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Build branch main with version main (fd0354d)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-kqfj7

Source commit: fd0354dae8

Source message: Point to new assets dir
This commit is contained in:
CI
2024-10-03 16:22:26 +00:00
parent c106022744
commit 2fadce912e
211 changed files with 621 additions and 532 deletions
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4
target/executable/bbmap_bbsplit/.config.vsh.yaml
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@@ -238,8 +238,8 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
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@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-10-01T10:01:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/bedtools_genomecov/bedtools_genomecov
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@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/cat_additional_fasta/cat_additional_fasta
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@@ -480,9 +480,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/cat_fastq/cat_fastq
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@@ -472,9 +472,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

20
target/executable/deseq2_qc/.config.vsh.yaml
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@@ -1,11 +1,11 @@
name: "deseq2_qc"
version: "main"
argument_groups:
- name: "Input"
- name: "input"
arguments:
- type: "file"
name: "--counts"
description: "Count file matrix where rows are genes and columns are samples"
description: "count file matrix where rows are genes and columns are samples"
info: null
must_exist: true
create_parent: true
@@ -104,7 +104,13 @@ resources:
is_executable: true
- type: "file"
path: "deseq2_qc.r"
description: "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples\
- type: "file"
path: "assets/multiqc/deseq2_pca_header.txt"
dest: "assets/multiqc/deseq2_pca_header.txt"
- type: "file"
path: "assets/multiqc/deseq2_clustering_header.txt"
dest: "assets/multiqc/deseq2_clustering_header.txt"
description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\
\ in the counts files\n"
test_resources:
- type: "bash_script"
@@ -112,10 +118,6 @@ test_resources:
is_executable: true
- type: "file"
path: "counts.tsv"
- type: "file"
path: "deseq2_pca_header.txt"
- type: "file"
path: "deseq2_clustering_header.txt"
info:
migration_info:
git_repo: "https://github.com/nf-core/rnaseq.git"
@@ -237,8 +239,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

12
target/executable/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt Normal file
View File

@@ -0,0 +1,12 @@
#id: 'deseq2_clustering'
#section_name: 'DESeq2 sample similarity'
#description: "is generated from clustering by Euclidean distances between
# <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html' target='_blank'>DESeq2</a>
# rlog values for each sample
# in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
#plot_type: 'heatmap'
#anchor: 'deseq2_clustering'
#pconfig:
# title: 'DESeq2: Heatmap of the sample-to-sample distances'
# xlab: True
# reverseColors: True

11
target/executable/deseq2_qc/assets/multiqc/deseq2_pca_header.txt Normal file
View File

@@ -0,0 +1,11 @@
#id: 'deseq2_pca'
#section_name: 'DESeq2 PCA plot'
#description: "PCA plot between samples in the experiment.
# These values are calculated using <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html'>DESeq2</a>
# in the <a href='https://github.com/nf-core/atacseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
#plot_type: 'scatter'
#anchor: 'deseq2_pca'
#pconfig:
# title: 'DESeq2: Principal component plot'
# xlab: PC1
# ylab: PC2

12
target/executable/deseq2_qc/deseq2_qc
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@@ -173,13 +173,13 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
function ViashHelp {
echo "deseq2_qc main"
echo ""
echo "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the"
echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the"
echo "counts files"
echo ""
echo "Input:"
echo "input:"
echo " --counts"
echo " type: file, file must exist"
echo " Count file matrix where rows are genes and columns are samples"
echo " count file matrix where rows are genes and columns are samples"
echo ""
echo " --pca_header_multiqc"
echo " type: file, file must exist"
@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/dupradar/dupradar
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@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/fastqc/fastqc
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@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/gtf2bed/gtf2bed
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/gtf_filter/gtf_filter
View File

@@ -470,9 +470,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/gunzip/gunzip
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -64,6 +64,9 @@ resources:
is_executable: true
- type: "file"
path: "mqc_features_stat.py"
- type: "file"
path: "assets/multiqc/biotypes_header.txt"
dest: "assets/multiqc/biotypes_header.txt"
description: "Calculate features percentage for biotype counts"
info: null
status: "enabled"
@@ -170,8 +173,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

11
target/executable/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt Normal file
View File

@@ -0,0 +1,11 @@
# id: 'biotype_counts'
# section_name: 'Biotype Counts'
# description: "shows reads overlapping genomic features of different biotypes,
# counted by <a href='http://bioinf.wehi.edu.au/featureCounts'>featureCounts</a>."
# plot_type: 'bargraph'
# anchor: 'featurecounts_biotype'
# pconfig:
# id: "featurecounts_biotype_plot"
# title: "featureCounts: Biotypes"
# xlab: "# Reads"
# cpswitch_counts_label: "Number of Reads"

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -481,9 +481,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
mv picard.jar /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -557,9 +557,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-10-01T10:02:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -462,9 +462,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -495,9 +495,9 @@ mkdir build && cd build && \
make && make install && make HAVE_HTSLIB=1 all
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
LABEL org.opencontainers.image.created="2024-10-01T10:01:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/qualimap/qualimap
View File

@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -483,9 +483,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -501,9 +501,9 @@ RUN apt-get update && \
RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/sortmerna/sortmerna
View File

@@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
bash sortmerna-4.3.6-Linux.sh --skip-license
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/stringtie/stringtie
View File

@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

4
target/executable/trimgalore/trimgalore
View File

@@ -858,9 +858,9 @@ ENTRYPOINT []
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
LABEL org.opencontainers.image.created="2024-10-01T10:02:08Z"
LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/tx2gene/tx2gene
View File

@@ -487,9 +487,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
LABEL org.opencontainers.image.created="2024-10-01T10:02:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/tximport/tximport
View File

@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component tximport"
LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-10-01T10:02:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-10-01T10:02:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
LABEL org.opencontainers.image.created="2024-10-01T10:02:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" "pysam"
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

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

@@ -496,8 +496,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"

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

@@ -283,8 +283,8 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

10
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -265,7 +265,7 @@ argument_groups:
name: "--biotypes_header"
info: null
default:
- "assets/multiqc/biotypes_header.txt"
- "src/assets/multiqc/biotypes_header.txt"
must_exist: true
create_parent: true
required: false
@@ -563,7 +563,7 @@ argument_groups:
name: "--pca_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_pca_header.txt"
- "src/assets/multiqc/deseq2_pca_header.txt"
must_exist: true
create_parent: true
required: false
@@ -574,7 +574,7 @@ argument_groups:
name: "--clustering_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_clustering_header.txt"
- "src/assets/multiqc/deseq2_clustering_header.txt"
must_exist: true
create_parent: true
required: false
@@ -1596,8 +1596,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"

12
target/executable/workflows/quality_control/quality_control
View File

@@ -296,7 +296,7 @@ function ViashHelp {
echo ""
echo " --biotypes_header"
echo " type: file, file must exist"
echo " default: assets/multiqc/biotypes_header.txt"
echo " default: src/assets/multiqc/biotypes_header.txt"
echo ""
echo " --biotype"
echo " type: string"
@@ -464,11 +464,11 @@ function ViashHelp {
echo ""
echo " --pca_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_pca_header.txt"
echo " default: src/assets/multiqc/deseq2_pca_header.txt"
echo ""
echo " --clustering_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_clustering_header.txt"
echo " default: src/assets/multiqc/deseq2_clustering_header.txt"
echo ""
echo " --deseq2_vst"
echo " type: boolean"
@@ -2477,7 +2477,7 @@ if [ -z ${VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE+x} ]; then
VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE="exon"
fi
if [ -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then
VIASH_PAR_BIOTYPES_HEADER="assets/multiqc/biotypes_header.txt"
VIASH_PAR_BIOTYPES_HEADER="src/assets/multiqc/biotypes_header.txt"
fi
if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then
VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
@@ -2546,10 +2546,10 @@ if [ -z ${VIASH_PAR_JAVA_MEMORY_SIZE+x} ]; then
VIASH_PAR_JAVA_MEMORY_SIZE="4G"
fi
if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then
VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt"
VIASH_PAR_PCA_HEADER_MULTIQC="src/assets/multiqc/deseq2_pca_header.txt"
fi
if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt"
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="src/assets/multiqc/deseq2_clustering_header.txt"
fi
if [ -z ${VIASH_PAR_EXTRA_DESEQ2_ARGS+x} ]; then
VIASH_PAR_EXTRA_DESEQ2_ARGS="--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"

14
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -295,7 +295,7 @@ argument_groups:
\ be used to create the database for SortMeRNA."
info: null
default:
- "assets/rrna-db-defaults.txt"
- "src/assets/rrna-db-defaults.txt"
must_exist: true
create_parent: true
required: false
@@ -683,7 +683,7 @@ argument_groups:
name: "--pca_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_pca_header.txt"
- "src/assets/multiqc/deseq2_pca_header.txt"
must_exist: true
create_parent: true
required: false
@@ -694,7 +694,7 @@ argument_groups:
name: "--clustering_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_clustering_header.txt"
- "src/assets/multiqc/deseq2_clustering_header.txt"
must_exist: true
create_parent: true
required: false
@@ -754,7 +754,7 @@ argument_groups:
name: "--multiqc_custom_config"
info: null
default:
- "assets/multiqc_config.yml"
- "src/assets/multiqc_config.yml"
must_exist: true
create_parent: true
required: false
@@ -772,7 +772,7 @@ argument_groups:
name: "--multiqc_methods_description"
info: null
default:
- "assets/methods_description_template.yml"
- "src/assets/methods_description_template.yml"
must_exist: true
create_parent: true
required: false
@@ -2117,8 +2117,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

20
target/executable/workflows/rnaseq/rnaseq
View File

@@ -314,7 +314,7 @@ function ViashHelp {
echo ""
echo " --ribo_database_manifest"
echo " type: file, file must exist"
echo " default: assets/rrna-db-defaults.txt"
echo " default: src/assets/rrna-db-defaults.txt"
echo " Text file containing paths to fasta files (one per line) that will be"
echo " used to create the database for SortMeRNA."
echo ""
@@ -545,11 +545,11 @@ function ViashHelp {
echo ""
echo " --pca_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_pca_header.txt"
echo " default: src/assets/multiqc/deseq2_pca_header.txt"
echo ""
echo " --clustering_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_clustering_header.txt"
echo " default: src/assets/multiqc/deseq2_clustering_header.txt"
echo ""
echo " --deseq2_vst"
echo " type: boolean"
@@ -576,14 +576,14 @@ function ViashHelp {
echo "Multiqc paramenters:"
echo " --multiqc_custom_config"
echo " type: file, file must exist"
echo " default: assets/multiqc_config.yml"
echo " default: src/assets/multiqc_config.yml"
echo ""
echo " --multiqc_title"
echo " type: string"
echo ""
echo " --multiqc_methods_description"
echo " type: file, file must exist"
echo " default: assets/methods_description_template.yml"
echo " default: src/assets/methods_description_template.yml"
echo ""
echo "Output:"
echo " --output_fasta"
@@ -3202,7 +3202,7 @@ if [ -z ${VIASH_PAR_REMOVE_RIBO_RNA+x} ]; then
VIASH_PAR_REMOVE_RIBO_RNA="false"
fi
if [ -z ${VIASH_PAR_RIBO_DATABASE_MANIFEST+x} ]; then
VIASH_PAR_RIBO_DATABASE_MANIFEST="assets/rrna-db-defaults.txt"
VIASH_PAR_RIBO_DATABASE_MANIFEST="src/assets/rrna-db-defaults.txt"
fi
if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then
VIASH_PAR_WITH_UMI="false"
@@ -3319,10 +3319,10 @@ if [ -z ${VIASH_PAR_EXTRA_PRESEQ_ARGS+x} ]; then
VIASH_PAR_EXTRA_PRESEQ_ARGS="-verbose -seed 1 -seg_len 100000000"
fi
if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then
VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt"
VIASH_PAR_PCA_HEADER_MULTIQC="src/assets/multiqc/deseq2_pca_header.txt"
fi
if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt"
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="src/assets/multiqc/deseq2_clustering_header.txt"
fi
if [ -z ${VIASH_PAR_DESEQ2_VST+x} ]; then
VIASH_PAR_DESEQ2_VST="true"
@@ -3337,10 +3337,10 @@ if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then
VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
fi
if [ -z ${VIASH_PAR_MULTIQC_CUSTOM_CONFIG+x} ]; then
VIASH_PAR_MULTIQC_CUSTOM_CONFIG="assets/multiqc_config.yml"
VIASH_PAR_MULTIQC_CUSTOM_CONFIG="src/assets/multiqc_config.yml"
fi
if [ -z ${VIASH_PAR_MULTIQC_METHODS_DESCRIPTION+x} ]; then
VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="assets/methods_description_template.yml"
VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="src/assets/methods_description_template.yml"
fi
if [ -z ${VIASH_PAR_OUTPUT_FASTA+x} ]; then
VIASH_PAR_OUTPUT_FASTA="reference/genome.fasta"