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Build branch main with version main (1d87dc7)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-g2rlq

Source commit: 1d87dc7c24

Source message: Multiple fixes (#23)

* multiple fixes

* update arguments and add test

* fix biobox module calls

* fix dependency

* add rsem merge counts

* exclude general stats in multiqc report

* output markduplicates metrics

* rename output reference files
This commit is contained in:
CI
2024-10-01 10:12:28 +00:00
parent 9b29e37466
commit c106022744
237 changed files with 9490 additions and 2187 deletions
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4
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
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@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
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@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
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@@ -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="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
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@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
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@@ -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="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
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@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

6
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
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@@ -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="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
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@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
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@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
View File

@@ -211,8 +211,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
View File

@@ -214,8 +214,8 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -501,9 +501,9 @@ RUN apt-get update && \
RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER