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Build branch main with version main (f52978a)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-k4ttq

Source commit: f52978a0e2

Source message: Fix summarizedexperiment build (#42)
This commit is contained in:
CI
2025-05-06 20:05:48 +00:00
parent d08ba5f5fa
commit c00bcda3f8
275 changed files with 31239 additions and 8651 deletions
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14
target/executable/tximport/.config.vsh.yaml
View File

@@ -143,6 +143,9 @@ info:
- "modules/local/tximport/main.nf"
last_sha: "489bcb4efdc7bd58839b22b0360d26b4d80b87a8"
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -245,6 +248,7 @@ engines:
- "tximport"
- "tximeta"
bioc_force_install: false
warnings_as_errors: true
entrypoint: []
cmd: null
- type: "native"
@@ -255,15 +259,15 @@ build_info:
engine: "docker|native"
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
viash_version: "0.9.2"
git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
git_remote: "https://github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
- path: "gs://viash-hub-resources/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
@@ -274,7 +278,7 @@ package_config:
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

148
target/executable/tximport/tximport
View File

@@ -2,7 +2,7 @@
# tximport 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.
#
@@ -169,57 +169,6 @@ 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 "tximport main"
echo ""
echo "Get dataframe linking transcript ID, gene ID, and gene name"
echo ""
echo "Input:"
echo " --quant_results"
echo " type: file, multiple values allowed, file must exist"
echo ""
echo " --tx2gene_tsv"
echo " type: file, file must exist"
echo ""
echo " --quant_type"
echo " type: string"
echo " choices: [ salmon, kallisto ]"
echo " Method used for quantification"
echo ""
echo "Output:"
echo " --tpm_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_tpm.tsv"
echo ""
echo " --counts_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_counts.tsv"
echo ""
echo " --counts_gene_length_scaled"
echo " type: file, output, file must exist"
echo " default: merged.gene_counts_length_scaled.tsv"
echo ""
echo " --counts_gene_scaled"
echo " type: file, output, file must exist"
echo " default: merged.gene_counts_scaled.tsv"
echo ""
echo " --lengths_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_lengths.tsv"
echo ""
echo " --tpm_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_tpm.tsv"
echo ""
echo " --counts_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_counts.tsv"
echo ""
echo " --lengths_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_lengths.tsv"
}
# initialise variables
VIASH_MODE='run'
@@ -500,17 +449,17 @@ RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y r-base libcurl4-openssl-dev libssl-dev libxml2-dev && \
rm -rf /var/lib/apt/lists/*
RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
Rscript -e 'if (!requireNamespace("SummarizedExperiment", quietly = TRUE)) BiocManager::install("SummarizedExperiment")' && \
Rscript -e 'if (!requireNamespace("tximport", quietly = TRUE)) BiocManager::install("tximport")' && \
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' && \
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
Rscript -e 'options(warn = 2); if (!requireNamespace("SummarizedExperiment", quietly = TRUE)) BiocManager::install("SummarizedExperiment")' && \
Rscript -e 'options(warn = 2); if (!requireNamespace("tximport", quietly = TRUE)) BiocManager::install("tximport")' && \
Rscript -e 'options(warn = 2); if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' && \
Rscript -e 'options(warn = 2); remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component tximport"
LABEL org.opencontainers.image.created="2024-12-05T14:40:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="2b3d511b34246648b934fd1dc99b22e0a71c37f2"
LABEL org.opencontainers.image.created="2025-05-06T19:18:29Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f52978a0e25cae182b7874b4b8aa3afc183e880e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -625,6 +574,83 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "tximport main"
echo ""
echo "Get dataframe linking transcript ID, gene ID, and gene name"
echo ""
echo "Input:"
echo " --quant_results"
echo " type: file, multiple values allowed, file must exist"
echo ""
echo " --tx2gene_tsv"
echo " type: file, file must exist"
echo ""
echo " --quant_type"
echo " type: string"
echo " choices: [ salmon, kallisto ]"
echo " Method used for quantification"
echo ""
echo "Output:"
echo " --tpm_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_tpm.tsv"
echo ""
echo " --counts_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_counts.tsv"
echo ""
echo " --counts_gene_length_scaled"
echo " type: file, output, file must exist"
echo " default: merged.gene_counts_length_scaled.tsv"
echo ""
echo " --counts_gene_scaled"
echo " type: file, output, file must exist"
echo " default: merged.gene_counts_scaled.tsv"
echo ""
echo " --lengths_gene"
echo " type: file, output, file must exist"
echo " default: merged.gene_lengths.tsv"
echo ""
echo " --tpm_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_tpm.tsv"
echo ""
echo " --counts_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_counts.tsv"
echo ""
echo " --lengths_transcript"
echo " type: file, output, file must exist"
echo " default: merged.transcript_lengths.tsv"
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=''