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Build branch main with version main (a4f2c7d)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-f78nc

Source commit: a4f2c7d5a1

Source message: multiple minor fixes
This commit is contained in:
CI
2024-11-21 08:37:00 +00:00
parent 2d86d22f22
commit 20fef7a87e
230 changed files with 736 additions and 661 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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z"
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.created="2024-11-21T08:06:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-11-13T12:42:22Z"
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.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:21Z"
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.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:20Z"
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.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:22Z"
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.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -266,8 +266,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:22Z"
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.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:25Z"
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.created="2024-11-21T08:06:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"

6
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-11-13T12:42:23Z"
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.created="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -167,8 +167,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:21Z"
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.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:23Z"
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.created="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:21Z"
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.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:16Z"
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.created="2024-11-21T08:05:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:17Z"
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.created="2024-11-21T08:06:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:17Z"
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.created="2024-11-21T08:06:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:20Z"
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.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:18Z"
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.created="2024-11-21T08:06:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:14Z"
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.created="2024-11-21T08:05:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:19Z"
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.created="2024-11-21T08:06:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:18Z"
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.created="2024-11-21T08:06:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:16Z"
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.created="2024-11-21T08:05:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:15Z"
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.created="2024-11-21T08:05:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:15Z"
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.created="2024-11-21T08:05:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:20Z"
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.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:22Z"
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.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:20Z"
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.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:20Z"
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.created="2024-11-21T08:06:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:21Z"
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.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:21Z"
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.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:19Z"
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.created="2024-11-21T08:06:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:21Z"
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.created="2024-11-21T08:06:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:24Z"
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.created="2024-11-21T08:06:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:25Z"
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.created="2024-11-21T08:06:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:23Z"
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.created="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:24Z"
LABEL org.opencontainers.image.created="2024-11-21T08:06:07Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:23Z"
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.created="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:22Z"
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.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:22Z"
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.created="2024-11-21T08:06:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:23Z"
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.created="2024-11-21T08:06:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:18Z"
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.created="2024-11-21T08:06:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:17Z"
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.created="2024-11-21T08:06:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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="2024-11-13T12:42:24Z"
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.created="2024-11-21T08:06:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

12
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -108,6 +108,14 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--star_sjdb_gtf_feature_exon"
description: "Feature type in GTF file to be used as exons for building transcripts"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_index"
description: "Path to directory or tar.gz archive for pre-built RSEM index."
@@ -501,8 +509,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@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

@@ -222,6 +222,10 @@ function ViashHelp {
echo " type: file, file must exist"
echo " Path to directory or tar.gz archive for pre-built STAR index."
echo ""
echo " --star_sjdb_gtf_feature_exon"
echo " type: string"
echo " Feature type in GTF file to be used as exons for building transcripts"
echo ""
echo " --rsem_index"
echo " type: file, file must exist"
echo " Path to directory or tar.gz archive for pre-built RSEM index."
@@ -471,6 +475,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_STAR_INDEX=$(ViashRemoveFlags "$1")
shift 1
;;
--star_sjdb_gtf_feature_exon)
[ -n "$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON" ] && ViashError Bad arguments for option \'--star_sjdb_gtf_feature_exon\': \'$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_sjdb_gtf_feature_exon. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--star_sjdb_gtf_feature_exon=*)
[ -n "$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON" ] && ViashError Bad arguments for option \'--star_sjdb_gtf_feature_exon=*\': \'$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON=$(ViashRemoveFlags "$1")
shift 1
;;
--rsem_index)
[ -n "$VIASH_PAR_RSEM_INDEX" ] && ViashError Bad arguments for option \'--rsem_index\': \'$VIASH_PAR_RSEM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_INDEX="$2"
@@ -1160,7 +1175,7 @@ workflow run_wf {
main:
output_ch = input_ch
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
@@ -1343,7 +1358,8 @@ workflow run_wf {
runIf: {id, state -> !state.star_index && !state.skip_alignment},
fromState: [
"genome_fasta_files": "fasta",
"sjdb_gtf_file": "gtf"
"sjdb_gtf_file": "gtf",
"sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
],
toState: [ "star_index": "index" ],
key: "generate_star_index",

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: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

28
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -181,38 +181,22 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
- type: "boolean_true"
name: "--skip_qc"
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
- type: "boolean_true"
name: "--skip_biotype_qc"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
- type: "boolean_true"
name: "--skip_align"
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
- type: "boolean_true"
name: "--skip_pseudo_align"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--skip_dupradar"
info: null
@@ -1572,8 +1556,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"

70
target/executable/workflows/quality_control/quality_control
View File

@@ -257,18 +257,16 @@ function ViashHelp {
echo " Expression counts on transcript level"
echo ""
echo " --skip_qc"
echo " type: boolean"
echo " default: false"
echo " type: boolean_true"
echo ""
echo " --skip_biotype_qc"
echo " type: boolean"
echo " type: boolean_true"
echo ""
echo " --skip_align"
echo " type: boolean"
echo " default: false"
echo " type: boolean_true"
echo ""
echo " --skip_pseudo_align"
echo " type: boolean"
echo " type: boolean_true"
echo ""
echo " --skip_dupradar"
echo " type: boolean_true"
@@ -1033,46 +1031,22 @@ while [[ $# -gt 0 ]]; do
;;
--skip_qc)
[ -n "$VIASH_PAR_SKIP_QC" ] && ViashError Bad arguments for option \'--skip_qc\': \'$VIASH_PAR_SKIP_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_QC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_qc. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--skip_qc=*)
[ -n "$VIASH_PAR_SKIP_QC" ] && ViashError Bad arguments for option \'--skip_qc=*\': \'$VIASH_PAR_SKIP_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_QC=$(ViashRemoveFlags "$1")
VIASH_PAR_SKIP_QC=true
shift 1
;;
--skip_biotype_qc)
[ -n "$VIASH_PAR_SKIP_BIOTYPE_QC" ] && ViashError Bad arguments for option \'--skip_biotype_qc\': \'$VIASH_PAR_SKIP_BIOTYPE_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_BIOTYPE_QC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_biotype_qc. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--skip_biotype_qc=*)
[ -n "$VIASH_PAR_SKIP_BIOTYPE_QC" ] && ViashError Bad arguments for option \'--skip_biotype_qc=*\': \'$VIASH_PAR_SKIP_BIOTYPE_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_BIOTYPE_QC=$(ViashRemoveFlags "$1")
VIASH_PAR_SKIP_BIOTYPE_QC=true
shift 1
;;
--skip_align)
[ -n "$VIASH_PAR_SKIP_ALIGN" ] && ViashError Bad arguments for option \'--skip_align\': \'$VIASH_PAR_SKIP_ALIGN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_ALIGN="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_align. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--skip_align=*)
[ -n "$VIASH_PAR_SKIP_ALIGN" ] && ViashError Bad arguments for option \'--skip_align=*\': \'$VIASH_PAR_SKIP_ALIGN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_ALIGN=$(ViashRemoveFlags "$1")
VIASH_PAR_SKIP_ALIGN=true
shift 1
;;
--skip_pseudo_align)
[ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGN" ] && ViashError Bad arguments for option \'--skip_pseudo_align\': \'$VIASH_PAR_SKIP_PSEUDO_ALIGN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_PSEUDO_ALIGN="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_pseudo_align. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--skip_pseudo_align=*)
[ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGN" ] && ViashError Bad arguments for option \'--skip_pseudo_align=*\': \'$VIASH_PAR_SKIP_PSEUDO_ALIGN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_PSEUDO_ALIGN=$(ViashRemoveFlags "$1")
VIASH_PAR_SKIP_PSEUDO_ALIGN=true
shift 1
;;
--skip_dupradar)
@@ -2433,9 +2407,15 @@ fi
if [ -z ${VIASH_PAR_SKIP_QC+x} ]; then
VIASH_PAR_SKIP_QC="false"
fi
if [ -z ${VIASH_PAR_SKIP_BIOTYPE_QC+x} ]; then
VIASH_PAR_SKIP_BIOTYPE_QC="false"
fi
if [ -z ${VIASH_PAR_SKIP_ALIGN+x} ]; then
VIASH_PAR_SKIP_ALIGN="false"
fi
if [ -z ${VIASH_PAR_SKIP_PSEUDO_ALIGN+x} ]; then
VIASH_PAR_SKIP_PSEUDO_ALIGN="false"
fi
if [ -z ${VIASH_PAR_SKIP_DUPRADAR+x} ]; then
VIASH_PAR_SKIP_DUPRADAR="false"
fi
@@ -2769,25 +2749,25 @@ if [[ -n "$VIASH_PAR_PAIRED" ]]; then
fi
if [[ -n "$VIASH_PAR_SKIP_QC" ]]; then
if ! [[ "$VIASH_PAR_SKIP_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_qc' has to be a boolean. Use "--help" to get more information on the parameters.
ViashError '--skip_qc' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_BIOTYPE_QC" ]]; then
if ! [[ "$VIASH_PAR_SKIP_BIOTYPE_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_biotype_qc' has to be a boolean. Use "--help" to get more information on the parameters.
ViashError '--skip_biotype_qc' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_ALIGN" ]]; then
if ! [[ "$VIASH_PAR_SKIP_ALIGN" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_align' has to be a boolean. Use "--help" to get more information on the parameters.
ViashError '--skip_align' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGN" ]]; then
if ! [[ "$VIASH_PAR_SKIP_PSEUDO_ALIGN" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_pseudo_align' has to be a boolean. Use "--help" to get more information on the parameters.
ViashError '--skip_pseudo_align' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
@@ -3749,12 +3729,12 @@ workflow run_wf {
passed_strand_check: passed_strand_check,
skip_align: skip_align,
skip_pseudo_align: skip_pseudo_align,
quant_results: quant_results,
rsem_counts_gene: rsem_counts_gene,
rsem_counts_transcripts: rsem_counts_transcripts,
pseudo_quant_out_dir: pseudo_quant_out_dir,
pseudo_salmon_quant_results: pseudo_salmon_quant_results,
pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
quant_results: quant_results.findAll { it != null },
rsem_counts_gene: rsem_counts_gene.findAll { it != null },
rsem_counts_transcripts: rsem_counts_transcripts.findAll { it != null },
pseudo_quant_out_dir: pseudo_quant_out_dir.findAll { it != null },
pseudo_salmon_quant_results: pseudo_salmon_quant_results.findAll { it != null },
pseudo_kallisto_quant_results: pseudo_kallisto_quant_results.findAll { it != null },
gtf: gtf,
gtf_extra_attributes: gtf_extra_attributes,
gtf_group_features: gtf_group_features,
@@ -3893,7 +3873,7 @@ workflow run_wf {
],
key: "deseq2_qc_pseuso_align_quant"
)
| niceView()
// Get list of samples that failed trimming, mapping, and strand check for MultiQC report
| map { id, state ->
def fail_trimming_header = ["Sample", "Reads after trimming"]

12
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -214,6 +214,14 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--star_sjdb_gtf_feature_exon"
description: "Feature type in GTF file to be used as exons for building transcripts"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Read trimming options"
arguments:
- type: "string"
@@ -2082,8 +2090,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "a04f9bab8aec1c4f5e8ade4d5b68c2d4c92a7814"
git_remote: "https://x-access-token:ghs_U4pAQwhSWAqkeDDEK1YyMxMtkXglzF3wJkYc@github.com/viash-hub/rnaseq"
git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

31
target/executable/workflows/rnaseq/rnaseq
View File

@@ -272,6 +272,10 @@ function ViashHelp {
echo " By default, the pipeline assigns reads based on the 'exon' attribute"
echo " within the GTF file."
echo ""
echo " --star_sjdb_gtf_feature_exon"
echo " type: string"
echo " Feature type in GTF file to be used as exons for building transcripts"
echo ""
echo "Read trimming options:"
echo " --trimmer"
echo " type: string"
@@ -1308,6 +1312,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE=$(ViashRemoveFlags "$1")
shift 1
;;
--star_sjdb_gtf_feature_exon)
[ -n "$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON" ] && ViashError Bad arguments for option \'--star_sjdb_gtf_feature_exon\': \'$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_sjdb_gtf_feature_exon. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--star_sjdb_gtf_feature_exon=*)
[ -n "$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON" ] && ViashError Bad arguments for option \'--star_sjdb_gtf_feature_exon=*\': \'$VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDB_GTF_FEATURE_EXON=$(ViashRemoveFlags "$1")
shift 1
;;
--trimmer)
[ -n "$VIASH_PAR_TRIMMER" ] && ViashError Bad arguments for option \'--trimmer\': \'$VIASH_PAR_TRIMMER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TRIMMER="$2"
@@ -4441,8 +4456,10 @@ workflow run_wf {
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0],
star_sjdb_gtf_feature_exon: list.collect { id, state -> state.star_sjdb_gtf_feature_exon }.unique()[0],
filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0],
pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ]
]
@@ -4472,7 +4489,8 @@ workflow run_wf {
"filter_gtf": "filter_gtf",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner",
"skip_alignment": "skip_alignment"
"skip_alignment": "skip_alignment",
"star_sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
],
toState: [
"fasta": "uncompressed_fasta",
@@ -4980,12 +4998,21 @@ def isBelowMaxContigSize(fai_file) {
return true
}
// Find a file in a directory
import java.nio.file.*
def findFile(Path dir, String fileName) {
Files.walk(dir)
.filter { Files.isRegularFile(it) && it.fileName.toString() == fileName }
.findFirst()
.orElse(null)
}
import groovy.json.JsonSlurper
//
// Function that parses Salmon quant 'meta_info.json' output file to get inferred strandedness
//
def getSalmonInferredStrandedness(salmon_quant_output) {
def json_file = new File(salmon_quant_output).listFiles().find { it.name == "meta_info.json" || it.isDirectory() && it.listFiles().find { it.name == "meta_info.json" } }
def json_file = findFile(salmon_quant_output, 'meta_info.json')
def lib_type = new JsonSlurper().parseText(json_file.text).get('library_types')[0]
def strandedness = 'reverse'
if (lib_type) {