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Build branch build/main with version build_main (408cceb)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-cvdhc

Source commit: 408cceb53b

Source message: deploy: bbebaa1a26a30c55af33fa6818c12123f9fe4824
This commit is contained in:
CI
2025-08-27 16:53:33 +00:00
parent 5273fbdd05
commit 3de8c3ee6d
384 changed files with 3422 additions and 19655 deletions
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26
target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
View File

@@ -555,18 +555,14 @@ dependencies:
- name: "workflows/multiomics/process_samples"
alias: "spatial_sample_processing"
repository:
type: "github"
repo: "openpipelines-bio/openpipeline"
tag: "disable-scrublet_build"
type: "vsh"
repo: "openpipeline"
tag: "v3.0.0"
repositories:
- type: "github"
- type: "vsh"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
- type: "github"
name: "openpipeline_scrublet"
repo: "openpipelines-bio/openpipeline"
tag: "disable-scrublet_build"
repo: "openpipeline"
tag: "v3.0.0"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
docker_registry: "ghcr.io"
@@ -644,10 +640,10 @@ build_info:
output: "target/nextflow/workflows/multiomics/spatial_process_samples"
executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
viash_version: "0.9.4"
git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
git_commit: "408cceb53bfbdaeaf2029527c4c5071776db5e7b"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples"
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"
package_config:
name: "openpipeline_spatial"
version: "build_main"
@@ -657,10 +653,10 @@ package_config:
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
dest: "resources_test"
repositories:
- type: "github"
- type: "vsh"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
repo: "openpipeline"
tag: "v3.0.0"
viash_version: "0.9.4"
source: "src"
target: "target"

30
target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
View File

@@ -3705,24 +3705,18 @@ meta = [
"name" : "workflows/multiomics/process_samples",
"alias" : "spatial_sample_processing",
"repository" : {
"type" : "github",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "disable-scrublet_build"
"type" : "vsh",
"repo" : "openpipeline",
"tag" : "v3.0.0"
}
}
],
"repositories" : [
{
"type" : "github",
"type" : "vsh",
"name" : "openpipeline",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "2.1.2"
},
{
"type" : "github",
"name" : "openpipeline_scrublet",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "disable-scrublet_build"
"repo" : "openpipeline",
"tag" : "v3.0.0"
}
],
"links" : {
@@ -3813,7 +3807,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
"viash_version" : "0.9.4",
"git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
"git_commit" : "408cceb53bfbdaeaf2029527c4c5071776db5e7b",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3830,10 +3824,10 @@ meta = [
},
"repositories" : [
{
"type" : "github",
"type" : "vsh",
"name" : "openpipeline",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "2.1.2"
"repo" : "openpipeline",
"tag" : "v3.0.0"
}
],
"viash_version" : "0.9.4",
@@ -3856,7 +3850,7 @@ meta = [
// resolve dependencies dependencies (if any)
meta["root_dir"] = getRootDir()
include { process_samples as spatial_sample_processing_viashalias } from "${meta.root_dir}/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples/main.nf"
include { process_samples as spatial_sample_processing_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples/main.nf"
spatial_sample_processing = spatial_sample_processing_viashalias.run(key: "spatial_sample_processing")
// inner workflow
@@ -3921,7 +3915,7 @@ workflow run_wf {
"output": state.workflow_output
]},
args: [
"skip_scrublet_filtering": "true",
"skip_scrublet_doublet_detection": "true",
],
toState: [
"output": "output"

22
target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
View File

@@ -302,14 +302,14 @@ dependencies:
- name: "workflows/qc/qc"
alias: "spatial_qc_workflow"
repository:
type: "github"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
type: "vsh"
repo: "openpipeline"
tag: "v3.0.0"
repositories:
- type: "github"
- type: "vsh"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
repo: "openpipeline"
tag: "v3.0.0"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
docker_registry: "ghcr.io"
@@ -387,10 +387,10 @@ build_info:
output: "target/nextflow/workflows/qc/spatial_qc"
executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
viash_version: "0.9.4"
git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
git_commit: "408cceb53bfbdaeaf2029527c4c5071776db5e7b"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc"
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"
package_config:
name: "openpipeline_spatial"
version: "build_main"
@@ -400,10 +400,10 @@ package_config:
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
dest: "resources_test"
repositories:
- type: "github"
- type: "vsh"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
repo: "openpipeline"
tag: "v3.0.0"
viash_version: "0.9.4"
source: "src"
target: "target"

22
target/nextflow/workflows/qc/spatial_qc/main.nf
View File

@@ -3403,18 +3403,18 @@ meta = [
"name" : "workflows/qc/qc",
"alias" : "spatial_qc_workflow",
"repository" : {
"type" : "github",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "2.1.2"
"type" : "vsh",
"repo" : "openpipeline",
"tag" : "v3.0.0"
}
}
],
"repositories" : [
{
"type" : "github",
"type" : "vsh",
"name" : "openpipeline",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "2.1.2"
"repo" : "openpipeline",
"tag" : "v3.0.0"
}
],
"links" : {
@@ -3505,7 +3505,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
"viash_version" : "0.9.4",
"git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
"git_commit" : "408cceb53bfbdaeaf2029527c4c5071776db5e7b",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3522,10 +3522,10 @@ meta = [
},
"repositories" : [
{
"type" : "github",
"type" : "vsh",
"name" : "openpipeline",
"repo" : "openpipelines-bio/openpipeline",
"tag" : "2.1.2"
"repo" : "openpipeline",
"tag" : "v3.0.0"
}
],
"viash_version" : "0.9.4",
@@ -3548,7 +3548,7 @@ meta = [
// resolve dependencies dependencies (if any)
meta["root_dir"] = getRootDir()
include { qc as spatial_qc_workflow_viashalias } from "${meta.root_dir}/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc/main.nf"
include { qc as spatial_qc_workflow_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc/main.nf"
spatial_qc_workflow = spatial_qc_workflow_viashalias.run(key: "spatial_qc_workflow")
// inner workflow