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Build branch main with version main (a04f9ba)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-xf2ql

Source commit: a04f9bab8a

Source message: avoid generating STAR index if alignment is skipped
This commit is contained in:
CI
2024-11-13 12:53:08 +00:00
parent bc17b94cd5
commit 2d86d22f22
194 changed files with 473 additions and 422 deletions
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3
src/workflows/prepare_genome/config.vsh.yaml
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@@ -80,6 +80,9 @@ argument_groups:
description: Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'.
choices: [salmon, kallisto]
default: "salmon"
- name: "--skip_alignment"
type: boolean_true
description: Skip all of the alignment-based processes within the pipeline.
- name: "Output"
arguments:

2
src/workflows/prepare_genome/main.nf
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@@ -185,7 +185,7 @@ workflow run_wf {
// TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode
| star_genome_generate.run (
runIf: {id, state -> !state.star_index},
runIf: {id, state -> !state.star_index && !state.skip_alignment},
fromState: [
"genome_fasta_files": "fasta",
"sjdb_gtf_file": "gtf"

3
src/workflows/rnaseq/main.nf
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@@ -69,7 +69,8 @@ workflow run_wf {
"biotype": "biotype",
"filter_gtf": "filter_gtf",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner"
"pseudo_aligner": "pseudo_aligner",
"skip_alignment": "skip_alignment"
],
toState: [
"fasta": "uncompressed_fasta",

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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:21Z"
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.created="2024-11-13T12:42:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:19Z"
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.created="2024-11-13T12:42:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:18Z"
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.created="2024-11-13T12:42:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:17Z"
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.created="2024-11-13T12:42:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:19Z"
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.created="2024-11-13T12:42:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:20Z"
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.created="2024-11-13T12:42:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/fastqc/.config.vsh.yaml
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@@ -198,8 +198,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:22Z"
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.created="2024-11-13T12:42:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/fq_subsample/fq_subsample
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@@ -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="2024-11-13T10:13:21Z"
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.created="2024-11-13T12:42:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:18Z"
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.created="2024-11-13T12:42:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:20Z"
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.created="2024-11-13T12:42:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:19Z"
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.created="2024-11-13T12:42:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:14Z"
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.created="2024-11-13T12:42:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:14Z"
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.created="2024-11-13T12:42:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:14Z"
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.created="2024-11-13T12:42:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:18Z"
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.created="2024-11-13T12:42:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:16Z"
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.created="2024-11-13T12:42:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:11Z"
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.created="2024-11-13T12:42:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:16Z"
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.created="2024-11-13T12:42:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:16Z"
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.created="2024-11-13T12:42:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:13Z"
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.created="2024-11-13T12:42:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:13Z"
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.created="2024-11-13T12:42:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:12Z"
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.created="2024-11-13T12:42:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:18Z"
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.created="2024-11-13T12:42:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:19Z"
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.created="2024-11-13T12:42:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:17Z"
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.created="2024-11-13T12:42:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:17Z"
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.created="2024-11-13T12:42:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:19Z"
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.created="2024-11-13T12:42:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:18Z"
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.created="2024-11-13T12:42:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:17Z"
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.created="2024-11-13T12:42:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:18Z"
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.created="2024-11-13T12:42:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:22Z"
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.created="2024-11-13T12:42:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:23Z"
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.created="2024-11-13T12:42:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:20Z"
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.created="2024-11-13T12:42:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:21Z"
LABEL org.opencontainers.image.created="2024-11-13T12:42:24Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:20Z"
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.created="2024-11-13T12:42:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:19Z"
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.created="2024-11-13T12:42:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:20Z"
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.created="2024-11-13T12:42:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:20Z"
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.created="2024-11-13T12:42:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:15Z"
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.created="2024-11-13T12:42:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:15Z"
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.created="2024-11-13T12:42:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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="2024-11-13T10:13:22Z"
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.created="2024-11-13T12:42:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

9
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -221,6 +221,11 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--skip_alignment"
description: "Skip all of the alignment-based processes within the pipeline."
info: null
direction: "input"
- name: "Output"
arguments:
- type: "file"
@@ -496,8 +501,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"

20
target/executable/workflows/prepare_genome/prepare_genome
View File

@@ -275,6 +275,10 @@ function ViashHelp {
echo " Specifies the pseudo aligner to use - available options are 'salmon'."
echo " Runs in addition to '--aligner'."
echo ""
echo " --skip_alignment"
echo " type: boolean_true"
echo " Skip all of the alignment-based processes within the pipeline."
echo ""
echo "Output:"
echo " --fasta_uncompressed"
echo " type: file, output, file must exist"
@@ -577,6 +581,11 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_PSEUDO_ALIGNER=$(ViashRemoveFlags "$1")
shift 1
;;
--skip_alignment)
[ -n "$VIASH_PAR_SKIP_ALIGNMENT" ] && ViashError Bad arguments for option \'--skip_alignment\': \'$VIASH_PAR_SKIP_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_ALIGNMENT=true
shift 1
;;
--fasta_uncompressed)
[ -n "$VIASH_PAR_FASTA_UNCOMPRESSED" ] && ViashError Bad arguments for option \'--fasta_uncompressed\': \'$VIASH_PAR_FASTA_UNCOMPRESSED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTA_UNCOMPRESSED="$2"
@@ -846,6 +855,9 @@ fi
if [ -z ${VIASH_PAR_PSEUDO_ALIGNER+x} ]; then
VIASH_PAR_PSEUDO_ALIGNER="salmon"
fi
if [ -z ${VIASH_PAR_SKIP_ALIGNMENT+x} ]; then
VIASH_PAR_SKIP_ALIGNMENT="false"
fi
if [ -z ${VIASH_PAR_FASTA_UNCOMPRESSED+x} ]; then
VIASH_PAR_FASTA_UNCOMPRESSED="reference_genome.fasta"
fi
@@ -959,6 +971,12 @@ if [[ -n "$VIASH_PAR_FILTER_GTF" ]]; then
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_ALIGNMENT" ]]; then
if ! [[ "$VIASH_PAR_SKIP_ALIGNMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_alignment' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
@@ -1322,7 +1340,7 @@ workflow run_wf {
// TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode
| star_genome_generate.run (
runIf: {id, state -> !state.star_index},
runIf: {id, state -> !state.star_index && !state.skip_alignment},
fromState: [
"genome_fasta_files": "fasta",
"sjdb_gtf_file": "gtf"

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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

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

@@ -1572,8 +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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"

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

@@ -2082,8 +2082,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

3
target/executable/workflows/rnaseq/rnaseq
View File

@@ -4471,7 +4471,8 @@ workflow run_wf {
"biotype": "biotype",
"filter_gtf": "filter_gtf",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner"
"pseudo_aligner": "pseudo_aligner",
"skip_alignment": "skip_alignment"
],
toState: [
"fasta": "uncompressed_fasta",

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

@@ -238,8 +238,8 @@ build_info:
output: "target/nextflow/bbmap_bbsplit"
executable: "target/nextflow/bbmap_bbsplit/main.nf"
viash_version: "0.9.0"
git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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

@@ -3104,8 +3104,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit",
"viash_version" : "0.9.0",
"git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
"git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
"git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814",
"git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
"git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
"git_commit" : "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814",
"git_remote" : "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@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: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

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