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Build branch main with version main (d63250a)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-p26ls

Source commit: d63250ae70

Source message: add checks
This commit is contained in:
CI
2024-11-27 17:19:29 +00:00
parent 93ac6aad2e
commit b649544267
134 changed files with 294 additions and 291 deletions
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1
src/workflows/quality_control/main.nf
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@@ -202,6 +202,7 @@ workflow run_wf {
// TODO: Add outdir as an output argument to the qualimap module on biobox.
// Qualimap ouputs a few more raw data files to outdir but since the module is using a temporary directory as output dir these files are lost.
| qualimap_rnaseq.run(
runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align },
fromState: [
"bam": "genome_bam",
"gtf": "gtf",

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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:49Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/deseq2_qc/.config.vsh.yaml
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@@ -237,8 +237,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/deseq2_qc/deseq2_qc
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@@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
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="2024-11-27T11:43:49Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/getchromsizes/.config.vsh.yaml
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@@ -167,8 +167,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/getchromsizes/getchromsizes
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@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-11-27T11:43:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/gtf2bed/.config.vsh.yaml
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@@ -145,8 +145,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/gtf_filter/.config.vsh.yaml
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@@ -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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/gtf_filter/gtf_filter
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@@ -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="2024-11-27T11:43:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/gunzip/.config.vsh.yaml
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@@ -144,8 +144,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/gunzip/gunzip
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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 gunzip"
LABEL org.opencontainers.image.created="2024-11-27T11:43:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -165,8 +165,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:49Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
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@@ -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="2024-11-27T11:43:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -181,8 +181,8 @@ build_info:
output: "target/executable/rsem_merge_counts"
executable: "target/executable/rsem_merge_counts/rsem_merge_counts"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/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_merge_counts"
LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:48Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:49Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:49Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:48Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:48Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -185,8 +185,8 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/tx2gene/tx2gene
View File

@@ -483,9 +483,9 @@ 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="2024-11-27T11:43:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -251,8 +251,8 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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="2024-11-27T11:43:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -590,8 +590,8 @@ 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

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

@@ -477,8 +477,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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

@@ -632,8 +632,8 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract"

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

@@ -502,8 +502,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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

@@ -285,8 +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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant"

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

@@ -1554,8 +1554,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment"

1
target/executable/workflows/quality_control/quality_control
View File

@@ -3505,6 +3505,7 @@ workflow run_wf {
// TODO: Add outdir as an output argument to the qualimap module on biobox.
// Qualimap ouputs a few more raw data files to outdir but since the module is using a temporary directory as output dir these files are lost.
| qualimap_rnaseq.run(
runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align },
fromState: [
"bam": "genome_bam",
"gtf": "gtf",

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

@@ -2061,8 +2061,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

4
target/nextflow/bedtools_genomecov/.config.vsh.yaml
View File

@@ -178,8 +178,8 @@ build_info:
output: "target/nextflow/bedtools_genomecov"
executable: "target/nextflow/bedtools_genomecov/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/bedtools_genomecov/main.nf
View File

@@ -3031,8 +3031,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

4
target/nextflow/cat_additional_fasta/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ build_info:
output: "target/nextflow/cat_additional_fasta"
executable: "target/nextflow/cat_additional_fasta/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/cat_additional_fasta/main.nf
View File

@@ -3032,8 +3032,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

4
target/nextflow/cat_fastq/.config.vsh.yaml
View File

@@ -169,8 +169,8 @@ build_info:
output: "target/nextflow/cat_fastq"
executable: "target/nextflow/cat_fastq/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/cat_fastq/main.nf
View File

@@ -3023,8 +3023,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/cat_fastq",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

4
target/nextflow/deseq2_qc/.config.vsh.yaml
View File

@@ -237,8 +237,8 @@ build_info:
output: "target/nextflow/deseq2_qc"
executable: "target/nextflow/deseq2_qc/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/deseq2_qc/main.nf
View File

@@ -3104,8 +3104,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/deseq2_qc",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

4
target/nextflow/dupradar/.config.vsh.yaml
View File

@@ -266,8 +266,8 @@ build_info:
output: "target/nextflow/dupradar"
executable: "target/nextflow/dupradar/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/dupradar/main.nf
View File

@@ -3136,8 +3136,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/dupradar",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -167,8 +167,8 @@ build_info:
output: "target/nextflow/getchromsizes"
executable: "target/nextflow/getchromsizes/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/getchromsizes/main.nf
View File

@@ -3013,8 +3013,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/getchromsizes",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -145,8 +145,8 @@ build_info:
output: "target/nextflow/gtf2bed"
executable: "target/nextflow/gtf2bed/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/gtf2bed/main.nf
View File

@@ -2995,8 +2995,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/gtf2bed",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -155,8 +155,8 @@ build_info:
output: "target/nextflow/gtf_filter"
executable: "target/nextflow/gtf_filter/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/gtf_filter/main.nf
View File

@@ -3003,8 +3003,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/gtf_filter",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -144,8 +144,8 @@ build_info:
output: "target/nextflow/gunzip"
executable: "target/nextflow/gunzip/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/gunzip/main.nf
View File

@@ -2992,8 +2992,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/gunzip",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -165,8 +165,8 @@ build_info:
output: "target/nextflow/multiqc_custom_biotype"
executable: "target/nextflow/multiqc_custom_biotype/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/multiqc_custom_biotype/main.nf
View File

@@ -3012,8 +3012,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -207,8 +207,8 @@ build_info:
output: "target/nextflow/picard_markduplicates"
executable: "target/nextflow/picard_markduplicates/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/picard_markduplicates/main.nf
View File

@@ -3063,8 +3063,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/picard_markduplicates",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -409,8 +409,8 @@ build_info:
output: "target/nextflow/prepare_multiqc_input"
executable: "target/nextflow/prepare_multiqc_input/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/prepare_multiqc_input/main.nf
View File

@@ -3277,8 +3277,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -138,8 +138,8 @@ build_info:
output: "target/nextflow/preprocess_transcripts_fasta"
executable: "target/nextflow/preprocess_transcripts_fasta/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/preprocess_transcripts_fasta/main.nf
View File

@@ -2982,8 +2982,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -191,8 +191,8 @@ build_info:
output: "target/nextflow/preseq_lcextrap"
executable: "target/nextflow/preseq_lcextrap/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/preseq_lcextrap/main.nf
View File

@@ -3035,8 +3035,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

4
target/nextflow/rsem_merge_counts/.config.vsh.yaml
View File

@@ -181,8 +181,8 @@ build_info:
output: "target/nextflow/rsem_merge_counts"
executable: "target/nextflow/rsem_merge_counts/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/rsem_merge_counts/main.nf
View File

@@ -3027,8 +3027,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/rsem_merge_counts",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -260,8 +260,8 @@ build_info:
output: "target/nextflow/rseqc/rseqc_junctionannotation"
executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/rseqc/rseqc_junctionannotation/main.nf
View File

@@ -3128,8 +3128,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -249,8 +249,8 @@ build_info:
output: "target/nextflow/rseqc/rseqc_junctionsaturation"
executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/rseqc/rseqc_junctionsaturation/main.nf
View File

@@ -3113,8 +3113,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation",
"viash_version" : "0.9.0",
"git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b",
"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -162,8 +162,8 @@ build_info:
output: "target/nextflow/rseqc/rseqc_readdistribution"
executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf"
viash_version: "0.9.0"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

4
target/nextflow/rseqc/rseqc_readdistribution/main.nf
View File

@@ -3017,8 +3017,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution",
"viash_version" : "0.9.0",
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"git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
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"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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