vsh/rnaseq
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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
Download Patch File Download Diff File Expand all files Collapse all files

13
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -107,6 +107,9 @@ info:
- "modules/nf-core/picard/markduplicates/meta.yml"
last_sha: "55398de6ab7577acfe9b1180016a93d7af7eb859"
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -211,15 +214,15 @@ build_info:
engine: "docker|native"
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
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"
@@ -230,7 +233,7 @@ 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:

118
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -2,7 +2,7 @@
# picard_markduplicates 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.
#
@@ -169,48 +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 "picard_markduplicates main"
echo ""
echo "Locate and tag duplicate reads in a BAM file"
echo ""
echo "Input:"
echo " --bam"
echo " type: file, file must exist"
echo " Input BAM file"
echo ""
echo " --fasta"
echo " type: file, file must exist"
echo " Reference genome FASTA file"
echo ""
echo " --fai"
echo " type: file, file must exist"
echo " Reference genome FASTA index"
echo ""
echo " --extra_picard_args"
echo " type: string"
echo " default: --ASSUME_SORTED true --REMOVE_DUPLICATES false"
echo "--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
echo " Additional argument to be passed to Picard MarkDuplicates"
echo ""
echo "Output:"
echo " --output_bam"
echo " type: file, output, file must exist"
echo " default: \$id.MarkDuplicates.bam"
echo " BAM file with duplicate reads marked/removed"
echo ""
echo " --bai"
echo " type: file, output"
echo " default: \$id.MarkDuplicates.bam.bai"
echo " An optional BAM index file. If desired, --CREATE_INDEX must be passed as"
echo " a flag"
echo ""
echo " --metrics"
echo " type: file, output, file must exist"
echo " default: \$id.MarkDuplicates.metrics.txt"
echo " Duplicate metrics file generated by picard"
}
# initialise variables
VIASH_MODE='run'
@@ -494,9 +452,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
mv picard.jar /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
LABEL org.opencontainers.image.created="2024-12-05T14:40:08Z"
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="2025-05-06T19:18:30Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f52978a0e25cae182b7874b4b8aa3afc183e880e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -611,6 +569,74 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "picard_markduplicates main"
echo ""
echo "Locate and tag duplicate reads in a BAM file"
echo ""
echo "Input:"
echo " --bam"
echo " type: file, file must exist"
echo " Input BAM file"
echo ""
echo " --fasta"
echo " type: file, file must exist"
echo " Reference genome FASTA file"
echo ""
echo " --fai"
echo " type: file, file must exist"
echo " Reference genome FASTA index"
echo ""
echo " --extra_picard_args"
echo " type: string"
echo " default: --ASSUME_SORTED true --REMOVE_DUPLICATES false"
echo "--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
echo " Additional argument to be passed to Picard MarkDuplicates"
echo ""
echo "Output:"
echo " --output_bam"
echo " type: file, output, file must exist"
echo " default: \$id.MarkDuplicates.bam"
echo " BAM file with duplicate reads marked/removed"
echo ""
echo " --bai"
echo " type: file, output"
echo " default: \$id.MarkDuplicates.bam.bai"
echo " An optional BAM index file. If desired, --CREATE_INDEX must be passed as"
echo " a flag"
echo ""
echo " --metrics"
echo " type: file, output, file must exist"
echo " default: \$id.MarkDuplicates.metrics.txt"
echo " Duplicate metrics file generated by picard"
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=''