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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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22
target/executable/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -140,6 +140,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -229,14 +238,23 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
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"
package_config:
version: "main"
info:
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"

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-09-13T10:19:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/bedtools_genomecov/.config.vsh.yaml
View File

@@ -80,6 +80,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -169,14 +178,23 @@ build_info:
output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
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"
package_config:
version: "main"
info:
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"

6
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/cat_additional_fasta/.config.vsh.yaml
View File

@@ -90,6 +90,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -173,14 +182,23 @@ build_info:
output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
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"
package_config:
version: "main"
info:
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"

6
target/executable/cat_additional_fasta/cat_additional_fasta
View File

@@ -480,9 +480,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
LABEL org.opencontainers.image.created="2024-09-13T10:19:17Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/cat_fastq/.config.vsh.yaml
View File

@@ -77,6 +77,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -160,14 +169,23 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
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"
package_config:
version: "main"
info:
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"

6
target/executable/cat_fastq/cat_fastq
View File

@@ -472,9 +472,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/deseq2_qc/.config.vsh.yaml
View File

@@ -126,6 +126,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -228,14 +237,23 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
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"
package_config:
version: "main"
info:
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"

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-09-13T10:19:30Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/dupradar/.config.vsh.yaml
View File

@@ -165,6 +165,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -257,14 +266,23 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
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"
package_config:
version: "main"
info:
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"

6
target/executable/dupradar/dupradar
View File

@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
LABEL org.opencontainers.image.created="2024-09-13T10:19:19Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/fastqc/.config.vsh.yaml
View File

@@ -101,6 +101,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -189,14 +198,23 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
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"
package_config:
version: "main"
info:
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"

6
target/executable/fastqc/fastqc
View File

@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/fq_subsample/.config.vsh.yaml
View File

@@ -74,6 +74,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -168,14 +177,23 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
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"
package_config:
version: "main"
info:
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"

6
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/getchromsizes/.config.vsh.yaml
View File

@@ -67,6 +67,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -158,14 +167,23 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
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"
package_config:
version: "main"
info:
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"

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/gtf2bed/.config.vsh.yaml
View File

@@ -48,6 +48,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -136,14 +145,23 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
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"
package_config:
version: "main"
info:
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"

6
target/executable/gtf2bed/gtf2bed
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/gtf_filter/.config.vsh.yaml
View File

@@ -63,6 +63,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -146,14 +155,23 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
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"
package_config:
version: "main"
info:
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"

6
target/executable/gtf_filter/gtf_filter
View File

@@ -470,9 +470,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/gunzip/.config.vsh.yaml
View File

@@ -47,6 +47,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -135,14 +144,23 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
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"
package_config:
version: "main"
info:
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"

6
target/executable/gunzip/gunzip
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/kallisto/kallisto_index/.config.vsh.yaml
View File

@@ -56,6 +56,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -146,14 +155,23 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
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"
package_config:
version: "main"
info:
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"

6
target/executable/kallisto/kallisto_index/kallisto_index
View File

@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/kallisto/kallisto_quant/.config.vsh.yaml
View File

@@ -154,6 +154,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -244,14 +253,23 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_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"
package_config:
version: "main"
info:
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"

6
target/executable/kallisto/kallisto_quant/kallisto_quant
View File

@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/multiqc_custom_biotype/.config.vsh.yaml
View File

@@ -70,6 +70,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -161,14 +170,23 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
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"
package_config:
version: "main"
info:
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"

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -481,9 +481,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -107,6 +107,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -198,14 +207,23 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
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"
package_config:
version: "main"
info:
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"

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -494,9 +494,9 @@ 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="2024-09-13T10:19:29Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/prepare_multiqc_input/.config.vsh.yaml
View File

@@ -317,6 +317,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -400,14 +409,23 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
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"
package_config:
version: "main"
info:
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"

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -557,9 +557,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
View File

@@ -46,6 +46,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -129,14 +138,23 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
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"
package_config:
version: "main"
info:
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"

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -462,9 +462,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/preseq_lcextrap/.config.vsh.yaml
View File

@@ -67,6 +67,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -182,14 +191,23 @@ build_info:
output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
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"
package_config:
version: "main"
info:
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"

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -495,9 +495,9 @@ mkdir build && cd build && \
make && make install && make HAVE_HTSLIB=1 all
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/qualimap/.config.vsh.yaml
View File

@@ -158,6 +158,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -262,14 +271,23 @@ build_info:
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
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"
package_config:
version: "main"
info:
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"

6
target/executable/qualimap/qualimap
View File

@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
View File

@@ -181,6 +181,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -299,14 +308,23 @@ build_info:
output: "target/executable/rsem/rsem_calculate_expression"
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
View File

@@ -545,9 +545,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -110,6 +110,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -193,14 +202,23 @@ build_info:
output: "target/executable/rsem/rsem_merge_counts"
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rsem/rsem_merge_counts/rsem_merge_counts
View File

@@ -490,9 +490,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
View File

@@ -61,6 +61,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -154,14 +163,23 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
View File

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
View File

@@ -84,6 +84,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -177,14 +186,23 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
View File

@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
View File

@@ -169,6 +169,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -263,14 +272,23 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
View File

@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
View File

@@ -157,6 +157,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -251,14 +260,23 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
View File

@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
View File

@@ -146,6 +146,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -240,14 +249,23 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
View File

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-09-13T10:19:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
View File

@@ -60,6 +60,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -153,14 +162,23 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
View File

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
View File

@@ -108,6 +108,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -202,14 +211,23 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
View File

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
View File

@@ -114,6 +114,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -205,14 +214,23 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
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"
package_config:
version: "main"
info:
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"

6
target/executable/rseqc/rseqc_tin/rseqc_tin
View File

@@ -501,9 +501,9 @@ RUN apt-get update && \
RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-09-13T10:19:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/sortmerna/.config.vsh.yaml
View File

@@ -100,6 +100,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -189,14 +198,23 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
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"
package_config:
version: "main"
info:
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"

6
target/executable/sortmerna/sortmerna
View File

@@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
bash sortmerna-4.3.6-Linux.sh --skip-license
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/stringtie/.config.vsh.yaml
View File

@@ -117,6 +117,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -207,14 +216,23 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
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"
package_config:
version: "main"
info:
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"

6
target/executable/stringtie/stringtie
View File

@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/summarizedexperiment/.config.vsh.yaml
View File

@@ -96,6 +96,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -190,14 +199,23 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
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"
package_config:
version: "main"
info:
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"

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/trimgalore/.config.vsh.yaml
View File

@@ -683,6 +683,15 @@ status: "enabled"
requirements:
commands:
- "ps"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
keywords:
- "trimming"
- "adapters"
@@ -779,14 +788,23 @@ build_info:
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
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"
package_config:
version: "main"
info:
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"

4
target/executable/trimgalore/trimgalore
View File

@@ -858,9 +858,9 @@ ENTRYPOINT []
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/tx2gene/.config.vsh.yaml
View File

@@ -91,6 +91,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -183,14 +192,23 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
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"
package_config:
version: "main"
info:
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"

6
target/executable/tx2gene/tx2gene
View File

@@ -487,9 +487,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/tximport/.config.vsh.yaml
View File

@@ -139,6 +139,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -238,14 +247,23 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
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"
package_config:
version: "main"
info:
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"

6
target/executable/tximport/tximport
View File

@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e '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="2024-09-13T10:19:17Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/ucsc/bedclip/.config.vsh.yaml
View File

@@ -62,6 +62,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -155,14 +164,23 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
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"
package_config:
version: "main"
info:
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"

6
target/executable/ucsc/bedclip/bedclip
View File

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
View File

@@ -62,6 +62,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -155,14 +164,23 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
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"
package_config:
version: "main"
info:
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"

6
target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
View File

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/umitools/umitools_dedup/.config.vsh.yaml
View File

@@ -93,6 +93,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -186,14 +195,23 @@ build_info:
output: "target/executable/umitools/umitools_dedup"
executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
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"
package_config:
version: "main"
info:
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"

6
target/executable/umitools/umitools_dedup/umitools_dedup
View File

@@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/umitools/umitools_extract/.config.vsh.yaml
View File

@@ -151,6 +151,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -244,14 +253,23 @@ build_info:
output: "target/executable/umitools/umitools_extract"
executable: "target/executable/umitools/umitools_extract/umitools_extract"
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"
package_config:
version: "main"
info:
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"

6
target/executable/umitools/umitools_extract/umitools_extract
View File

@@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

22
target/executable/umitools_prepareforquant/.config.vsh.yaml
View File

@@ -53,6 +53,15 @@ status: "enabled"
requirements:
commands:
- "ps"
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"
@@ -147,14 +156,23 @@ build_info:
output: "target/executable/umitools_prepareforquant"
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
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"
package_config:
version: "main"
info:
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"

6
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" "pysam"
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -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
View File

@@ -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"