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Build branch main with version main (dc7b33d)

Browse Source 
Build pipeline: viash-hub.biobox.main-62lvg

Source commit: dc7b33d51f

Source message: Bcftools Norm (#144)

* Initial Commit

* config and help.txt

* script.sh

* test template

* More tests and debugging

* test 5 and 6

* test 7, 8, 9

* Update test.sh

* fixing bug on config

* Changelog

* Update config.vsh.yaml

* Requested changes

* Bug fixing

---------

Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
This commit is contained in:
CI
2024-09-10 14:36:08 +00:00
parent db2f4203b8
commit 2a330fe450
235 changed files with 7748 additions and 280 deletions
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2
target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
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@@ -187,7 +187,7 @@ build_info:
output: "target/executable/bedtools/bedtools_bamtofastq"
executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
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@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:47Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
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@@ -176,7 +176,7 @@ build_info:
output: "target/executable/bedtools/bedtools_bed12tobed6"
executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
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@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
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@@ -214,7 +214,7 @@ build_info:
output: "target/executable/bedtools/bedtools_bedtobam"
executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
View File

@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:48Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
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@@ -337,7 +337,7 @@ build_info:
output: "target/executable/bedtools/bedtools_genomecov"
executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
View File

@@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
View File

@@ -232,7 +232,7 @@ build_info:
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
View File

@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
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@@ -273,7 +273,7 @@ build_info:
output: "target/executable/bedtools/bedtools_groupby"
executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_groupby/bedtools_groupby
View File

@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:48Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
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@@ -410,7 +410,7 @@ build_info:
output: "target/executable/bedtools/bedtools_intersect"
executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_intersect/bedtools_intersect
View File

@@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:47Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_links/.config.vsh.yaml
View File

@@ -210,7 +210,7 @@ build_info:
output: "target/executable/bedtools/bedtools_links"
executable: "target/executable/bedtools/bedtools_links/bedtools_links"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_links/bedtools_links
View File

@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:47Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_merge/.config.vsh.yaml
View File

@@ -279,7 +279,7 @@ build_info:
output: "target/executable/bedtools/bedtools_merge"
executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_merge/bedtools_merge
View File

@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bedtools/bedtools_sort/.config.vsh.yaml
View File

@@ -222,7 +222,7 @@ build_info:
output: "target/executable/bedtools/bedtools_sort"
executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
viash_version: "0.9.0-RC7"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_sort/bedtools_sort
View File

@@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
LABEL org.opencontainers.image.created="2024-09-10T14:19:48Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER