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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/rseqc/rseqc_bamstat/.config.vsh.yaml
View File

@@ -68,6 +68,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -174,16 +177,16 @@ build_info:
engine: "docker|native"
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
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:

76
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
View File

@@ -2,7 +2,7 @@
# rseqc_bamstat 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.
#
@@ -172,28 +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 "rseqc_bamstat main"
echo ""
echo "Generate statistics from a bam file."
echo ""
echo "Input:"
echo " -i, --input_file"
echo " type: file, required parameter, file must exist"
echo " Input alignment file in BAM or SAM format."
echo ""
echo " -q, --mapq"
echo " type: integer"
echo " example: 30"
echo " Minimum mapping quality (phred scaled) to determine uniquely mapped"
echo " reads. Default: '30'."
echo ""
echo "Output:"
echo " --output"
echo " type: file, output, file must exist"
echo " Output file (txt) with mapping quality statistics."
}
# initialise variables
VIASH_MODE='run'
@@ -477,9 +455,9 @@ RUN echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/s
LABEL org.opencontainers.image.authors="Emma Rousseau"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -594,6 +572,54 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "rseqc_bamstat main"
echo ""
echo "Generate statistics from a bam file."
echo ""
echo "Input:"
echo " -i, --input_file"
echo " type: file, required parameter, file must exist"
echo " Input alignment file in BAM or SAM format."
echo ""
echo " -q, --mapq"
echo " type: integer"
echo " example: 30"
echo " Minimum mapping quality (phred scaled) to determine uniquely mapped"
echo " reads. Default: '30'."
echo ""
echo "Output:"
echo " --output"
echo " type: file, output, file must exist"
echo " Output file (txt) with mapping quality statistics."
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/rseqc/rseqc_inferexperiment/.config.vsh.yaml
View File

@@ -96,6 +96,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -200,16 +203,16 @@ build_info:
engine: "docker|native"
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
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:

98
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
View File

@@ -2,7 +2,7 @@
# rseqc_inferexperiment 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.
#
@@ -172,39 +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 "rseqc_inferexperiment main"
echo ""
echo "Infer strandedness from sequencing reads"
echo ""
echo "Input:"
echo " -i, --input_file"
echo " type: file, required parameter, file must exist"
echo " input alignment file in BAM or SAM format"
echo ""
echo " -r, --refgene"
echo " type: file, required parameter, file must exist"
echo " Reference gene model in bed format"
echo ""
echo "Output:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: \$id.strandedness.txt"
echo " Output file (txt) of strandness report."
echo ""
echo "Options:"
echo " -s, --sample_size"
echo " type: integer"
echo " example: 200000"
echo " Number of reads sampled from SAM/BAM file. Default: 200000"
echo ""
echo " -q, --mapq"
echo " type: integer"
echo " example: 30"
echo " Minimum mapping quality (phred scaled) to determine uniquely mapped"
echo " reads. Default: 30"
}
# initialise variables
VIASH_MODE='run'
@@ -488,9 +455,9 @@ RUN echo "RSeQC - infer_experiment.py: $(infer_experiment.py --version | cut -d'
LABEL org.opencontainers.image.authors="Emma Rousseau"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -605,6 +572,65 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "rseqc_inferexperiment main"
echo ""
echo "Infer strandedness from sequencing reads"
echo ""
echo "Input:"
echo " -i, --input_file"
echo " type: file, required parameter, file must exist"
echo " input alignment file in BAM or SAM format"
echo ""
echo " -r, --refgene"
echo " type: file, required parameter, file must exist"
echo " Reference gene model in bed format"
echo ""
echo "Output:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: \$id.strandedness.txt"
echo " Output file (txt) of strandness report."
echo ""
echo "Options:"
echo " -s, --sample_size"
echo " type: integer"
echo " example: 200000"
echo " Number of reads sampled from SAM/BAM file. Default: 200000"
echo ""
echo " -q, --mapq"
echo " type: integer"
echo " example: 30"
echo " Minimum mapping quality (phred scaled) to determine uniquely mapped"
echo " reads. Default: 30"
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/rseqc/rseqc_inner_distance/.config.vsh.yaml
View File

@@ -185,6 +185,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -293,16 +296,16 @@ build_info:
engine: "docker|native"
output: "target/executable/rseqc/rseqc_inner_distance"
executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance"
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:

178
target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance
View File

@@ -2,7 +2,7 @@
# rseqc_inner_distance 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.
#
@@ -172,79 +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 "rseqc_inner_distance main"
echo ""
echo "Calculate inner distance between read pairs."
echo ""
echo "Input:"
echo " -i, --input_file"
echo " type: file, required parameter, file must exist"
echo " input alignment file in BAM or SAM format"
echo ""
echo " -r, --refgene"
echo " type: file, required parameter, file must exist"
echo " Reference gene model in bed format"
echo ""
echo " -k, --sample_size"
echo " type: integer"
echo " example: 1000000"
echo " Numer of reads sampled from SAM/BAM file, default = 1000000."
echo ""
echo " -q, --mapq"
echo " type: integer"
echo " example: 30"
echo " Minimum mapping quality (phred scaled) to determine uniquely mapped"
echo " reads, default=30."
echo ""
echo " -l, --lower_bound"
echo " type: integer"
echo " example: -250"
echo " Lower bound of inner distance (bp). This option is used for ploting"
echo " histograme, default=-250."
echo ""
echo " -u, --upper_bound"
echo " type: integer"
echo " example: 250"
echo " Upper bound of inner distance (bp). This option is used for ploting"
echo " histograme, default=250."
echo ""
echo " -s, --step"
echo " type: integer"
echo " example: 5"
echo " Step size (bp) of histograme. This option is used for plotting"
echo " histogram, default=5."
echo ""
echo "Output:"
echo " -o, --output_prefix"
echo " type: string, required parameter"
echo " Rrefix of output files."
echo ""
echo " --output_stats"
echo " type: file, output, file must exist"
echo " output file (txt) with summary statistics of inner distances of paired"
echo " reads"
echo ""
echo " --output_dist"
echo " type: file, output, file must exist"
echo " output file (txt) with inner distances of all paired reads"
echo ""
echo " --output_freq"
echo " type: file, output, file must exist"
echo " output file (txt) with frequencies of inner distances of all paired"
echo " reads"
echo ""
echo " --output_plot"
echo " type: file, output, file must exist"
echo " output file (pdf) with histogram plot of of inner distances of all"
echo " paired reads"
echo ""
echo " --output_plot_r"
echo " type: file, output, file must exist"
echo " output file (R) with script of histogram plot of of inner distances of"
echo " all paired reads"
}
# initialise variables
VIASH_MODE='run'
@@ -532,9 +459,9 @@ RUN echo "RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' ' -
LABEL org.opencontainers.image.authors="Emma Rousseau"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inner_distance"
LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -649,6 +576,105 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "rseqc_inner_distance main"
echo ""
echo "Calculate inner distance between read pairs."
echo ""
echo "Input:"
echo " -i, --input_file"
echo " type: file, required parameter, file must exist"
echo " input alignment file in BAM or SAM format"
echo ""
echo " -r, --refgene"
echo " type: file, required parameter, file must exist"
echo " Reference gene model in bed format"
echo ""
echo " -k, --sample_size"
echo " type: integer"
echo " example: 1000000"
echo " Numer of reads sampled from SAM/BAM file, default = 1000000."
echo ""
echo " -q, --mapq"
echo " type: integer"
echo " example: 30"
echo " Minimum mapping quality (phred scaled) to determine uniquely mapped"
echo " reads, default=30."
echo ""
echo " -l, --lower_bound"
echo " type: integer"
echo " example: -250"
echo " Lower bound of inner distance (bp). This option is used for ploting"
echo " histograme, default=-250."
echo ""
echo " -u, --upper_bound"
echo " type: integer"
echo " example: 250"
echo " Upper bound of inner distance (bp). This option is used for ploting"
echo " histograme, default=250."
echo ""
echo " -s, --step"
echo " type: integer"
echo " example: 5"
echo " Step size (bp) of histograme. This option is used for plotting"
echo " histogram, default=5."
echo ""
echo "Output:"
echo " -o, --output_prefix"
echo " type: string, required parameter"
echo " Rrefix of output files."
echo ""
echo " --output_stats"
echo " type: file, output, file must exist"
echo " output file (txt) with summary statistics of inner distances of paired"
echo " reads"
echo ""
echo " --output_dist"
echo " type: file, output, file must exist"
echo " output file (txt) with inner distances of all paired reads"
echo ""
echo " --output_freq"
echo " type: file, output, file must exist"
echo " output file (txt) with frequencies of inner distances of all paired"
echo " reads"
echo ""
echo " --output_plot"
echo " type: file, output, file must exist"
echo " output file (pdf) with histogram plot of of inner distances of all"
echo " paired reads"
echo ""
echo " --output_plot_r"
echo " type: file, output, file must exist"
echo " output file (R) with script of histogram plot of of inner distances of"
echo " all paired reads"
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=''