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Build branch main with version main (5fbd530)

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

Source commit: 5fbd530a7c

Source message: add arguments to skip qc components
This commit is contained in:
CI
2024-11-13 10:26:31 +00:00
parent fe41adb0c7
commit bc17b94cd5
228 changed files with 846 additions and 656 deletions
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4
target/executable/bbmap_bbsplit/.config.vsh.yaml
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@@ -238,8 +238,8 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
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@@ -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="2024-10-25T08:58:48Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/bedtools_genomecov/.config.vsh.yaml
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@@ -178,8 +178,8 @@ build_info:
output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/bedtools_genomecov/bedtools_genomecov
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@@ -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="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/cat_additional_fasta/.config.vsh.yaml
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@@ -182,8 +182,8 @@ build_info:
output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/cat_additional_fasta/cat_additional_fasta
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@@ -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="2024-10-25T08:58:38Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/cat_fastq/.config.vsh.yaml
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@@ -169,8 +169,8 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/cat_fastq/cat_fastq
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@@ -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="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

7
target/executable/deseq2_qc/.config.vsh.yaml
View File

@@ -222,10 +222,9 @@ engines:
- "RColorBrewer"
- "pheatmap"
- "stringr"
- "matrixStats"
bioc:
- "DESeq2"
url:
- "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"
bioc_force_install: false
entrypoint: []
cmd: null
@@ -238,8 +237,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

9
target/executable/deseq2_qc/deseq2_qc
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@@ -503,13 +503,12 @@ ENTRYPOINT []
RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
Rscript -e 'if (!requireNamespace("DESeq2", quietly = TRUE)) BiocManager::install("DESeq2")' && \
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr"), repos = "https://cran.rstudio.com")' && \
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")'
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/dupradar/.config.vsh.yaml
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@@ -266,8 +266,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/dupradar/dupradar
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@@ -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="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/fastqc/.config.vsh.yaml
View File

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/fastqc/fastqc
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@@ -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="2024-10-25T08:58:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/fq_subsample/.config.vsh.yaml
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@@ -177,8 +177,8 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/getchromsizes/.config.vsh.yaml
View File

@@ -167,8 +167,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/gtf2bed/.config.vsh.yaml
View File

@@ -145,8 +145,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/gtf2bed/gtf2bed
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@@ -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="2024-10-25T08:58:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/gtf_filter/.config.vsh.yaml
View File

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/gunzip/.config.vsh.yaml
View File

@@ -144,8 +144,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/kallisto/kallisto_index/.config.vsh.yaml
View File

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/kallisto/kallisto_quant/.config.vsh.yaml
View File

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/multiqc_custom_biotype/.config.vsh.yaml
View File

@@ -161,8 +161,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -476,9 +476,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -207,8 +207,8 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/prepare_multiqc_input/.config.vsh.yaml
View File

@@ -409,8 +409,8 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
View File

@@ -138,8 +138,8 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/preseq_lcextrap/.config.vsh.yaml
View File

@@ -191,8 +191,8 @@ build_info:
output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/qualimap/.config.vsh.yaml
View File

@@ -271,8 +271,8 @@ build_info:
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
View File

@@ -299,8 +299,8 @@ 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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

@@ -542,9 +542,9 @@ 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="2024-10-25T08:58:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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

@@ -483,9 +483,9 @@ 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="2024-10-25T08:58:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
View File

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
View File

@@ -186,8 +186,8 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
View File

@@ -272,8 +272,8 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
View File

@@ -260,8 +260,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
View File

@@ -249,8 +249,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
View File

@@ -162,8 +162,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
View File

@@ -211,8 +211,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
View File

@@ -214,8 +214,8 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/sortmerna/.config.vsh.yaml
View File

@@ -192,8 +192,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/sortmerna/sortmerna
View File

@@ -486,9 +486,9 @@ function ViashDockerfile {
FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stringtie/.config.vsh.yaml
View File

@@ -216,8 +216,8 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/summarizedexperiment/.config.vsh.yaml
View File

@@ -199,8 +199,8 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/trimgalore/.config.vsh.yaml
View File

@@ -788,8 +788,8 @@ build_info:
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/tx2gene/.config.vsh.yaml
View File

@@ -192,8 +192,8 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/tximport/.config.vsh.yaml
View File

@@ -247,8 +247,8 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:38Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/ucsc/bedclip/.config.vsh.yaml
View File

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
View File

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/umitools/umitools_dedup/.config.vsh.yaml
View File

@@ -195,8 +195,8 @@ build_info:
output: "target/executable/umitools/umitools_dedup"
executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/umitools/umitools_extract/.config.vsh.yaml
View File

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/umitools/umitools_extract"
executable: "target/executable/umitools/umitools_extract/umitools_extract"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/umitools_prepareforquant/.config.vsh.yaml
View File

@@ -156,8 +156,8 @@ build_info:
output: "target/executable/umitools_prepareforquant"
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -603,8 +603,8 @@ 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

4
target/executable/workflows/merge_quant_results/.config.vsh.yaml
View File

@@ -278,8 +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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

4
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -486,8 +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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

4
target/executable/workflows/pre_processing/.config.vsh.yaml
View File

@@ -673,8 +673,8 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

4
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"

4
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
View File

@@ -283,8 +283,8 @@ 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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

20
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -213,6 +213,22 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--skip_dupradar"
info: null
direction: "input"
- type: "boolean_true"
name: "--skip_qualimap"
info: null
direction: "input"
- type: "boolean_true"
name: "--skip_rseqc"
info: null
direction: "input"
- type: "boolean_true"
name: "--skip_multiqc"
info: null
direction: "input"
- type: "boolean"
name: "--skip_preseq"
info: null
@@ -1556,8 +1572,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"

102
target/executable/workflows/quality_control/quality_control
View File

@@ -270,6 +270,18 @@ function ViashHelp {
echo " --skip_pseudo_align"
echo " type: boolean"
echo ""
echo " --skip_dupradar"
echo " type: boolean_true"
echo ""
echo " --skip_qualimap"
echo " type: boolean_true"
echo ""
echo " --skip_rseqc"
echo " type: boolean_true"
echo ""
echo " --skip_multiqc"
echo " type: boolean_true"
echo ""
echo " --skip_preseq"
echo " type: boolean"
echo " default: false"
@@ -1063,6 +1075,26 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_SKIP_PSEUDO_ALIGN=$(ViashRemoveFlags "$1")
shift 1
;;
--skip_dupradar)
[ -n "$VIASH_PAR_SKIP_DUPRADAR" ] && ViashError Bad arguments for option \'--skip_dupradar\': \'$VIASH_PAR_SKIP_DUPRADAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_DUPRADAR=true
shift 1
;;
--skip_qualimap)
[ -n "$VIASH_PAR_SKIP_QUALIMAP" ] && ViashError Bad arguments for option \'--skip_qualimap\': \'$VIASH_PAR_SKIP_QUALIMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_QUALIMAP=true
shift 1
;;
--skip_rseqc)
[ -n "$VIASH_PAR_SKIP_RSEQC" ] && ViashError Bad arguments for option \'--skip_rseqc\': \'$VIASH_PAR_SKIP_RSEQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_RSEQC=true
shift 1
;;
--skip_multiqc)
[ -n "$VIASH_PAR_SKIP_MULTIQC" ] && ViashError Bad arguments for option \'--skip_multiqc\': \'$VIASH_PAR_SKIP_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_MULTIQC=true
shift 1
;;
--skip_preseq)
[ -n "$VIASH_PAR_SKIP_PRESEQ" ] && ViashError Bad arguments for option \'--skip_preseq\': \'$VIASH_PAR_SKIP_PRESEQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_PRESEQ="$2"
@@ -2404,6 +2436,18 @@ fi
if [ -z ${VIASH_PAR_SKIP_ALIGN+x} ]; then
VIASH_PAR_SKIP_ALIGN="false"
fi
if [ -z ${VIASH_PAR_SKIP_DUPRADAR+x} ]; then
VIASH_PAR_SKIP_DUPRADAR="false"
fi
if [ -z ${VIASH_PAR_SKIP_QUALIMAP+x} ]; then
VIASH_PAR_SKIP_QUALIMAP="false"
fi
if [ -z ${VIASH_PAR_SKIP_RSEQC+x} ]; then
VIASH_PAR_SKIP_RSEQC="false"
fi
if [ -z ${VIASH_PAR_SKIP_MULTIQC+x} ]; then
VIASH_PAR_SKIP_MULTIQC="false"
fi
if [ -z ${VIASH_PAR_SKIP_PRESEQ+x} ]; then
VIASH_PAR_SKIP_PRESEQ="false"
fi
@@ -2747,6 +2791,30 @@ if [[ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGN" ]]; then
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_DUPRADAR" ]]; then
if ! [[ "$VIASH_PAR_SKIP_DUPRADAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_QUALIMAP" ]]; then
if ! [[ "$VIASH_PAR_SKIP_QUALIMAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_qualimap' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_RSEQC" ]]; then
if ! [[ "$VIASH_PAR_SKIP_RSEQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_MULTIQC" ]]; then
if ! [[ "$VIASH_PAR_SKIP_MULTIQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_PRESEQ" ]]; then
if ! [[ "$VIASH_PAR_SKIP_PRESEQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_preseq' has to be a boolean. Use "--help" to get more information on the parameters.
@@ -3305,7 +3373,7 @@ workflow run_wf {
}
| featurecounts.run (
runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf },
runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf && !state.skip_align },
fromState: [
"paired": "paired",
"strand": "strand",
@@ -3326,7 +3394,7 @@ workflow run_wf {
)
| multiqc_custom_biotype.run (
runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts },
runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align },
fromState: [
"id": "id",
"biocounts": "featurecounts",
@@ -3339,7 +3407,7 @@ workflow run_wf {
)
| preseq_lcextrap.run (
runIf: { id, state -> !state.skip_qc && !state.skip_preseq },
runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align },
fromState: [
"paired": "paired",
"input": "genome_bam",
@@ -3349,7 +3417,7 @@ workflow run_wf {
)
| rseqc_bamstat.run (
runIf: { id, state -> "bam_stat" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align },
fromState: [
"input": "genome_bam",
"map_qual": "map_qual"
@@ -3357,7 +3425,7 @@ workflow run_wf {
toState: [ "bamstat_output": "output" ]
)
| rseqc_inferexperiment.run(
runIf: { id, state -> "infer_experiment" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align },
fromState: [
"input": "genome_bam",
"refgene": "gene_bed",
@@ -3373,7 +3441,7 @@ workflow run_wf {
[ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ]
}
| rseqc_innerdistance.run(
runIf: { id, state -> state.paired && "inner_distance" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align },
key: "inner_distance",
fromState: [
"input": "genome_bam",
@@ -3393,7 +3461,7 @@ workflow run_wf {
]
)
| rseqc_junctionannotation.run(
runIf: { id, state -> "junction_annotation" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align },
fromState: [
"input": "genome_bam",
"refgene": "gene_bed",
@@ -3411,7 +3479,7 @@ workflow run_wf {
]
)
| rseqc_junctionsaturation.run(
runIf: { id, state -> "junction_saturation" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align },
fromState: [
"input": "genome_bam",
"refgene": "gene_bed",
@@ -3428,7 +3496,7 @@ workflow run_wf {
]
)
| rseqc_readdistribution.run(
runIf: { id, state -> "read_distribution" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align },
fromState: [
"input": "genome_bam",
"refgene": "gene_bed",
@@ -3436,7 +3504,7 @@ workflow run_wf {
toState: [ "read_distribution_output": "output" ]
)
| rseqc_readduplication.run(
runIf: { id, state -> "read_duplication" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align },
fromState: [
"input": "genome_bam",
"read_count_upper_limit": "read_count_upper_limit",
@@ -3450,7 +3518,7 @@ workflow run_wf {
]
)
| rseqc_tin.run(
runIf: { id, state -> "tin" in state.rseqc_modules },
runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align },
fromState: [
"bam_input": "genome_bam",
"bai_input": "genome_bam_index",
@@ -3466,6 +3534,7 @@ workflow run_wf {
)
| dupradar.run(
runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align },
fromState: [
"id": "id",
"input": "genome_bam",
@@ -3485,6 +3554,7 @@ workflow run_wf {
)
| qualimap.run(
runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align },
fromState: [
"input": "genome_bam",
"gtf": "gtf",
@@ -3505,7 +3575,7 @@ workflow run_wf {
| toSortedList
| map { list ->
def ids = list.collect { id, state -> state.id }
def ids = list.collect { id, state -> id }
def strandedness = list.collect { id, state -> state.strandedness }
def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
@@ -3811,7 +3881,7 @@ workflow run_wf {
| deseq2_qc.run (
runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align },
fromState: [
"counts": "counts",
"counts": "pseudo_counts_gene_length_scaled",
"vst": "deseq2_vst",
"label": "pseudo_aligner"
],
@@ -3823,7 +3893,7 @@ workflow run_wf {
],
key: "deseq2_qc_pseuso_align_quant"
)
| niceView()
// Get list of samples that failed trimming, mapping, and strand check for MultiQC report
| map { id, state ->
def fail_trimming_header = ["Sample", "Reads after trimming"]
@@ -3846,7 +3916,7 @@ workflow run_wf {
fail_mapping_multiqc += tsv_data.join('\\n')
}
if (!state.passed_strand_check[i]) {
tsv_data = ([ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\\t')
tsv_data = ([state.ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\\t')
fail_strand_multiqc += tsv_data.join('\\n')
}
}
@@ -3866,6 +3936,7 @@ workflow run_wf {
}
| prepare_multiqc_input.run(
runIf: { id, state -> !state.skip_qc && !state.skip_multiqc },
fromState: [
"fail_trimming_multiqc": "fail_trimming_multiqc",
"fail_mapping_multiqc": "fail_mapping_multiqc",
@@ -3906,6 +3977,7 @@ workflow run_wf {
)
| multiqc.run (
runIf: { id, state -> !state.skip_qc && !state.skip_multiqc },
fromState: [
"title": "multiqc_title",
"input": "multiqc_input",

15
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -607,17 +607,22 @@ argument_groups:
info: null
direction: "input"
- type: "boolean_true"
name: "skip_dupradar"
name: "--skip_dupradar"
description: "Skip dupRadar."
info: null
direction: "input"
- type: "boolean_true"
name: "skip_rseqc"
name: "--skip_qualimap"
description: "Skip Qualimap."
info: null
direction: "input"
- type: "boolean_true"
name: "--skip_rseqc"
description: "Skip RSeQC."
info: null
direction: "input"
- type: "boolean_true"
name: "skip_multiqc"
name: "--skip_multiqc"
description: "Skip MultiQC."
info: null
direction: "input"
@@ -2077,8 +2082,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

66
target/executable/workflows/rnaseq/rnaseq
View File

@@ -499,15 +499,19 @@ function ViashHelp {
echo " type: boolean_true"
echo " Skip DESeq2 PCA and heatmap plotting."
echo ""
echo " skip_dupradar"
echo " --skip_dupradar"
echo " type: boolean_true"
echo " Skip dupRadar."
echo ""
echo " skip_rseqc"
echo " --skip_qualimap"
echo " type: boolean_true"
echo " Skip Qualimap."
echo ""
echo " --skip_rseqc"
echo " type: boolean_true"
echo " Skip RSeQC."
echo ""
echo " skip_multiqc"
echo " --skip_multiqc"
echo " type: boolean_true"
echo " Skip MultiQC."
echo ""
@@ -1675,6 +1679,26 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_SKIP_DESEQ2_QC=true
shift 1
;;
--skip_dupradar)
[ -n "$VIASH_PAR_SKIP_DUPRADAR" ] && ViashError Bad arguments for option \'--skip_dupradar\': \'$VIASH_PAR_SKIP_DUPRADAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_DUPRADAR=true
shift 1
;;
--skip_qualimap)
[ -n "$VIASH_PAR_SKIP_QUALIMAP" ] && ViashError Bad arguments for option \'--skip_qualimap\': \'$VIASH_PAR_SKIP_QUALIMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_QUALIMAP=true
shift 1
;;
--skip_rseqc)
[ -n "$VIASH_PAR_SKIP_RSEQC" ] && ViashError Bad arguments for option \'--skip_rseqc\': \'$VIASH_PAR_SKIP_RSEQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_RSEQC=true
shift 1
;;
--skip_multiqc)
[ -n "$VIASH_PAR_SKIP_MULTIQC" ] && ViashError Bad arguments for option \'--skip_multiqc\': \'$VIASH_PAR_SKIP_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_MULTIQC=true
shift 1
;;
--extra_fq_subsample_args)
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="$2"
@@ -3059,20 +3083,6 @@ if [ -z "$VIASH_META_CPUS" ]; then
fi
# storing leftover values in positionals
if [[ $# -gt 0 ]]; then
VIASH_PAR_SKIP_DUPRADAR="$1"
shift 1
fi
if [[ $# -gt 0 ]]; then
VIASH_PAR_SKIP_RSEQC="$1"
shift 1
fi
if [[ $# -gt 0 ]]; then
VIASH_PAR_SKIP_MULTIQC="$1"
shift 1
fi
# check whether required parameters exist
if [ -z ${VIASH_PAR_ID+x} ]; then
ViashError '--id' is a required argument. Use "--help" to get more information on the parameters.
@@ -3235,6 +3245,9 @@ fi
if [ -z ${VIASH_PAR_SKIP_DUPRADAR+x} ]; then
VIASH_PAR_SKIP_DUPRADAR="false"
fi
if [ -z ${VIASH_PAR_SKIP_QUALIMAP+x} ]; then
VIASH_PAR_SKIP_QUALIMAP="false"
fi
if [ -z ${VIASH_PAR_SKIP_RSEQC+x} ]; then
VIASH_PAR_SKIP_RSEQC="false"
fi
@@ -3827,19 +3840,25 @@ if [[ -n "$VIASH_PAR_SKIP_DESEQ2_QC" ]]; then
fi
if [[ -n "$VIASH_PAR_SKIP_DUPRADAR" ]]; then
if ! [[ "$VIASH_PAR_SKIP_DUPRADAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError 'skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters.
ViashError '--skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_QUALIMAP" ]]; then
if ! [[ "$VIASH_PAR_SKIP_QUALIMAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_qualimap' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_RSEQC" ]]; then
if ! [[ "$VIASH_PAR_SKIP_RSEQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError 'skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters.
ViashError '--skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_MULTIQC" ]]; then
if ! [[ "$VIASH_PAR_SKIP_MULTIQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError 'skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters.
ViashError '--skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
@@ -4624,7 +4643,7 @@ workflow run_wf {
// Filter channels to get samples that passed STAR minimum mapping percentage
| map { id, state ->
def percent_mapped = getStarPercentMapped(state.star_multiqc)
def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0
def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false
[ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ]
}
@@ -4719,6 +4738,11 @@ workflow run_wf {
"strandedness": "strandedness",
"skip_align": "skip_alignment",
"skip_pseudo_align": "skip_pseudo_alignment",
"skip_dupradar": "skip_dupradar",
"skip_qualimap": "skip_qualimap",
"skip_rseqc": "skip_rseqc",
"skip_multiqc": "skip_multiqc",
"skip_preseq": "skip_preseq",
"gtf": "gtf",
"num_trimmed_reads": "num_trimmed_reads",
"passed_trimmed_reads": "passed_trimmed_reads",