_tag"
+    description: "The primary_tag corresponds to the data type and is stored in 3rd\
+      \ field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
+    info: null
+    example:
+    - "gene"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--inflate_type"
+    description: "Feature type (3rd column in gff) created when inflate parameter\
+      \ activated [default: exon].\n"
+    info: null
+    example:
+    - "exon"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "add verbosity"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
+      \ shipped with AGAT. The `--config` option gives you the possibility to use\
+      \ your own AGAT config file (located elsewhere or named differently).\n"
+    info: null
+    example:
+    - "custom_agat_config.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "The script takes a GENSCAN file as input, and will translate it in gff\n\
+  format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).\n\
+  \n**Known problem** \n\nYou must have submited only DNA sequence, without any header!!\
+  \ Indeed the tool expects only DNA\nsequences and does not crash/warn if an header\
+  \ is submited along the\nsequence. e.g If you have an header \">seq\" s-e-q are\
+  \ seen as the 3 first\nnucleotides of the sequence. Then all prediction location\
+  \ are shifted\naccordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html).\
+  \ \nI don't know if there is the same problem elsewhere.)\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:
+- "gene annotations"
+- "GFF conversion"
+- "GENSCAN"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.5281/zenodo.3552717"
+links:
+  repository: "https://github.com/NBISweden/AGAT"
+  homepage: "https://github.com/NBISweden/AGAT"
+  documentation: "https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.html"
+  issue_tracker: "https://github.com/NBISweden/AGAT/issues"
+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/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/agat/agat_convert_genscan2gff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_genscan2gff"
+  executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
+++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -227,15 +227,16 @@ build_info:
  engine: "docker|native"
  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-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -2,9 +2,9 @@

 # agat_convert_sp_gff2gtf main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:17Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:34Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -187,15 +187,16 @@ build_info:
  engine: "docker|native"
  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-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -2,9 +2,9 @@

 # agat_convert_sp_gff2tsv main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:16Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:33Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -194,15 +194,16 @@ build_info:
  engine: "docker|native"
  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-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -2,9 +2,9 @@

 # agat_convert_sp_gxf2gxf main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:16Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:33Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -705,15 +705,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -2,9 +2,9 @@

 # arriba main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:19Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:36Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -468,15 +468,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bcftools/bcftools_annotate"
  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -2,9 +2,9 @@

 # bcftools_annotate main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:10Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:28Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
@@ -334,15 +334,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bcftools/bcftools_concat"
  executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bcftools/bcftools_concat/bcftools_concat
+++ b/target/executable/bcftools/bcftools_concat/bcftools_concat
@@ -2,9 +2,9 @@

 # bcftools_concat main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:10Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:28Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -415,15 +415,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bcftools/bcftools_norm"
  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
@@ -2,9 +2,9 @@

 # bcftools_norm main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:11Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:29Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -184,15 +184,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -2,9 +2,9 @@

 # bcftools_sort main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:09Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:27Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -457,15 +457,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bcftools/bcftools_stats"
  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -2,9 +2,9 @@

 # bcftools_stats main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:10Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:28Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -417,15 +417,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -2,9 +2,9 @@

 # bcl_convert main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:18Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:35Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -269,15 +269,16 @@ build_info:
  engine: "docker|native"
  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-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- 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
@@ -2,9 +2,9 @@

 # bd_rhapsody_make_reference main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -549,9 +549,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-09-16T07:55:21Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:38Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -186,15 +186,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_bamtofastq"
  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -2,9 +2,9 @@

 # bedtools_bamtofastq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:02Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:20Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -175,15 +175,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -2,9 +2,9 @@

 # bedtools_bed12tobed6 main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:01Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:19Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -213,15 +213,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_bedtobam"
  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -2,9 +2,9 @@

 # bedtools_bedtobam main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:03Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:21Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -336,15 +336,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -2,9 +2,9 @@

 # bedtools_genomecov main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:00Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:19Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -231,15 +231,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -2,9 +2,9 @@

 # bedtools_getfasta main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:01Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:19Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -272,15 +272,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -2,9 +2,9 @@

 # bedtools_groupby main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:02Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:21Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -409,15 +409,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -2,9 +2,9 @@

 # bedtools_intersect main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:01Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:20Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -209,15 +209,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -2,9 +2,9 @@

 # bedtools_links main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:02Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:20Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -278,15 +278,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -2,9 +2,9 @@

 # bedtools_merge main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:00Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:18Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -221,15 +221,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_sort"
  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -2,9 +2,9 @@

 # bedtools_sort main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:03Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:21Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -157,15 +157,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -2,9 +2,9 @@

 # busco_download_datasets main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:14Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:31Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -144,15 +144,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -2,9 +2,9 @@

 # busco_list_datasets main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:14Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:32Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -422,15 +422,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -2,9 +2,9 @@

 # busco_run main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:14Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:32Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -739,15 +739,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -2,9 +2,9 @@

 # cutadapt main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:20Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:37Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -316,15 +316,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -2,9 +2,9 @@

 # falco main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:21Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:38Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1082,15 +1082,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -2,9 +2,9 @@

 # fastp main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:17Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:35Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -339,15 +339,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -2,9 +2,9 @@

 # fastqc main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:08Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:26Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -644,15 +644,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -2,9 +2,9 @@

 # featurecounts main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:12Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:30Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -189,15 +189,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -2,9 +2,9 @@

 # fq_subsample main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:07Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:25Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -684,15 +684,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -2,9 +2,9 @@

 # gffread main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:54:59Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:18Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -217,15 +217,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -2,9 +2,9 @@

 # kallisto_index main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:15Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:33Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -506,15 +506,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -2,9 +2,9 @@

 # lofreq_call main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:12Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -214,15 +214,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -2,9 +2,9 @@

 # lofreq_indelqual main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:11Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -455,15 +455,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -2,9 +2,9 @@

 # multiqc main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:20Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:38Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -397,15 +397,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -2,9 +2,9 @@

 # pear main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:03Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:21Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -263,15 +263,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -2,9 +2,9 @@

 # qualimap_rnaseq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:07Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:25Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -415,15 +415,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/rsem/rsem_prepare_reference"
  executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -2,9 +2,9 @@

 # rsem_prepare_reference main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:15Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:32Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -276,15 +276,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -2,9 +2,9 @@

 # salmon_index main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:19Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:36Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1172,15 +1172,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/salmon/salmon_quant"
  executable: "target/executable/salmon/salmon_quant/salmon_quant"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -2,9 +2,9 @@

 # salmon_quant main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:19Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:37Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -263,15 +263,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -2,9 +2,9 @@

 # samtools_collate main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:06Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:24Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -242,15 +242,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/samtools/samtools_faidx"
  executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -2,9 +2,9 @@

 # samtools_faidx main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# 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
@@ -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="2024-09-16T07:55:05Z"
+LABEL org.opencontainers.image.created="2024-09-17T06:47:23Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
+LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -432,15 +432,16 @@ build_info:
  engine: "docker|native"
  output: "target/executable/samtools/samtools_fasta"
  executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 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-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/Show More
+++ b/Show More