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Build branch main with version main (05d48ac)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-c7sdt

Source commit: 05d48ac2f8

Source message: Multiple fixes (#26)

* unset argument if not paired

* fix argument name

* add count_read_pairs argument

* output star log

* move biotypes header file into multiqc_custom_biotype component

* move deseq2 header files into deseq2_qc component

* update output defaults

* use biobox main

* add parameters to example

* update component

* update component

* ribo database processing moved to workflow

* clean code, remove unused arguments
This commit is contained in:
CI
2024-10-25 09:08:46 +00:00
parent 54557aa596
commit fe41adb0c7
298 changed files with 3125 additions and 3983 deletions
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9
target/executable/ucsc/bedclip/.config.vsh.yaml
View File

@@ -66,7 +66,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -164,9 +164,10 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -176,7 +177,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/ucsc/bedclip/bedclip
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@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-10-04T07:06:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedclip:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedclip:main'
fi
# print dockerfile

9
target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
View File

@@ -66,7 +66,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -164,9 +164,10 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -176,7 +177,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
View File

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-10-04T07:06:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:47Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedgraphtobigwig:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedgraphtobigwig:main'
fi
# print dockerfile