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Build branch main with version main (8f9353f)

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Build pipeline: viash-hub.craftbox.main-w5ngd

Source commit: 8f9353f15e

Source message: add documentation and bump viash (#9)
This commit is contained in:
CI
2025-04-08 07:56:01 +00:00
parent 249b9a0c8f
commit 953f3df186
28 changed files with 2101 additions and 504 deletions
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43
target/executable/csv2fasta/.config.vsh.yaml
View File

@@ -1,5 +1,36 @@
name: "csv2fasta"
version: "main"
authors:
- name: "Dries Schaumont"
roles:
- "author"
- "maintainer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Robrecht Cannoodt"
roles:
- "reviewer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
argument_groups:
- name: "Inputs"
arguments:
@@ -104,6 +135,7 @@ resources:
- type: "python_script"
path: "script.py"
is_executable: true
summary: "Convert a CSV file to FASTA entries"
description: "Convert two columns from a CSV file to FASTA entries. The CSV file can\n\
contain an optional header and each row (other than the header) becomes\na single\
\ FASTA record. One of the two columns will be used as the names\nfor the FASTA\
@@ -116,6 +148,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -221,16 +256,16 @@ build_info:
engine: "docker|native"
output: "target/executable/csv2fasta"
executable: "target/executable/csv2fasta/csv2fasta"
viash_version: "0.9.0"
git_commit: "3c8413009764e3a6839e3e8b038857caf7047593"
viash_version: "0.9.3"
git_commit: "8f9353f15e4d6952eca57e896f962a60b42b0a3c"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-3-g3c84130"
git_tag: "v0.1.0-4-g8f9353f"
package_config:
name: "craftbox"
version: "main"
description: "A collection of custom-tailored scripts and applied tools.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.3"
source: "src"
target: "target"
config_mods:

181
target/executable/csv2fasta/csv2fasta
View File

@@ -2,7 +2,7 @@
# csv2fasta 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 0.9.3 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -10,6 +10,10 @@
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
#
# Component authors:
# * Dries Schaumont (author, maintainer)
# * Robrecht Cannoodt (reviewer)
set -e
@@ -169,78 +173,6 @@ 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 "csv2fasta main"
echo ""
echo "Convert two columns from a CSV file to FASTA entries. The CSV file can"
echo "contain an optional header and each row (other than the header) becomes"
echo "a single FASTA record. One of the two columns will be used as the names"
echo "for the FASTA entries, while the other become the sequences. The sequences"
echo "column must only contain characters that are valid IUPAC notation for"
echo "nucleotides or a group thereof (wildcard characters)."
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " example: barcodes.csv"
echo " CSV file to be processed."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Parse the first line of the CSV file as a header."
echo ""
echo "CSV dialect options:"
echo " Options that can be used to override the automatically detected"
echo " dialect of the CSV file."
echo ""
echo " --delimiter"
echo " type: string"
echo " Overwrite the column delimiter character."
echo ""
echo " --quote_character"
echo " type: string"
echo " Overwrite the character used to denote the start and end of a quoted"
echo " item."
echo ""
echo "CSV column arguments:"
echo " Parameters for the selection of columns from the CSV file."
echo " Only required when your CSV file contains more than 2 columns,"
echo " otherwise the first column will be used for the FASTA header"
echo " and the second for the FASTA nucleotide sequences. This default"
echo " can still be overwritten by using the options below."
echo ""
echo " --sequence_column"
echo " type: string"
echo " Name of the column containing the sequences. Implies 'header'."
echo " Cannot be used together with 'sequence_column_index'."
echo ""
echo " --name_column"
echo " type: string"
echo " Name of the column describing the FASTA headers. Implies 'header'."
echo " Cannot be used together with 'name_column_index'."
echo ""
echo " --sequence_column_index"
echo " type: integer"
echo " min: 0"
echo " Index of the column to use as the FASTA sequences, counter from the left"
echo " and"
echo " starting from 0. Cannot be used in combination with the"
echo " 'sequence_column' argument."
echo ""
echo " --name_column_index"
echo " type: integer"
echo " min: 0"
echo " Index of the column to use as the FASTA headers, counter from the left"
echo " and"
echo " starting from 0. Cannot be used in combination with 'name_column'."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, output, file must exist"
echo " example: barcodes.fasta"
echo " Output fasta file."
}
# initialise variables
VIASH_MODE='run'
@@ -524,10 +456,11 @@ RUN apt-get update && \
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "dnaio"
LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
LABEL org.opencontainers.image.created="2025-04-08T07:25:22Z"
LABEL org.opencontainers.image.created="2025-04-08T07:49:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
LABEL org.opencontainers.image.revision="3c8413009764e3a6839e3e8b038857caf7047593"
LABEL org.opencontainers.image.revision="8f9353f15e4d6952eca57e896f962a60b42b0a3c"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -642,6 +575,104 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "csv2fasta main"
echo ""
echo "Convert two columns from a CSV file to FASTA entries. The CSV file can"
echo "contain an optional header and each row (other than the header) becomes"
echo "a single FASTA record. One of the two columns will be used as the names"
echo "for the FASTA entries, while the other become the sequences. The sequences"
echo "column must only contain characters that are valid IUPAC notation for"
echo "nucleotides or a group thereof (wildcard characters)."
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " example: barcodes.csv"
echo " CSV file to be processed."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Parse the first line of the CSV file as a header."
echo ""
echo "CSV dialect options:"
echo " Options that can be used to override the automatically detected"
echo " dialect of the CSV file."
echo ""
echo " --delimiter"
echo " type: string"
echo " Overwrite the column delimiter character."
echo ""
echo " --quote_character"
echo " type: string"
echo " Overwrite the character used to denote the start and end of a quoted"
echo " item."
echo ""
echo "CSV column arguments:"
echo " Parameters for the selection of columns from the CSV file."
echo " Only required when your CSV file contains more than 2 columns,"
echo " otherwise the first column will be used for the FASTA header"
echo " and the second for the FASTA nucleotide sequences. This default"
echo " can still be overwritten by using the options below."
echo ""
echo " --sequence_column"
echo " type: string"
echo " Name of the column containing the sequences. Implies 'header'."
echo " Cannot be used together with 'sequence_column_index'."
echo ""
echo " --name_column"
echo " type: string"
echo " Name of the column describing the FASTA headers. Implies 'header'."
echo " Cannot be used together with 'name_column_index'."
echo ""
echo " --sequence_column_index"
echo " type: integer"
echo " min: 0"
echo " Index of the column to use as the FASTA sequences, counter from the left"
echo " and"
echo " starting from 0. Cannot be used in combination with the"
echo " 'sequence_column' argument."
echo ""
echo " --name_column_index"
echo " type: integer"
echo " min: 0"
echo " Index of the column to use as the FASTA headers, counter from the left"
echo " and"
echo " starting from 0. Cannot be used in combination with 'name_column'."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, output, file must exist"
echo " example: barcodes.fasta"
echo " Output fasta file."
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=''