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Build branch multiple_fixes with version multiple_fixes (b291665)

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Build pipeline: viash-hub.rnaseq.multiple-fixes-kj62j

Source commit: b291665ddc

Source message: minor changes
This commit is contained in:
CI
2024-09-24 10:36:19 +00:00
parent 29c8cdb0a2
commit 0e55094fd4
209 changed files with 15628 additions and 2971 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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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="2024-09-23T13:49:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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="2024-09-23T13:49:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

8
target/executable/cat_fastq/.config.vsh.yaml
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@@ -30,7 +30,7 @@ argument_groups:
description: "Concatenated read 1 fastq"
info: null
default:
- "$id_merged.fastq"
- "$id_r1_merged.fastq"
must_exist: true
create_parent: true
required: false
@@ -42,7 +42,7 @@ argument_groups:
description: "Concatenated read 2 fastq"
info: null
default:
- "$id_merged.fastq"
- "$id_r2_merged.fastq"
must_exist: false
create_parent: true
required: false
@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

14
target/executable/cat_fastq/cat_fastq
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@@ -187,12 +187,12 @@ function ViashHelp {
echo "Output:"
echo " --fastq_1"
echo " type: file, output, file must exist"
echo " default: \$id_merged.fastq"
echo " default: \$id_r1_merged.fastq"
echo " Concatenated read 1 fastq"
echo ""
echo " --fastq_2"
echo " type: file, output"
echo " default: \$id_merged.fastq"
echo " default: \$id_r2_merged.fastq"
echo " Concatenated read 2 fastq"
}
@@ -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="2024-09-23T13:50:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -869,10 +869,10 @@ fi
# filling in defaults
if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then
VIASH_PAR_FASTQ_1="\$id_merged.fastq"
VIASH_PAR_FASTQ_1="\$id_r1_merged.fastq"
fi
if [ -z ${VIASH_PAR_FASTQ_2+x} ]; then
VIASH_PAR_FASTQ_2="\$id_merged.fastq"
VIASH_PAR_FASTQ_2="\$id_r2_merged.fastq"
fi
# check whether required files exist

4
target/executable/deseq2_qc/.config.vsh.yaml
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@@ -237,8 +237,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -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="2024-09-23T13:50:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:49:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

4
target/executable/fq_subsample/.config.vsh.yaml
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@@ -177,8 +177,8 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:49:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:49:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:49:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -170,8 +170,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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="2024-09-23T13:50:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

11
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="2024-09-23T13:50:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -2285,7 +2285,8 @@ IFS="," read -ra star_multiqc <<< \$par_star_multiqc && for file in "\${star_mul
IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
# TODO: Fetch Salmon meta info
# IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra samtools_stats <<< \$par_samtools_stats && for file in "\${samtools_stats[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done
@@ -2300,7 +2301,7 @@ IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseu
IFS="," read -ra featurecounts_multiqc <<< \$par_featurecounts_multiqc && for file in "\${featurecounts_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc&& for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc && for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
[ -e "\$par_aligner_pca_multiqc" ] && cp -r "\$par_aligner_pca_multiqc" "\$par_output/"

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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:49:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:49:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

24
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -24,15 +24,6 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--versions"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
@@ -83,17 +74,6 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--updated_versions"
info: null
default:
- "versions.yml"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
@@ -202,8 +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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

62
target/executable/rsem/rsem_merge_counts/rsem_merge_counts
View File

@@ -185,9 +185,6 @@ function ViashHelp {
echo " type: file, file must exist"
echo " Expression counts on transcript level (isoforms)"
echo ""
echo " --versions"
echo " type: file"
echo ""
echo "Output:"
echo " --merged_gene_counts"
echo " type: file, output, file must exist"
@@ -208,10 +205,6 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: rsem.merged.transcript_tpm.tsv"
echo " File containing transcript TPM across all samples."
echo ""
echo " --updated_versions"
echo " type: file, output, file must exist"
echo " default: versions.yml"
}
# initialise variables
@@ -490,9 +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="2024-09-23T13:50:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -654,17 +647,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashRemoveFlags "$1")
shift 1
;;
--versions)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--versions=*)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
--merged_gene_counts)
[ -n "$VIASH_PAR_MERGED_GENE_COUNTS" ] && ViashError Bad arguments for option \'--merged_gene_counts\': \'$VIASH_PAR_MERGED_GENE_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MERGED_GENE_COUNTS="$2"
@@ -709,17 +691,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashRemoveFlags "$1")
shift 1
;;
--updated_versions)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --updated_versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--updated_versions=*)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions=*\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
@@ -930,9 +901,6 @@ fi
if [ -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM="rsem.merged.transcript_tpm.tsv"
fi
if [ -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then
VIASH_PAR_UPDATED_VERSIONS="versions.yml"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
@@ -1031,9 +999,6 @@ fi
if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -d "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")"
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
@@ -1055,10 +1020,6 @@ if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS_TRANSCRIPTS")" )
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_VERSIONS")" )
VIASH_PAR_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MERGED_GENE_COUNTS")" )
VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_GENE_COUNTS")
@@ -1079,11 +1040,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" )
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_UPDATED_VERSIONS")" )
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_UPDATED_VERSIONS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_UPDATED_VERSIONS" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1155,12 +1111,10 @@ cat > "\$tempscript" << 'VIASHMAIN'
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_COUNTS_GENE+x} ]; then echo "${VIASH_PAR_COUNTS_GENE}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_gene='&'#" ; else echo "# par_counts_gene="; fi )
$( if [ ! -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_COUNTS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_transcripts='&'#" ; else echo "# par_counts_transcripts="; fi )
$( if [ ! -z ${VIASH_PAR_VERSIONS+x} ]; then echo "${VIASH_PAR_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_versions='&'#" ; else echo "# par_versions="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_GENE_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_GENE_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_counts='&'#" ; else echo "# par_merged_gene_counts="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_GENE_TPM+x} ]; then echo "${VIASH_PAR_MERGED_GENE_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_tpm='&'#" ; else echo "# par_merged_gene_tpm="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_counts='&'#" ; else echo "# par_merged_transcript_counts="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_tpm='&'#" ; else echo "# par_merged_transcript_tpm="; fi )
$( if [ ! -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then echo "${VIASH_PAR_UPDATED_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_updated_versions='&'#" ; else echo "# par_updated_versions="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1225,9 +1179,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_PAR_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_GENE_COUNTS")
fi
@@ -1240,9 +1191,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_UPDATED_VERSIONS")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
@@ -1275,10 +1223,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -e "$VIASH_PAR_MERGED_TRAN
ViashError "Output file '$VIASH_PAR_MERGED_TRANSCRIPT_TPM' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -e "$VIASH_PAR_UPDATED_VERSIONS" ]; then
ViashError "Output file '$VIASH_PAR_UPDATED_VERSIONS' does not exist."
exit 1
fi
exit 0

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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:08Z"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
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="2024-09-23T13:50:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

16
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -242,7 +242,7 @@ argument_groups:
name: "--star_multiqc"
info: null
default:
- "$id.log"
- "$id_star.log"
must_exist: true
create_parent: true
required: false
@@ -382,7 +382,7 @@ argument_groups:
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_gene"
name: "--rsem_counts_gene"
description: "Expression counts on gene level"
info: null
default:
@@ -496,11 +496,9 @@ dependencies:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "umi_tools/umi_tools_dedup"
- name: "umitools/umitools_dedup"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
type: "local"
- name: "umitools_prepareforquant"
repository:
type: "local"
@@ -596,8 +594,8 @@ 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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@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"
@@ -605,7 +603,7 @@ build_info:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_dedup"
- "target/nextflow/umitools/umitools_dedup"
- "target/nextflow/umitools_prepareforquant"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/rsem/rsem_calculate_expression"

34
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -291,7 +291,7 @@ function ViashHelp {
echo "Output:"
echo " --star_multiqc"
echo " type: file, output, file must exist"
echo " default: \$id.log"
echo " default: \$id_star.log"
echo ""
echo " --genome_bam_sorted"
echo " type: file, output, file must exist"
@@ -341,7 +341,7 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: \$id.quant.sf"
echo ""
echo " --counts_gene"
echo " --rsem_counts_gene"
echo " type: file, output, file must exist"
echo " default: \$id.genes.results"
echo " Expression counts on gene level"
@@ -792,15 +792,15 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
shift 1
;;
--counts_gene)
[ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNTS_GENE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene. Use "--help" to get more information on the parameters. && exit 1
--rsem_counts_gene)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --rsem_counts_gene. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--counts_gene=*)
[ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene=*\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNTS_GENE=$(ViashRemoveFlags "$1")
--rsem_counts_gene=*)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene=*\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE=$(ViashRemoveFlags "$1")
shift 1
;;
--counts_transcripts)
@@ -1023,7 +1023,7 @@ if [ -z ${VIASH_PAR_ALIGNER+x} ]; then
VIASH_PAR_ALIGNER="star_salmon"
fi
if [ -z ${VIASH_PAR_STAR_MULTIQC+x} ]; then
VIASH_PAR_STAR_MULTIQC="\$id.log"
VIASH_PAR_STAR_MULTIQC="\$id_star.log"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_SORTED+x} ]; then
VIASH_PAR_GENOME_BAM_SORTED="\$id.genome.bam"
@@ -1061,8 +1061,8 @@ fi
if [ -z ${VIASH_PAR_QUANT_RESULTS_FILE+x} ]; then
VIASH_PAR_QUANT_RESULTS_FILE="\$id.quant.sf"
fi
if [ -z ${VIASH_PAR_COUNTS_GENE+x} ]; then
VIASH_PAR_COUNTS_GENE="\$id.genes.results"
if [ -z ${VIASH_PAR_RSEM_COUNTS_GENE+x} ]; then
VIASH_PAR_RSEM_COUNTS_GENE="\$id.genes.results"
fi
if [ -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then
VIASH_PAR_COUNTS_TRANSCRIPTS="\$id.isoforms.results"
@@ -1273,8 +1273,8 @@ fi
if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")"
fi
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE")"
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")"
fi
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPTS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPTS")"
@@ -1303,6 +1303,7 @@ fi
# set dependency paths
VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_dedup/main.nf"
VIASH_DEP_UMITOOLS_PREPAREFORQUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools_prepareforquant/main.nf"
VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_calculate_expression/main.nf"
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf"
@@ -1311,7 +1312,6 @@ VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_DEDUP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_dedup/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
@@ -1772,8 +1772,8 @@ if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_QUANT_RESULTS_
ViashError "Output file '$VIASH_PAR_QUANT_RESULTS_FILE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
ViashError "Output file '$VIASH_PAR_COUNTS_GENE' does not exist."
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_GENE" ]; then
ViashError "Output file '$VIASH_PAR_RSEM_COUNTS_GENE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ] && [ ! -e "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then

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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@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

@@ -285,8 +285,8 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

34
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -97,7 +97,7 @@ argument_groups:
multiple_sep: ";"
- type: "file"
name: "--quant_out_dir"
description: "Directory containing quantification results."
description: "Directory containing Salmon quantification results."
info: null
must_exist: true
create_parent: true
@@ -107,7 +107,7 @@ argument_groups:
multiple_sep: ";"
- type: "file"
name: "--quant_results_file"
description: "Quantification file."
description: "Salmon quantification file."
info: null
must_exist: true
create_parent: true
@@ -155,12 +155,32 @@ argument_groups:
multiple_sep: ";"
- type: "string"
name: "--pseudo_aligner"
description: "Method used for [seudo alignment and quantification."
description: "Method used for pseudo alignment and quantification."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_counts_gene"
description: "Expression counts on gene level"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_counts_transcripts"
description: "Expression counts on transcript level"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_qc"
info: null
@@ -1505,6 +1525,9 @@ dependencies:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "rsem/rsem_merge_counts"
repository:
type: "local"
- name: "workflows/merge_quant_results"
repository:
type: "local"
@@ -1592,8 +1615,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"
@@ -1611,6 +1634,7 @@ build_info:
- "target/nextflow/deseq2_qc"
- "target/nextflow/prepare_multiqc_input"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
- "target/nextflow/rsem/rsem_merge_counts"
- "target/nextflow/workflows/merge_quant_results"
package_config:
version: "multiple_fixes"

97
target/executable/workflows/quality_control/quality_control
View File

@@ -222,11 +222,11 @@ function ViashHelp {
echo ""
echo " --quant_out_dir"
echo " type: file, file must exist"
echo " Directory containing quantification results."
echo " Directory containing Salmon quantification results."
echo ""
echo " --quant_results_file"
echo " type: file, file must exist"
echo " Quantification file."
echo " Salmon quantification file."
echo ""
echo " --pseudo_quant_out_dir"
echo " type: file, file must exist"
@@ -246,7 +246,15 @@ function ViashHelp {
echo ""
echo " --pseudo_aligner"
echo " type: string"
echo " Method used for [seudo alignment and quantification."
echo " Method used for pseudo alignment and quantification."
echo ""
echo " --rsem_counts_gene"
echo " type: file, file must exist"
echo " Expression counts on gene level"
echo ""
echo " --rsem_counts_transcripts"
echo " type: file, file must exist"
echo " Expression counts on transcript level"
echo ""
echo " --skip_qc"
echo " type: boolean"
@@ -1012,6 +1020,28 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_PSEUDO_ALIGNER=$(ViashRemoveFlags "$1")
shift 1
;;
--rsem_counts_gene)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --rsem_counts_gene. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--rsem_counts_gene=*)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene=*\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE=$(ViashRemoveFlags "$1")
shift 1
;;
--rsem_counts_transcripts)
[ -n "$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS" ] && ViashError Bad arguments for option \'--rsem_counts_transcripts\': \'$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --rsem_counts_transcripts. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--rsem_counts_transcripts=*)
[ -n "$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS" ] && ViashError Bad arguments for option \'--rsem_counts_transcripts=*\': \'$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS=$(ViashRemoveFlags "$1")
shift 1
;;
--skip_qc)
[ -n "$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="$2"
@@ -2762,6 +2792,14 @@ if [ ! -z "$VIASH_PAR_PSEUDO_KALLISTO_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PA
ViashError "Input file '$VIASH_PAR_PSEUDO_KALLISTO_QUANT_RESULTS_FILE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_GENE" ]; then
ViashError "Input file '$VIASH_PAR_RSEM_COUNTS_GENE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS" ]; then
ViashError "Input file '$VIASH_PAR_RSEM_COUNTS_TRANSCRIPTS' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ] && [ ! -e "$VIASH_PAR_BIOTYPES_HEADER" ]; then
ViashError "Input file '$VIASH_PAR_BIOTYPES_HEADER' does not exist."
exit 1
@@ -3342,6 +3380,7 @@ VIASH_DEP_PRESEQ_LCEXTRAP="$VIASH_META_RESOURCES_DIR/../../../nextflow/preseq_lc
VIASH_DEP_MULTIQC_CUSTOM_BIOTYPE="$VIASH_META_RESOURCES_DIR/../../../nextflow/multiqc_custom_biotype/main.nf"
VIASH_DEP_DESEQ2_QC="$VIASH_META_RESOURCES_DIR/../../../nextflow/deseq2_qc/main.nf"
VIASH_DEP_PREPARE_MULTIQC_INPUT="$VIASH_META_RESOURCES_DIR/../../../nextflow/prepare_multiqc_input/main.nf"
VIASH_DEP_RSEM_RSEM_MERGE_COUNTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_merge_counts/main.nf"
VIASH_DEP_WORKFLOWS_MERGE_QUANT_RESULTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/merge_quant_results/main.nf"
VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf"
VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"
@@ -3581,6 +3620,7 @@ workflow run_wf {
| toSortedList
// TODO: Get Salmon meta info
| map { list ->
def ids = list.collect { id, state -> state.id }
def strandedness = list.collect { id, state -> state.strandedness }
@@ -3620,6 +3660,14 @@ workflow run_wf {
(state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ?
state.quant_results_file :
null }
def rsem_counts_gene = list.collect { id, state ->
(state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ?
state.rsem_counts_gene :
null }
def rsem_counts_transcripts = list.collect { id, state ->
(state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ?
state.rsem_counts_transcripts :
null }
def pseudo_salmon_quant_results = list.collect { id, state ->
(state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ?
state.pseudo_salmon_quant_results_file :
@@ -3714,9 +3762,9 @@ workflow run_wf {
def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc } .unique()[0]
def aligner = list.collect { id, state -> state.aligner } .unique()[0]
def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner } .unique()[0]
def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
def aligner = list.collect { id, state -> state.aligner }.unique()[0]
def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
@@ -3754,6 +3802,8 @@ workflow run_wf {
read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping,
tin_output_summary: tin_output_summary,
quant_results: quant_results,
rsem_counts_gene: rsem_counts_gene,
rsem_counts_transcripts: rsem_counts_transcripts,
pseudo_salmon_quant_results: pseudo_salmon_quant_results,
pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
gtf: gtf,
@@ -3781,7 +3831,7 @@ workflow run_wf {
// Merge quantification results of alignment
| merge_quant_results.run (
runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' },
runIf: { id, state -> (!state.skip_align && state.aligner == 'star_salmon') || !skip_pseudo_align },
fromState: [
"salmon_quant_results": "quant_results",
"gtf": "gtf",
@@ -3803,16 +3853,33 @@ workflow run_wf {
key: "merge_qunat_results"
)
| rsem_merge_counts.run (
runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [
"counts_gene": "rsem_counts_gene",
"counts_transcripts": "rsem_counts_transcripts"
],
toState: [
"tpm_gene": "merged_gene_tpm",
"counts_gene": "merged_gene_counts",
"tpm_transcript": "merged_transcript_tpm",
"counts_transcript": "merged_transcript_counts"
]
)
| deseq2_qc.run (
runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_align },
fromState: [
"counts": "counts_gene_length_scaled",
"pca_header_multiqc": "pca_header_multiqc",
"clustering_header_multiqc": "clustering_header_multiqc",
"deseq2_vst": "deseq2_vst",
"extra_deseq2_args": "extra_deseq2_args",
"extra_deseq2_args2": "extra_deseq2_args2"
],
fromState: { id, state ->
def counts = (state.aligner == "star_rsem") ? state.counts_gene : state.counts_gene_length_scaled
[
counts: counts,
pca_header_multiqc: state.pca_header_multiqc,
clustering_header_multiqc: state.clustering_header_multiqc,
deseq2_vst: state.deseq2_vst,
extra_deseq2_args: state.extra_deseq2_args,
extra_deseq2_args2: state.extra_deseq2_args2
]
},
toState: [
"deseq2_output": "deseq2_output",
"deseq2_pca_multiqc": "pca_multiqc",

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