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Build branch main with version main (5f6516e)

Browse Source 
Build pipeline: viash-hub.biobox.main-v9whr

Source commit: 5f6516e9c0

Source message: Bump viash version (#172)

* bump viash version

* fix agat requirements
This commit is contained in:
CI
2025-03-06 09:35:27 +00:00
parent 6f8d68b9cc
commit a518d2ead8
343 changed files with 40275 additions and 18530 deletions
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13
target/executable/busco/busco_download_datasets/.config.vsh.yaml
View File

@@ -58,6 +58,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -157,16 +160,16 @@ 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"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
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"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

78
target/executable/busco/busco_download_datasets/busco_download_datasets
View File

@@ -2,7 +2,7 @@
# busco_download_datasets main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,29 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "busco_download_datasets main"
echo ""
echo "Downloads available busco datasets"
echo ""
echo "Inputs:"
echo " --download"
echo " type: string, required parameter"
echo " example: stramenopiles_odb10"
echo " Download dataset. Possible values are a specific dataset name, \"all\","
echo " \"prokaryota\", \"eukaryota\", or \"virus\"."
echo " The full list of available datasets can be viewed"
echo " [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
echo " busco/busco_list_datasets component."
echo ""
echo "Outputs:"
echo " --download_path"
echo " type: file, output, file must exist"
echo " default: busco_downloads"
echo " example: busco_downloads"
echo " Local filepath for storing BUSCO dataset downloads"
}
# initialise variables
VIASH_MODE='run'
@@ -475,9 +452,9 @@ 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="2024-12-03T10:34:01Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -592,6 +569,55 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "busco_download_datasets main"
echo ""
echo "Downloads available busco datasets"
echo ""
echo "Inputs:"
echo " --download"
echo " type: string, required parameter"
echo " example: stramenopiles_odb10"
echo " Download dataset. Possible values are a specific dataset name, \"all\","
echo " \"prokaryota\", \"eukaryota\", or \"virus\"."
echo " The full list of available datasets can be viewed"
echo " [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
echo " busco/busco_list_datasets component."
echo ""
echo "Outputs:"
echo " --download_path"
echo " type: file, output, file must exist"
echo " default: busco_downloads"
echo " example: busco_downloads"
echo " Local filepath for storing BUSCO dataset downloads"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/busco/busco_list_datasets/.config.vsh.yaml
View File

@@ -45,6 +45,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -144,16 +147,16 @@ 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"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
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"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

58
target/executable/busco/busco_list_datasets/busco_list_datasets
View File

@@ -2,7 +2,7 @@
# busco_list_datasets main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,19 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "busco_list_datasets main"
echo ""
echo "Lists the available busco datasets"
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " default: busco_dataset_list.txt"
echo " example: file.txt"
echo " Output file of the available busco datasets"
}
# initialise variables
VIASH_MODE='run'
@@ -465,9 +452,9 @@ 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="2024-12-03T10:34:00Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -582,6 +569,45 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "busco_list_datasets main"
echo ""
echo "Lists the available busco datasets"
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " default: busco_dataset_list.txt"
echo " example: file.txt"
echo " Output file of the available busco datasets"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/busco/busco_run/.config.vsh.yaml
View File

@@ -322,6 +322,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -422,16 +425,16 @@ build_info:
engine: "docker|native"
output: "target/executable/busco/busco_run"
executable: "target/executable/busco/busco_run/busco_run"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
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"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

392
target/executable/busco/busco_run/busco_run
View File

@@ -2,7 +2,7 @@
# busco_run main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,186 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "busco_run main"
echo ""
echo "Assessment of genome assembly and annotation completeness with single copy"
echo "orthologs"
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " example: file.fasta"
echo " Input sequence file in FASTA format. Can be an assembled genome or"
echo " transcriptome (DNA), or protein sequences from an annotated gene set."
echo " Also possible to use a path to a directory containing multiple input"
echo " files."
echo ""
echo " -m, --mode"
echo " type: string, required parameter"
echo " example: proteins"
echo " choices: [ genome, geno, transcriptome, tran, proteins, prot ]"
echo " Specify which BUSCO analysis mode to run. There are three valid modes:"
echo " - geno or genome, for genome assemblies (DNA)"
echo " - tran or transcriptome, for transcriptome assemblies (DNA)"
echo " - prot or proteins, for annotated gene sets (protein)"
echo ""
echo " -l, --lineage_dataset"
echo " type: string"
echo " example: stramenopiles_odb10"
echo " Specify a BUSCO lineage dataset that is most closely related to the"
echo " assembly or gene set being assessed."
echo " The full list of available datasets can be viewed"
echo " [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
echo " busco/busco_list_datasets component."
echo " When unsure, the \"--auto_lineage\" flag can be set to automatically find"
echo " the optimal lineage path."
echo " BUSCO will automatically download the requested dataset if it is not"
echo " already present in the download folder."
echo " You can optionally provide a path to a local dataset instead of a name,"
echo " e.g. path/to/dataset."
echo " Datasets can be downloaded using the busco/busco_download_dataset"
echo " component."
echo ""
echo "Outputs:"
echo " --short_summary_json"
echo " type: file, output, file must exist"
echo " example: short_summary.json"
echo " Output file for short summary in JSON format."
echo ""
echo " --short_summary_txt"
echo " type: file, output, file must exist"
echo " example: short_summary.txt"
echo " Output file for short summary in TXT format."
echo ""
echo " --full_table"
echo " type: file, output, file must exist"
echo " example: full_table.tsv"
echo " Full table output in TSV format."
echo ""
echo " --missing_busco_list"
echo " type: file, output, file must exist"
echo " example: missing_busco_list.tsv"
echo " Missing list output in TSV format."
echo ""
echo " --output_dir"
echo " type: file, output, file must exist"
echo " example: output_dir"
echo " The full output directory, if so desired."
echo ""
echo "Resource and Run Settings:"
echo " --force"
echo " type: boolean_true"
echo " Force rewriting of existing files. Must be used when output files with"
echo " the provided name already exist."
echo ""
echo " -q, --quiet"
echo " type: boolean_true"
echo " Disable the info logs, displays only errors."
echo ""
echo " -r, --restart"
echo " type: boolean_true"
echo " Continue a run that had already partially completed. Restarting skips"
echo " calls to tools that have completed but performs all pre- and"
echo " post-processing steps."
echo ""
echo " --tar"
echo " type: boolean_true"
echo " Compress some subdirectories with many files to save space."
echo ""
echo "Lineage Dataset Settings:"
echo " --auto_lineage"
echo " type: boolean_true"
echo " Run auto-lineage pipelilne to automatically determine BUSCO lineage"
echo " dataset that is most closely related to the assembly or gene set being"
echo " assessed."
echo ""
echo " --auto_lineage_euk"
echo " type: boolean_true"
echo " Run auto-placement just on eukaryota tree to find optimal lineage path."
echo ""
echo " --auto_lineage_prok"
echo " type: boolean_true"
echo " Run auto_lineage just on prokaryota trees to find optimum lineage path."
echo ""
echo " --datasets_version"
echo " type: string"
echo " example: odb10"
echo " Specify the version of BUSCO datasets"
echo ""
echo "Augustus Settings:"
echo " --augustus"
echo " type: boolean_true"
echo " Use augustus gene predictor for eukaryote runs."
echo ""
echo " --augustus_parameters"
echo " type: string"
echo " example: --PARAM1=VALUE1,--PARAM2=VALUE2"
echo " Additional parameters to be passed to Augustus (see Augustus"
echo " documentation:"
echo " "
echo "https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md)."
echo " Parameters should be contained within a single string, without"
echo " whitespace and seperated by commas."
echo ""
echo " --augustus_species"
echo " type: string"
echo " Specify the augustus species"
echo ""
echo " --long"
echo " type: boolean_true"
echo " Optimize Augustus self-training mode. This adds considerably to the run"
echo " time, but can improve results for some non-model organisms."
echo ""
echo "BBTools Settings:"
echo " --contig_break"
echo " type: integer"
echo " Number of contiguous Ns to signify a break between contigs in BBTools"
echo " analysis."
echo ""
echo " --limit"
echo " type: integer"
echo " Number of candidate regions (contig or transcript) from the BLAST output"
echo " to consider per BUSCO."
echo " This option is only effective in pipelines using BLAST, i.e. the genome"
echo " pipeline (see --augustus) or the prokaryota transcriptome pipeline."
echo ""
echo " --scaffold_composition"
echo " type: boolean_true"
echo " Writes ACGTN content per scaffold to a file scaffold_composition.txt."
echo ""
echo "BLAST Settings:"
echo " --e_value"
echo " type: double"
echo " E-value cutoff for BLAST searches."
echo ""
echo "Protein Gene Prediction settings:"
echo " --miniprot"
echo " type: boolean_true"
echo " Use Miniprot gene predictor."
echo ""
echo "MetaEuk Settings:"
echo " --metaeuk"
echo " type: boolean_true"
echo " Use Metaeuk gene predictor."
echo ""
echo " --metaeuk_parameters"
echo " type: string"
echo " example: --max-overlap=15,--min-exon-aa=15"
echo " Pass additional arguments to Metaeuk for the first run (see Metaeuk"
echo " documentation https://github.com/soedinglab/metaeuk)."
echo " All parameters should be contained within a single string with no white"
echo " space, with each parameter separated by a comma."
echo ""
echo " --metaeuk_rerun_parameters"
echo " type: string"
echo " example: --max-overlap=15,--min-exon-aa=15"
echo " Pass additional arguments to Metaeuk for the second run (see Metaeuk"
echo " documentation https://github.com/soedinglab/metaeuk)."
echo " All parameters should be contained within a single string with no white"
echo " space, with each parameter separated by a comma."
}
# initialise variables
VIASH_MODE='run'
@@ -632,9 +452,9 @@ 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="2024-12-03T10:34:00Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -749,6 +569,212 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "busco_run main"
echo ""
echo "Assessment of genome assembly and annotation completeness with single copy"
echo "orthologs"
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " example: file.fasta"
echo " Input sequence file in FASTA format. Can be an assembled genome or"
echo " transcriptome (DNA), or protein sequences from an annotated gene set."
echo " Also possible to use a path to a directory containing multiple input"
echo " files."
echo ""
echo " -m, --mode"
echo " type: string, required parameter"
echo " example: proteins"
echo " choices: [ genome, geno, transcriptome, tran, proteins, prot ]"
echo " Specify which BUSCO analysis mode to run. There are three valid modes:"
echo " - geno or genome, for genome assemblies (DNA)"
echo " - tran or transcriptome, for transcriptome assemblies (DNA)"
echo " - prot or proteins, for annotated gene sets (protein)"
echo ""
echo " -l, --lineage_dataset"
echo " type: string"
echo " example: stramenopiles_odb10"
echo " Specify a BUSCO lineage dataset that is most closely related to the"
echo " assembly or gene set being assessed."
echo " The full list of available datasets can be viewed"
echo " [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
echo " busco/busco_list_datasets component."
echo " When unsure, the \"--auto_lineage\" flag can be set to automatically find"
echo " the optimal lineage path."
echo " BUSCO will automatically download the requested dataset if it is not"
echo " already present in the download folder."
echo " You can optionally provide a path to a local dataset instead of a name,"
echo " e.g. path/to/dataset."
echo " Datasets can be downloaded using the busco/busco_download_dataset"
echo " component."
echo ""
echo "Outputs:"
echo " --short_summary_json"
echo " type: file, output, file must exist"
echo " example: short_summary.json"
echo " Output file for short summary in JSON format."
echo ""
echo " --short_summary_txt"
echo " type: file, output, file must exist"
echo " example: short_summary.txt"
echo " Output file for short summary in TXT format."
echo ""
echo " --full_table"
echo " type: file, output, file must exist"
echo " example: full_table.tsv"
echo " Full table output in TSV format."
echo ""
echo " --missing_busco_list"
echo " type: file, output, file must exist"
echo " example: missing_busco_list.tsv"
echo " Missing list output in TSV format."
echo ""
echo " --output_dir"
echo " type: file, output, file must exist"
echo " example: output_dir"
echo " The full output directory, if so desired."
echo ""
echo "Resource and Run Settings:"
echo " --force"
echo " type: boolean_true"
echo " Force rewriting of existing files. Must be used when output files with"
echo " the provided name already exist."
echo ""
echo " -q, --quiet"
echo " type: boolean_true"
echo " Disable the info logs, displays only errors."
echo ""
echo " -r, --restart"
echo " type: boolean_true"
echo " Continue a run that had already partially completed. Restarting skips"
echo " calls to tools that have completed but performs all pre- and"
echo " post-processing steps."
echo ""
echo " --tar"
echo " type: boolean_true"
echo " Compress some subdirectories with many files to save space."
echo ""
echo "Lineage Dataset Settings:"
echo " --auto_lineage"
echo " type: boolean_true"
echo " Run auto-lineage pipelilne to automatically determine BUSCO lineage"
echo " dataset that is most closely related to the assembly or gene set being"
echo " assessed."
echo ""
echo " --auto_lineage_euk"
echo " type: boolean_true"
echo " Run auto-placement just on eukaryota tree to find optimal lineage path."
echo ""
echo " --auto_lineage_prok"
echo " type: boolean_true"
echo " Run auto_lineage just on prokaryota trees to find optimum lineage path."
echo ""
echo " --datasets_version"
echo " type: string"
echo " example: odb10"
echo " Specify the version of BUSCO datasets"
echo ""
echo "Augustus Settings:"
echo " --augustus"
echo " type: boolean_true"
echo " Use augustus gene predictor for eukaryote runs."
echo ""
echo " --augustus_parameters"
echo " type: string"
echo " example: --PARAM1=VALUE1,--PARAM2=VALUE2"
echo " Additional parameters to be passed to Augustus (see Augustus"
echo " documentation:"
echo " "
echo "https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md)."
echo " Parameters should be contained within a single string, without"
echo " whitespace and seperated by commas."
echo ""
echo " --augustus_species"
echo " type: string"
echo " Specify the augustus species"
echo ""
echo " --long"
echo " type: boolean_true"
echo " Optimize Augustus self-training mode. This adds considerably to the run"
echo " time, but can improve results for some non-model organisms."
echo ""
echo "BBTools Settings:"
echo " --contig_break"
echo " type: integer"
echo " Number of contiguous Ns to signify a break between contigs in BBTools"
echo " analysis."
echo ""
echo " --limit"
echo " type: integer"
echo " Number of candidate regions (contig or transcript) from the BLAST output"
echo " to consider per BUSCO."
echo " This option is only effective in pipelines using BLAST, i.e. the genome"
echo " pipeline (see --augustus) or the prokaryota transcriptome pipeline."
echo ""
echo " --scaffold_composition"
echo " type: boolean_true"
echo " Writes ACGTN content per scaffold to a file scaffold_composition.txt."
echo ""
echo "BLAST Settings:"
echo " --e_value"
echo " type: double"
echo " E-value cutoff for BLAST searches."
echo ""
echo "Protein Gene Prediction settings:"
echo " --miniprot"
echo " type: boolean_true"
echo " Use Miniprot gene predictor."
echo ""
echo "MetaEuk Settings:"
echo " --metaeuk"
echo " type: boolean_true"
echo " Use Metaeuk gene predictor."
echo ""
echo " --metaeuk_parameters"
echo " type: string"
echo " example: --max-overlap=15,--min-exon-aa=15"
echo " Pass additional arguments to Metaeuk for the first run (see Metaeuk"
echo " documentation https://github.com/soedinglab/metaeuk)."
echo " All parameters should be contained within a single string with no white"
echo " space, with each parameter separated by a comma."
echo ""
echo " --metaeuk_rerun_parameters"
echo " type: string"
echo " example: --max-overlap=15,--min-exon-aa=15"
echo " Pass additional arguments to Metaeuk for the second run (see Metaeuk"
echo " documentation https://github.com/soedinglab/metaeuk)."
echo " All parameters should be contained within a single string with no white"
echo " space, with each parameter separated by a comma."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''