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Build branch main with version main (64aad6a)

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Build pipeline: viash-hub.rnaseq.main-4gbdz

Source commit: 64aad6a006

Source message: Merge pull request #22 from viash-hub/define_repositories_in_package_config

define dependency repositories once in the package config
This commit is contained in:
CI
2024-09-14 09:49:51 +00:00
parent 92b5a42360
commit 9b29e37466
237 changed files with 3667 additions and 685 deletions
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17
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
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@@ -443,6 +443,10 @@ repositories:
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -518,8 +522,8 @@ build_info:
output: "target/executable/workflows/genome_alignment_and_quant"
executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
@@ -537,6 +541,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

22
target/executable/workflows/merge_quant_results/.config.vsh.yaml
View File

@@ -194,6 +194,15 @@ dependencies:
- name: "summarizedexperiment"
repository:
type: "local"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -269,8 +278,8 @@ build_info:
output: "target/executable/workflows/merge_quant_results"
executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"
@@ -281,6 +290,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

17
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -407,6 +407,10 @@ repositories:
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -482,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
@@ -501,6 +505,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

17
target/executable/workflows/pre_processing/.config.vsh.yaml
View File

@@ -565,6 +565,10 @@ repositories:
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -640,8 +644,8 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"
@@ -657,6 +661,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

23
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -369,7 +369,7 @@ dependencies:
- name: "gffread"
repository:
type: "vsh"
repo: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "cat_additional_fasta"
repository:
@@ -386,7 +386,7 @@ dependencies:
- name: "rsem/rsem_prepare_reference"
repository:
type: "vsh"
repo: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "getchromsizes"
repository:
@@ -399,7 +399,7 @@ dependencies:
- name: "star/star_genome_generate"
repository:
type: "vsh"
repo: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "bbmap_bbsplit"
repository:
@@ -407,7 +407,7 @@ dependencies:
- name: "salmon/salmon_index"
repository:
type: "vsh"
repo: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "kallisto/kallisto_index"
repository:
@@ -415,7 +415,7 @@ dependencies:
repositories:
- type: "vsh"
name: "biobox"
repo: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
@@ -496,8 +496,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
@@ -518,6 +518,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

17
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
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@@ -206,6 +206,10 @@ repositories:
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -281,8 +285,8 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"
@@ -292,6 +296,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

17
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -1513,6 +1513,10 @@ repositories:
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -1588,8 +1592,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"
@@ -1614,6 +1618,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"

22
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -1881,6 +1881,15 @@ dependencies:
- name: "workflows/quality_control"
repository:
type: "local"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -1956,8 +1965,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"
@@ -1972,6 +1981,15 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"