vsh/biobox
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (3481750)

Browse Source 
Build pipeline: viash-hub.biobox.main-2mtst

Source commit: 3481750f6e

Source message: Output alignments to the transcriptome (#56)

* Output alignments to  the transcriptome

* Change argument name
This commit is contained in:
CI
2024-06-24 09:29:59 +00:00
parent 9c30676332
commit 9747a7a8d9
117 changed files with 243 additions and 286 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
target/executable/arriba/.config.vsh.yaml
View File

@@ -688,7 +688,7 @@ build_info:
output: "target/executable/arriba"
executable: "target/executable/arriba/arriba"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/arriba/arriba
View File

@@ -749,9 +749,9 @@ ENTRYPOINT []
RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component arriba"
LABEL org.opencontainers.image.created="2024-06-24T08:36:43Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:58Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/bcl_convert/.config.vsh.yaml
View File

@@ -386,7 +386,7 @@ build_info:
output: "target/executable/bcl_convert"
executable: "target/executable/bcl_convert/bcl_convert"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bcl_convert/bcl_convert
View File

@@ -593,9 +593,9 @@ rm /tmp/bcl-convert.rpm
RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
LABEL org.opencontainers.image.created="2024-06-24T08:36:37Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:52Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -217,7 +217,7 @@ build_info:
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -521,9 +521,9 @@ RUN apt-get update && \
RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2024-06-24T08:36:44Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/busco/busco_download_datasets/.config.vsh.yaml
View File

@@ -144,7 +144,7 @@ build_info:
output: "target/executable/busco/busco_download_datasets"
executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/busco/busco_download_datasets/busco_download_datasets
View File

@@ -470,9 +470,9 @@ ENTRYPOINT []
RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
LABEL org.opencontainers.image.created="2024-06-24T08:36:44Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/busco/busco_list_datasets/.config.vsh.yaml
View File

@@ -131,7 +131,7 @@ build_info:
output: "target/executable/busco/busco_list_datasets"
executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/busco/busco_list_datasets/busco_list_datasets
View File

@@ -460,9 +460,9 @@ ENTRYPOINT []
RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
LABEL org.opencontainers.image.created="2024-06-24T08:36:43Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/busco/busco_run/.config.vsh.yaml
View File

@@ -404,7 +404,7 @@ build_info:
output: "target/executable/busco/busco_run"
executable: "target/executable/busco/busco_run/busco_run"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/busco/busco_run/busco_run
View File

@@ -623,9 +623,9 @@ ENTRYPOINT []
RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
LABEL org.opencontainers.image.created="2024-06-24T08:36:43Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:59Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/cutadapt/.config.vsh.yaml
View File

@@ -707,7 +707,7 @@ build_info:
output: "target/executable/cutadapt"
executable: "target/executable/cutadapt/cutadapt"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/cutadapt/cutadapt
View File

@@ -810,9 +810,9 @@ RUN pip install --upgrade pip && \
RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
LABEL org.opencontainers.image.created="2024-06-24T08:36:37Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:52Z"
LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/falco/.config.vsh.yaml
View File

@@ -304,7 +304,7 @@ build_info:
output: "target/executable/falco"
executable: "target/executable/falco/falco"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/falco/falco
View File

@@ -584,9 +584,9 @@ make install
RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component falco"
LABEL org.opencontainers.image.created="2024-06-24T08:36:47Z"
LABEL org.opencontainers.image.created="2024-06-24T09:15:02Z"
LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/fastp/.config.vsh.yaml
View File

@@ -1065,7 +1065,7 @@ build_info:
output: "target/executable/fastp"
executable: "target/executable/fastp/fastp"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/fastp/fastp
View File

@@ -1023,9 +1023,9 @@ ENTRYPOINT []
RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component fastp"
LABEL org.opencontainers.image.created="2024-06-24T08:36:44Z"
LABEL org.opencontainers.image.created="2024-06-24T09:15:00Z"
LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/featurecounts/.config.vsh.yaml
View File

@@ -631,7 +631,7 @@ build_info:
output: "target/executable/featurecounts"
executable: "target/executable/featurecounts/featurecounts"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/featurecounts/featurecounts
View File

@@ -749,9 +749,9 @@ ENTRYPOINT []
RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
LABEL org.opencontainers.image.created="2024-06-24T08:36:36Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:51Z"
LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/gffread/.config.vsh.yaml
View File

@@ -671,7 +671,7 @@ build_info:
output: "target/executable/gffread"
executable: "target/executable/gffread/gffread"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/gffread/gffread
View File

@@ -802,9 +802,9 @@ ENTRYPOINT []
RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component gffread"
LABEL org.opencontainers.image.created="2024-06-24T08:36:41Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:57Z"
LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/lofreq/lofreq_call/.config.vsh.yaml
View File

@@ -489,7 +489,7 @@ build_info:
output: "target/executable/lofreq/lofreq_call"
executable: "target/executable/lofreq/lofreq_call/lofreq_call"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/lofreq/lofreq_call/lofreq_call
View File

@@ -651,9 +651,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
echo "lofreq: $version" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
LABEL org.opencontainers.image.created="2024-06-24T08:36:46Z"
LABEL org.opencontainers.image.created="2024-06-24T09:15:02Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
View File

@@ -197,7 +197,7 @@ build_info:
output: "target/executable/lofreq/lofreq_indelqual"
executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
View File

@@ -496,9 +496,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
echo "lofreq: $version" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
LABEL org.opencontainers.image.created="2024-06-24T08:36:46Z"
LABEL org.opencontainers.image.created="2024-06-24T09:15:02Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/multiqc/.config.vsh.yaml
View File

@@ -438,7 +438,7 @@ build_info:
output: "target/executable/multiqc"
executable: "target/executable/multiqc/multiqc"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/multiqc/multiqc
View File

@@ -632,9 +632,9 @@ ENTRYPOINT []
RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component multiqc"
LABEL org.opencontainers.image.created="2024-06-24T08:36:38Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:53Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/pear/.config.vsh.yaml
View File

@@ -380,7 +380,7 @@ build_info:
output: "target/executable/pear"
executable: "target/executable/pear/pear"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/pear/pear
View File

@@ -592,9 +592,9 @@ RUN version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \
echo "pear: $version" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component pear"
LABEL org.opencontainers.image.created="2024-06-24T08:36:41Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:56Z"
LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/salmon/salmon_index/.config.vsh.yaml
View File

@@ -263,7 +263,7 @@ build_info:
output: "target/executable/salmon/salmon_index"
executable: "target/executable/salmon/salmon_index/salmon_index"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/salmon/salmon_index/salmon_index
View File

@@ -541,9 +541,9 @@ ENTRYPOINT []
RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
LABEL org.opencontainers.image.created="2024-06-24T08:36:42Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:58Z"
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/salmon/salmon_quant/.config.vsh.yaml
View File

@@ -1159,7 +1159,7 @@ build_info:
output: "target/executable/salmon/salmon_quant"
executable: "target/executable/salmon/salmon_quant/salmon_quant"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/salmon/salmon_quant/salmon_quant
View File

@@ -1163,9 +1163,9 @@ ENTRYPOINT []
RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
LABEL org.opencontainers.image.created="2024-06-24T08:36:42Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:57Z"
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_collate/.config.vsh.yaml
View File

@@ -250,7 +250,7 @@ build_info:
output: "target/executable/samtools/samtools_collate"
executable: "target/executable/samtools/samtools_collate/samtools_collate"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_collate/samtools_collate
View File

@@ -514,9 +514,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
LABEL org.opencontainers.image.created="2024-06-24T08:36:40Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:56Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_faidx/.config.vsh.yaml
View File

@@ -229,7 +229,7 @@ build_info:
output: "target/executable/samtools/samtools_faidx"
executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_faidx/samtools_faidx
View File

@@ -507,9 +507,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
LABEL org.opencontainers.image.created="2024-06-24T08:36:38Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:54Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_fastq/.config.vsh.yaml
View File

@@ -417,7 +417,7 @@ build_info:
output: "target/executable/samtools/samtools_fastq"
executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_fastq/samtools_fastq
View File

@@ -620,9 +620,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
LABEL org.opencontainers.image.created="2024-06-24T08:36:41Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:56Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_flagstat/.config.vsh.yaml
View File

@@ -159,7 +159,7 @@ build_info:
output: "target/executable/samtools/samtools_flagstat"
executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_flagstat/samtools_flagstat
View File

@@ -469,9 +469,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
LABEL org.opencontainers.image.created="2024-06-24T08:36:40Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:55Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_idxstats/.config.vsh.yaml
View File

@@ -169,7 +169,7 @@ build_info:
output: "target/executable/samtools/samtools_idxstats"
executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_idxstats/samtools_idxstats
View File

@@ -473,9 +473,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
LABEL org.opencontainers.image.created="2024-06-24T08:36:39Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:54Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_index/.config.vsh.yaml
View File

@@ -175,7 +175,7 @@ build_info:
output: "target/executable/samtools/samtools_index"
executable: "target/executable/samtools/samtools_index/samtools_index"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_index/samtools_index
View File

@@ -480,9 +480,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
LABEL org.opencontainers.image.created="2024-06-24T08:36:40Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:55Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_sort/.config.vsh.yaml
View File

@@ -318,7 +318,7 @@ build_info:
output: "target/executable/samtools/samtools_sort"
executable: "target/executable/samtools/samtools_sort/samtools_sort"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_sort/samtools_sort
View File

@@ -551,9 +551,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
LABEL org.opencontainers.image.created="2024-06-24T08:36:39Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:54Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_stats/.config.vsh.yaml
View File

@@ -380,7 +380,7 @@ build_info:
output: "target/executable/samtools/samtools_stats"
executable: "target/executable/samtools/samtools_stats/samtools_stats"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_stats/samtools_stats
View File

@@ -568,9 +568,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
LABEL org.opencontainers.image.created="2024-06-24T08:36:39Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:55Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_view/.config.vsh.yaml
View File

@@ -651,7 +651,7 @@ build_info:
output: "target/executable/samtools/samtools_view"
executable: "target/executable/samtools/samtools_view/samtools_view"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_view/samtools_view
View File

@@ -820,9 +820,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
LABEL org.opencontainers.image.created="2024-06-24T08:36:38Z"
LABEL org.opencontainers.image.created="2024-06-24T09:14:53Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

15
target/executable/star/star_align_reads/.config.vsh.yaml
View File

@@ -1966,6 +1966,19 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--reads_aligned_to_transcriptome"
description: "The output file containing the alignments to transcriptome in BAM\
\ formats. This file is generated when --quantMode is set to TranscriptomeSAM."
info: null
example:
- "transcriptome_aligned.bam"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
@@ -2095,7 +2108,7 @@ build_info:
output: "target/executable/star/star_align_reads"
executable: "target/executable/star/star_align_reads/star_align_reads"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

43
target/executable/star/star_align_reads/star_align_reads
View File

@@ -1360,6 +1360,13 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " example: splice_junctions.tsv"
echo " The output file containing the splice junctions."
echo ""
echo " --reads_aligned_to_transcriptome"
echo " type: file, output, file must exist"
echo " example: transcriptome_aligned.bam"
echo " The output file containing the alignments to transcriptome in BAM"
echo " formats. This file is generated when --quantMode is set to"
echo " TranscriptomeSAM."
}
# initialise variables
@@ -1658,9 +1665,9 @@ RUN apt-get update && \
RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
LABEL org.opencontainers.image.created="2024-06-24T08:36:45Z"
LABEL org.opencontainers.image.created="2024-06-24T09:15:00Z"
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -3821,6 +3828,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_SPLICE_JUNCTIONS=$(ViashRemoveFlags "$1")
shift 1
;;
--reads_aligned_to_transcriptome)
[ -n "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && ViashError Bad arguments for option \'--reads_aligned_to_transcriptome\': \'$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --reads_aligned_to_transcriptome. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--reads_aligned_to_transcriptome=*)
[ -n "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && ViashError Bad arguments for option \'--reads_aligned_to_transcriptome=*\': \'$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
@@ -4814,6 +4832,9 @@ fi
if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_SPLICE_JUNCTIONS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_SPLICE_JUNCTIONS")"
fi
if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && [ ! -d "$(dirname "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
@@ -4907,6 +4928,11 @@ if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ]; then
VIASH_PAR_SPLICE_JUNCTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_SPLICE_JUNCTIONS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SPLICE_JUNCTIONS" )
fi
if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")" )
VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME=$(ViashDockerAutodetectMount "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -5146,7 +5172,8 @@ par = {
'unmapped_r2': $( if [ ! -z ${VIASH_PAR_UNMAPPED_R2+x} ]; then echo "r'${VIASH_PAR_UNMAPPED_R2//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'chimeric_junctions': $( if [ ! -z ${VIASH_PAR_CHIMERIC_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_CHIMERIC_JUNCTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'log': $( if [ ! -z ${VIASH_PAR_LOG+x} ]; then echo "r'${VIASH_PAR_LOG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'splice_junctions': $( if [ ! -z ${VIASH_PAR_SPLICE_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_SPLICE_JUNCTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi )
'splice_junctions': $( if [ ! -z ${VIASH_PAR_SPLICE_JUNCTIONS+x} ]; then echo "r'${VIASH_PAR_SPLICE_JUNCTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'reads_aligned_to_transcriptome': $( if [ ! -z ${VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME+x} ]; then echo "r'${VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME//\'/\'\"\'\"r\'}'"; else echo None; fi )
}
meta = {
'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
@@ -5210,7 +5237,8 @@ expected_outputs = {
"log": "Log.final.out",
"splice_junctions": "SJ.out.tab",
"unmapped": "Unmapped.out.mate1",
"unmapped_r2": "Unmapped.out.mate2"
"unmapped_r2": "Unmapped.out.mate2",
"reads_aligned_to_transcriptome": "Aligned.toTranscriptome.out.bam"
}
output_paths = {name: par[name] for name in expected_outputs.keys()}
for name in expected_outputs.keys():
@@ -5338,6 +5366,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ]; then
VIASH_PAR_SPLICE_JUNCTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_SPLICE_JUNCTIONS")
fi
if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ]; then
VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME=$(ViashDockerStripAutomount "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
@@ -5382,6 +5413,10 @@ if [ ! -z "$VIASH_PAR_SPLICE_JUNCTIONS" ] && [ ! -e "$VIASH_PAR_SPLICE_JUNCTIONS
ViashError "Output file '$VIASH_PAR_SPLICE_JUNCTIONS' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ] && [ ! -e "$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME" ]; then
ViashError "Output file '$VIASH_PAR_READS_ALIGNED_TO_TRANSCRIPTOME' does not exist."
exit 1
fi
exit 0

2
target/executable/star/star_genome_generate/.config.vsh.yaml
View File

@@ -319,7 +319,7 @@ build_info:
output: "target/executable/star/star_genome_generate"
executable: "target/executable/star/star_genome_generate/star_genome_generate"
viash_version: "0.9.0-RC6"
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
git_commit: "3481750f6e2d77defa28423d832ff251da3a1f9e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/star/star_genome_generate/star_genome_generate
View File

@@ -572,9 +572,9 @@ RUN apt-get update && \
RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
LABEL org.opencontainers.image.created="2024-06-24T08:36:46Z"
LABEL org.opencontainers.image.created="2024-06-24T09:15:01Z"
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
LABEL org.opencontainers.image.revision="d0c648fb7eefe067f5b5b3d402a204354bb37198"
LABEL org.opencontainers.image.revision="3481750f6e2d77defa28423d832ff251da3a1f9e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER