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Build branch seqtk_sample with version seqtk_sample (796c3bc)

Browse Source 
Build pipeline: viash-hub.biobox.seqtk-sample-plh2n

Source commit: 796c3bcdbb

Source message: changelog entry added
This commit is contained in:
CI
2024-06-27 09:43:57 +00:00
parent bffa3e8e13
commit 8ccd0dfd21
114 changed files with 828 additions and 988 deletions
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3
CHANGELOG.md
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@@ -50,6 +50,9 @@
* `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
* `seqtk/seqtk_sample`: Sample sequences from FASTA/Q(.gz) files
to FASTA/Q (PR #68).
## MAJOR CHANGES

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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:32Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:51Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

2
target/executable/bcl_convert/.config.vsh.yaml
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@@ -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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:30Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:49Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobbox"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

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

@@ -256,7 +256,7 @@ build_info:
output: "target/executable/bgzip"
executable: "target/executable/bgzip/bgzip"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bgzip/bgzip
View File

@@ -508,9 +508,9 @@ ENTRYPOINT []
RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bgzip"
LABEL org.opencontainers.image.created="2024-06-27T09:24:22Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:41Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/htslib"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:25Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:44Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:26Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:44Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:26Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:45Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

2
target/executable/falco/.config.vsh.yaml
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@@ -304,7 +304,7 @@ build_info:
output: "target/executable/falco"
executable: "target/executable/falco/falco"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/falco/falco
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@@ -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="2024-06-27T09:24:23Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:42Z"
LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:24Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:43Z"
LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:32Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:51Z"
LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:24Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:42Z"
LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:26Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:45Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobbox"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:26Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:45Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobbox"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:23Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:42Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobbox"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:30Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:49Z"
LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:31Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:50Z"
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

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

@@ -1153,7 +1153,7 @@ build_info:
output: "target/executable/salmon/salmon_quant"
executable: "target/executable/salmon/salmon_quant/salmon_quant"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -1157,9 +1157,9 @@ 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="2024-06-27T09:24:31Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:50Z"
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:28Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:47Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:29Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:48Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:28Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:47Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:29Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:48Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:29Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:48Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:27Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:46Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:29Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:48Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:28Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:47Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
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="2024-06-27T09:24:27Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:46Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

2
target/executable/seqtk/seqtk_sample/.config.vsh.yaml
View File

@@ -163,7 +163,7 @@ build_info:
output: "target/executable/seqtk/seqtk_sample"
executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/seqtk/seqtk_sample/seqtk_sample
View File

@@ -477,9 +477,9 @@ function ViashDockerfile {
FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
LABEL org.opencontainers.image.created="2024-06-27T09:24:31Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:49Z"
LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

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

@@ -2095,7 +2095,7 @@ 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: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/star/star_align_reads/star_align_reads
View File

@@ -1658,9 +1658,9 @@ 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="2024-06-27T09:24:24Z"
LABEL org.opencontainers.image.created="2024-06-27T09:29:43Z"
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
LABEL org.opencontainers.image.revision="0edf4d8d6700495424c4910e0c5047693d015b63"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"
VIASHDOCKER

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

@@ -688,7 +688,7 @@ build_info:
output: "target/nextflow/arriba"
executable: "target/nextflow/arriba/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/arriba/main.nf
View File

@@ -3534,7 +3534,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/arriba",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

467
target/nextflow/arriba/nextflow_schema.json
View File

@@ -1,467 +0,0 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "arriba",
"description": "Detect gene fusions from RNA-Seq data",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"bam": {
"type":
"string",
"description": "Type: `file`, required, example: `Aligned.out.bam`. File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned",
"help_text": "Type: `file`, required, example: `Aligned.out.bam`. File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned.out.sam). Arriba extracts candidate reads from this file.\n"
}
,
"genome": {
"type":
"string",
"description": "Type: `file`, required, example: `assembly.fa`. FastA file with genome sequence (assembly)",
"help_text": "Type: `file`, required, example: `assembly.fa`. FastA file with genome sequence (assembly). The file may be gzip-compressed. An \nindex with the file extension .fai must exist only if CRAM files are processed.\n"
}
,
"gene_annotation": {
"type":
"string",
"description": "Type: `file`, required, example: `annotation.gtf`. GTF file with gene annotation",
"help_text": "Type: `file`, required, example: `annotation.gtf`. GTF file with gene annotation. The file may be gzip-compressed.\n"
}
,
"known_fusions": {
"type":
"string",
"description": "Type: `file`, example: `known_fusions.tsv`. File containing known/recurrent fusions",
"help_text": "Type: `file`, example: `known_fusions.tsv`. File containing known/recurrent fusions. Some cancer entities are often \ncharacterized by fusions between the same pair of genes. In order to boost \nsensitivity, a list of known fusions can be supplied using this parameter. The list \nmust contain two columns with the names of the fused genes, separated by tabs.\n"
}
,
"blacklist": {
"type":
"string",
"description": "Type: `file`, example: `blacklist.tsv`. File containing blacklisted events (recurrent artifacts and transcripts \nobserved in healthy tissue)",
"help_text": "Type: `file`, example: `blacklist.tsv`. File containing blacklisted events (recurrent artifacts and transcripts \nobserved in healthy tissue).\n"
}
,
"structural_variants": {
"type":
"string",
"description": "Type: `file`, example: `structural_variants_from_WGS.tsv`. Tab-separated file with coordinates of structural variants found using \nwhole-genome sequencing data",
"help_text": "Type: `file`, example: `structural_variants_from_WGS.tsv`. Tab-separated file with coordinates of structural variants found using \nwhole-genome sequencing data. These coordinates serve to increase sensitivity \ntowards weakly expressed fusions and to eliminate fusions with low evidence. \n"
}
,
"tags": {
"type":
"string",
"description": "Type: `file`, example: `tags.tsv`. Tab-separated file containing fusions to annotate with tags in the \u0027tags\u0027 column",
"help_text": "Type: `file`, example: `tags.tsv`. Tab-separated file containing fusions to annotate with tags in the \u0027tags\u0027 column. \nThe first two columns specify the genes; the third column specifies the tag. The \nfile may be gzip-compressed. \n"
}
,
"protein_domains": {
"type":
"string",
"description": "Type: `file`, example: `protein_domains.gff3`. File in GFF3 format containing coordinates of the protein domains of genes",
"help_text": "Type: `file`, example: `protein_domains.gff3`. File in GFF3 format containing coordinates of the protein domains of genes. The\nprotein domains retained in a fusion are listed in the column\n\u0027retained_protein_domains\u0027. The file may be gzip-compressed.\n"
}
}
},
"outputs" : {
"title": "Outputs",
"type": "object",
"description": "No description",
"properties": {
"fusions": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.fusions.tsv`, example: `fusions.tsv`. Output file with fusions that have passed all filters",
"help_text": "Type: `file`, required, default: `$id.$key.fusions.tsv`, example: `fusions.tsv`. Output file with fusions that have passed all filters.\n"
,
"default": "$id.$key.fusions.tsv"
}
,
"fusions_discarded": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.fusions_discarded.tsv`, example: `fusions.discarded.tsv`. Output file with fusions that were discarded due to filtering",
"help_text": "Type: `file`, default: `$id.$key.fusions_discarded.tsv`, example: `fusions.discarded.tsv`. Output file with fusions that were discarded due to filtering. \n"
,
"default": "$id.$key.fusions_discarded.tsv"
}
}
},
"arguments" : {
"title": "Arguments",
"type": "object",
"description": "No description",
"properties": {
"max_genomic_breakpoint_distance": {
"type":
"string",
"description": "Type: `long`. When a file with genomic breakpoints obtained via \nwhole-genome sequencing is supplied via the --structural_variants\nparameter, this parameter determines how far a \ngenomic breakpoint may be away from a \ntranscriptomic breakpoint to consider it as a \nrelated event",
"help_text": "Type: `long`. When a file with genomic breakpoints obtained via \nwhole-genome sequencing is supplied via the --structural_variants\nparameter, this parameter determines how far a \ngenomic breakpoint may be away from a \ntranscriptomic breakpoint to consider it as a \nrelated event. For events inside genes, the \ndistance is added to the end of the gene; for \nintergenic events, the distance threshold is \napplied as is. Default: 100000.\n"
}
,
"strandedness": {
"type":
"string",
"description": "Type: `string`, choices: ``auto`, `yes`, `no`, `reverse``. Whether a strand-specific protocol was used for library preparation, \nand if so, the type of strandedness (auto/yes/no/reverse)",
"help_text": "Type: `string`, choices: ``auto`, `yes`, `no`, `reverse``. Whether a strand-specific protocol was used for library preparation, \nand if so, the type of strandedness (auto/yes/no/reverse). When \nunstranded data is processed, the strand can sometimes be inferred from \nsplice-patterns. But in unclear situations, stranded data helps \nresolve ambiguities. Default: auto\n",
"enum": ["auto", "yes", "no", "reverse"]
}
,
"interesting_contigs": {
"type":
"string",
"description": "Type: List of `string`, example: `1:2:AC_*:NC_*`, multiple_sep: `\":\"`. List of interesting contigs",
"help_text": "Type: List of `string`, example: `1:2:AC_*:NC_*`, multiple_sep: `\":\"`. List of interesting contigs. Fusions between genes \non other contigs are ignored. Contigs can be specified with or without the \nprefix \"chr\". Asterisks (*) are treated as wild-cards. \nDefault: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*\n"
}
,
"viral_contigs": {
"type":
"string",
"description": "Type: List of `string`, example: `AC_*:NC_*`, multiple_sep: `\":\"`. List of viral contigs",
"help_text": "Type: List of `string`, example: `AC_*:NC_*`, multiple_sep: `\":\"`. List of viral contigs. Asterisks (*) are treated as \nwild-cards.\nDefault: AC_* NC_*\n"
}
,
"disable_filters": {
"type":
"string",
"description": "Type: List of `string`, multiple_sep: `\":\"`, choices: ``homologs`, `low_entropy`, `isoforms`, `top_expressed_viral_contigs`, `viral_contigs`, `uninteresting_contigs`, `non_coding_neighbors`, `mismatches`, `duplicates`, `no_genomic_support`, `genomic_support`, `intronic`, `end_to_end`, `relative_support`, `low_coverage_viral_contigs`, `merge_adjacent`, `mismappers`, `multimappers`, `same_gene`, `long_gap`, `internal_tandem_duplication`, `small_insert_size`, `read_through`, `inconsistently_clipped`, `intragenic_exonic`, `marginal_read_through`, `spliced`, `hairpin`, `blacklist`, `min_support`, `select_best`, `in_vitro`, `short_anchor`, `known_fusions`, `no_coverage`, `homopolymer`, `many_spliced``. List of filters to disable",
"help_text": "Type: List of `string`, multiple_sep: `\":\"`, choices: ``homologs`, `low_entropy`, `isoforms`, `top_expressed_viral_contigs`, `viral_contigs`, `uninteresting_contigs`, `non_coding_neighbors`, `mismatches`, `duplicates`, `no_genomic_support`, `genomic_support`, `intronic`, `end_to_end`, `relative_support`, `low_coverage_viral_contigs`, `merge_adjacent`, `mismappers`, `multimappers`, `same_gene`, `long_gap`, `internal_tandem_duplication`, `small_insert_size`, `read_through`, `inconsistently_clipped`, `intragenic_exonic`, `marginal_read_through`, `spliced`, `hairpin`, `blacklist`, `min_support`, `select_best`, `in_vitro`, `short_anchor`, `known_fusions`, `no_coverage`, `homopolymer`, `many_spliced``. List of filters to disable. By default all filters are \nenabled. \n",
"enum": ["homologs", "low_entropy", "isoforms", "top_expressed_viral_contigs", "viral_contigs", "uninteresting_contigs", "non_coding_neighbors", "mismatches", "duplicates", "no_genomic_support", "genomic_support", "intronic", "end_to_end", "relative_support", "low_coverage_viral_contigs", "merge_adjacent", "mismappers", "multimappers", "same_gene", "long_gap", "internal_tandem_duplication", "small_insert_size", "read_through", "inconsistently_clipped", "intragenic_exonic", "marginal_read_through", "spliced", "hairpin", "blacklist", "min_support", "select_best", "in_vitro", "short_anchor", "known_fusions", "no_coverage", "homopolymer", "many_spliced"]
}
,
"max_e_value": {
"type":
"number",
"description": "Type: `double`. Arriba estimates the number of fusions with a given number of supporting \nreads which one would expect to see by random chance",
"help_text": "Type: `double`. Arriba estimates the number of fusions with a given number of supporting \nreads which one would expect to see by random chance. If the expected number \nof fusions (e-value) is higher than this threshold, the fusion is \ndiscarded by the \u0027relative_support\u0027 filter. Note: Increasing this \nthreshold can dramatically increase the number of false positives and may \nincrease the runtime of resource-intensive steps. Fractional values are \npossible. Default: 0.300000 \n"
}
,
"min_supporting_reads": {
"type":
"integer",
"description": "Type: `integer`, example: `2`. The \u0027min_support\u0027 filter discards all fusions with fewer than \nthis many supporting reads (split reads and discordant mates \ncombined)",
"help_text": "Type: `integer`, example: `2`. The \u0027min_support\u0027 filter discards all fusions with fewer than \nthis many supporting reads (split reads and discordant mates \ncombined). Default: 2 \n"
}
,
"max_mismappers": {
"type":
"number",
"description": "Type: `double`, example: `0.8`. When more than this fraction of supporting reads turns out to be \nmismappers, the \u0027mismappers\u0027 filter discards the fusion",
"help_text": "Type: `double`, example: `0.8`. When more than this fraction of supporting reads turns out to be \nmismappers, the \u0027mismappers\u0027 filter discards the fusion. Default: \n0.800000\n"
}
,
"max_homolog_identity": {
"type":
"number",
"description": "Type: `double`, example: `0.3`. Genes with more than the given fraction of sequence identity are \nconsidered homologs and removed by the \u0027homologs\u0027 filter",
"help_text": "Type: `double`, example: `0.3`. Genes with more than the given fraction of sequence identity are \nconsidered homologs and removed by the \u0027homologs\u0027 filter. \nDefault: 0.300000 \n"
}
,
"homopolymer_length": {
"type":
"integer",
"description": "Type: `integer`, example: `6`. The \u0027homopolymer\u0027 filter removes breakpoints adjacent to \nhomopolymers of the given length or more",
"help_text": "Type: `integer`, example: `6`. The \u0027homopolymer\u0027 filter removes breakpoints adjacent to \nhomopolymers of the given length or more. Default: 6\n"
}
,
"read_through_distance": {
"type":
"integer",
"description": "Type: `integer`, example: `10000`. The \u0027read_through\u0027 filter removes read-through fusions \nwhere the breakpoints are less than the given distance away \nfrom each other",
"help_text": "Type: `integer`, example: `10000`. The \u0027read_through\u0027 filter removes read-through fusions \nwhere the breakpoints are less than the given distance away \nfrom each other. Default: 10000 \n"
}
,
"min_anchor_length": {
"type":
"integer",
"description": "Type: `integer`, example: `23`. Alignment artifacts are often characterized by split reads coming \nfrom only one gene and no discordant mates",
"help_text": "Type: `integer`, example: `23`. Alignment artifacts are often characterized by split reads coming \nfrom only one gene and no discordant mates. Moreover, the split \nreads only align to a short stretch in one of the genes. The \n\u0027short_anchor\u0027 filter removes these fusions. This parameter sets \nthe threshold in bp for what the filter considers short. Default: 23 \n"
}
,
"many_spliced_events": {
"type":
"integer",
"description": "Type: `integer`, example: `4`. The \u0027many_spliced\u0027 filter recovers fusions between genes that \nhave at least this many spliced breakpoints",
"help_text": "Type: `integer`, example: `4`. The \u0027many_spliced\u0027 filter recovers fusions between genes that \nhave at least this many spliced breakpoints. Default: 4\n"
}
,
"max_kmer_content": {
"type":
"number",
"description": "Type: `double`, example: `0.6`. The \u0027low_entropy\u0027 filter removes reads with repetitive 3-mers",
"help_text": "Type: `double`, example: `0.6`. The \u0027low_entropy\u0027 filter removes reads with repetitive 3-mers. If \nthe 3-mers make up more than the given fraction of the sequence, then \nthe read is discarded. Default: 0.600000 \n"
}
,
"max_mismatch_pvalue": {
"type":
"number",
"description": "Type: `double`, example: `0.05`. The \u0027mismatches\u0027 filter uses a binomial model to calculate a \np-value for observing a given number of mismatches in a read",
"help_text": "Type: `double`, example: `0.05`. The \u0027mismatches\u0027 filter uses a binomial model to calculate a \np-value for observing a given number of mismatches in a read. If \nthe number of mismatches is too high, the read is discarded. \nDefault: 0.010000 \n"
}
,
"fragment_length": {
"type":
"integer",
"description": "Type: `integer`, example: `200`. When paired-end data is given, the fragment length is estimated \nautomatically and this parameter has no effect",
"help_text": "Type: `integer`, example: `200`. When paired-end data is given, the fragment length is estimated \nautomatically and this parameter has no effect. But when single-end \ndata is given, the mean fragment length should be specified to \neffectively filter fusions that arise from hairpin structures. \nDefault: 200 \n"
}
,
"max_reads": {
"type":
"integer",
"description": "Type: `integer`, example: `300`. Subsample fusions with more than the given number of supporting reads",
"help_text": "Type: `integer`, example: `300`. Subsample fusions with more than the given number of supporting reads. This \nimproves performance without compromising sensitivity, as long as the \nthreshold is high. Counting of supporting reads beyond the threshold is \ninaccurate, obviously. Default: 300 \n"
}
,
"quantile": {
"type":
"number",
"description": "Type: `double`, example: `0.998`. Highly expressed genes are prone to produce artifacts during library \npreparation",
"help_text": "Type: `double`, example: `0.998`. Highly expressed genes are prone to produce artifacts during library \npreparation. Genes with an expression above the given quantile are eligible \nfor filtering by the \u0027in_vitro\u0027 filter. Default: 0.998000\n"
}
,
"exonic_fraction": {
"type":
"number",
"description": "Type: `double`, example: `0.33`. The breakpoints of false-positive predictions of intragenic events \nare often both in exons",
"help_text": "Type: `double`, example: `0.33`. The breakpoints of false-positive predictions of intragenic events \nare often both in exons. True predictions are more likely to have at \nleast one breakpoint in an intron, because introns are larger. If the \nfraction of exonic sequence between two breakpoints is smaller than \nthe given fraction, the \u0027intragenic_exonic\u0027 filter discards the \nevent. Default: 0.330000 \n"
}
,
"top_n": {
"type":
"integer",
"description": "Type: `integer`, example: `5`. Only report viral integration sites of the top N most highly expressed viral \ncontigs",
"help_text": "Type: `integer`, example: `5`. Only report viral integration sites of the top N most highly expressed viral \ncontigs. Default: 5\n"
}
,
"covered_fraction": {
"type":
"number",
"description": "Type: `double`, example: `0.05`. Ignore virally associated events if the virus is not fully \nexpressed, i",
"help_text": "Type: `double`, example: `0.05`. Ignore virally associated events if the virus is not fully \nexpressed, i.e., less than the given fraction of the viral contig is \ntranscribed. Default: 0.050000 \n"
}
,
"max_itd_length": {
"type":
"integer",
"description": "Type: `integer`, example: `100`. Maximum length of internal tandem duplications",
"help_text": "Type: `integer`, example: `100`. Maximum length of internal tandem duplications. Note: Increasing \nthis value beyond the default can impair performance and lead to many \nfalse positives. Default: 100 \n"
}
,
"min_itd_allele_fraction": {
"type":
"number",
"description": "Type: `double`, example: `0.07`. Required fraction of supporting reads to report an internal \ntandem duplication",
"help_text": "Type: `double`, example: `0.07`. Required fraction of supporting reads to report an internal \ntandem duplication. Default: 0.070000 \n"
}
,
"min_itd_supporting_reads": {
"type":
"integer",
"description": "Type: `integer`, example: `10`. Required absolute number of supporting reads to report an \ninternal tandem duplication",
"help_text": "Type: `integer`, example: `10`. Required absolute number of supporting reads to report an \ninternal tandem duplication. Default: 10 \n"
}
,
"skip_duplicate_marking": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a \npreceding program using the BAM_FDUP flag",
"help_text": "Type: `boolean_true`, default: `false`. Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a \npreceding program using the BAM_FDUP flag. This makes sense when unique molecular \nidentifiers (UMI) are used.\n"
,
"default": "False"
}
,
"extra_information": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. To reduce the runtime and file size, by default, the columns \u0027fusion_transcript\u0027, \n\u0027peptide_sequence\u0027, and \u0027read_identifiers\u0027 are left empty in the file containing \ndiscarded fusion candidates (see parameter -O)",
"help_text": "Type: `boolean_true`, default: `false`. To reduce the runtime and file size, by default, the columns \u0027fusion_transcript\u0027, \n\u0027peptide_sequence\u0027, and \u0027read_identifiers\u0027 are left empty in the file containing \ndiscarded fusion candidates (see parameter -O). When this flag is set, this extra \ninformation is reported in the discarded fusions file.\n"
,
"default": "False"
}
,
"fill_gaps": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. If assembly of the fusion transcript sequence from the supporting reads is incomplete \n(denoted as \u0027",
"help_text": "Type: `boolean_true`, default: `false`. If assembly of the fusion transcript sequence from the supporting reads is incomplete \n(denoted as \u0027...\u0027), fill the gaps using the assembly sequence wherever possible. \n"
,
"default": "False"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/inputs"
},
{
"$ref": "#/definitions/outputs"
},
{
"$ref": "#/definitions/arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

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

@@ -386,7 +386,7 @@ build_info:
output: "target/nextflow/bcl_convert"
executable: "target/nextflow/bcl_convert/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/bcl_convert/main.nf
View File

@@ -3249,7 +3249,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bcl_convert",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

2
target/nextflow/bgzip/.config.vsh.yaml
View File

@@ -256,7 +256,7 @@ build_info:
output: "target/nextflow/bgzip"
executable: "target/nextflow/bgzip/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/bgzip/main.nf
View File

@@ -3063,7 +3063,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bgzip",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -144,7 +144,7 @@ build_info:
output: "target/nextflow/busco/busco_download_datasets"
executable: "target/nextflow/busco/busco_download_datasets/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/busco/busco_download_datasets/main.nf
View File

@@ -2959,7 +2959,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/busco/busco_download_datasets",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -131,7 +131,7 @@ build_info:
output: "target/nextflow/busco/busco_list_datasets"
executable: "target/nextflow/busco/busco_list_datasets/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/busco/busco_list_datasets/main.nf
View File

@@ -2945,7 +2945,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/busco/busco_list_datasets",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -404,7 +404,7 @@ build_info:
output: "target/nextflow/busco/busco_run"
executable: "target/nextflow/busco/busco_run/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/busco/busco_run/main.nf
View File

@@ -3251,7 +3251,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/busco/busco_run",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -304,7 +304,7 @@ build_info:
output: "target/nextflow/falco"
executable: "target/nextflow/falco/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/falco/main.nf
View File

@@ -3119,7 +3119,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/falco",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

2
target/nextflow/fastp/.config.vsh.yaml
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@@ -1065,7 +1065,7 @@ build_info:
output: "target/nextflow/fastp"
executable: "target/nextflow/fastp/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/fastp/main.nf
View File

@@ -3965,7 +3965,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/fastp",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -631,7 +631,7 @@ build_info:
output: "target/nextflow/featurecounts"
executable: "target/nextflow/featurecounts/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/featurecounts/main.nf
View File

@@ -3497,7 +3497,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/featurecounts",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

2
target/nextflow/gffread/.config.vsh.yaml
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@@ -671,7 +671,7 @@ build_info:
output: "target/nextflow/gffread"
executable: "target/nextflow/gffread/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/gffread/main.nf
View File

@@ -3554,7 +3554,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/gffread",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -489,7 +489,7 @@ build_info:
output: "target/nextflow/lofreq/lofreq_call"
executable: "target/nextflow/lofreq/lofreq_call/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/lofreq/lofreq_call/main.nf
View File

@@ -3356,7 +3356,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/lofreq/lofreq_call",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

454
target/nextflow/lofreq/lofreq_call/nextflow_schema.json Normal file
View File

@@ -0,0 +1,454 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "lofreq_call",
"description": "Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.\n\nLoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.\n",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: `file`, required, example: `normal.bam`. Input BAM file",
"help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n"
}
,
"input_bai": {
"type":
"string",
"description": "Type: `file`, required, example: `normal.bai`. Index file for the input BAM file",
"help_text": "Type: `file`, required, example: `normal.bai`. Index file for the input BAM file.\n"
}
,
"ref": {
"type":
"string",
"description": "Type: `file`, required, example: `reference.fasta`. Indexed reference fasta file (gzip supported)",
"help_text": "Type: `file`, required, example: `reference.fasta`. Indexed reference fasta file (gzip supported). Default: none.\n"
}
}
},
"outputs" : {
"title": "Outputs",
"type": "object",
"description": "No description",
"properties": {
"out": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.out.vcf`, example: `output.vcf`. Vcf output file",
"help_text": "Type: `file`, required, default: `$id.$key.out.vcf`, example: `output.vcf`. Vcf output file. Default: stdout.\n"
,
"default": "$id.$key.out.vcf"
}
}
},
"arguments" : {
"title": "Arguments",
"type": "object",
"description": "No description",
"properties": {
"region": {
"type":
"string",
"description": "Type: `string`, example: `chr1:1000-2000`. Limit calls to this region (chrom:start-end)",
"help_text": "Type: `string`, example: `chr1:1000-2000`. Limit calls to this region (chrom:start-end). Default: none.\n"
}
,
"bed": {
"type":
"string",
"description": "Type: `file`, example: `regions.bed`. List of positions (chr pos) or regions (BED)",
"help_text": "Type: `file`, example: `regions.bed`. List of positions (chr pos) or regions (BED). Default: none.\n"
}
,
"min_bq": {
"type":
"integer",
"description": "Type: `integer`, example: `6`. Skip any base with baseQ smaller than INT",
"help_text": "Type: `integer`, example: `6`. Skip any base with baseQ smaller than INT. Default: 6.\n"
}
,
"min_alt_bq": {
"type":
"integer",
"description": "Type: `integer`, example: `6`. Skip alternate bases with baseQ smaller than INT",
"help_text": "Type: `integer`, example: `6`. Skip alternate bases with baseQ smaller than INT. Default: 6.\n"
}
,
"def_alt_bq": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep)",
"help_text": "Type: `integer`, example: `0`. Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep). Default: 0.\n"
}
,
"min_jq": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Skip any base with joinedQ smaller than INT",
"help_text": "Type: `integer`, example: `0`. Skip any base with joinedQ smaller than INT. Default: 0.\n"
}
,
"min_alt_jq": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Skip alternate bases with joinedQ smaller than INT",
"help_text": "Type: `integer`, example: `0`. Skip alternate bases with joinedQ smaller than INT. Default: 0.\n"
}
,
"def_alt_jq": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)",
"help_text": "Type: `integer`, example: `0`. Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep). Default: 0.\n"
}
,
"no_baq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Disable use of base-alignment quality (BAQ)",
"help_text": "Type: `boolean_true`, default: `false`. Disable use of base-alignment quality (BAQ).\n"
,
"default": "False"
}
,
"no_idaq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Don\u0027t use IDAQ values (NOT recommended under ANY circumstances other than debugging)",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t use IDAQ values (NOT recommended under ANY circumstances other than debugging).\n"
,
"default": "False"
}
,
"del_baq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Delete pre-existing BAQ values, i",
"help_text": "Type: `boolean_true`, default: `false`. Delete pre-existing BAQ values, i.e. compute even if already present in BAM.\n"
,
"default": "False"
}
,
"no_ext_baq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Use \u0027normal\u0027 BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)",
"help_text": "Type: `boolean_true`, default: `false`. Use \u0027normal\u0027 BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag).\n"
,
"default": "False"
}
,
"min_mq": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Skip reads with mapping quality smaller than INT",
"help_text": "Type: `integer`, example: `0`. Skip reads with mapping quality smaller than INT. Default: 0.\n"
}
,
"max_mq": {
"type":
"integer",
"description": "Type: `integer`, example: `255`. Cap mapping quality at INT",
"help_text": "Type: `integer`, example: `255`. Cap mapping quality at INT. Default: 255.\n"
}
,
"no_mq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Don\u0027t merge mapping quality in LoFreq\u0027s model",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t merge mapping quality in LoFreq\u0027s model.\n"
,
"default": "False"
}
,
"call_indels": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Enable indel calls (note: preprocess your file to include indel alignment qualities!)",
"help_text": "Type: `boolean_true`, default: `false`. Enable indel calls (note: preprocess your file to include indel alignment qualities!).\n"
,
"default": "False"
}
,
"only_indels": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Only call indels; no SNVs",
"help_text": "Type: `boolean_true`, default: `false`. Only call indels; no SNVs.\n"
,
"default": "False"
}
,
"src_qual": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Enable computation of source quality",
"help_text": "Type: `boolean_true`, default: `false`. Enable computation of source quality.\n"
,
"default": "False"
}
,
"ign_vcf": {
"type":
"string",
"description": "Type: `file`, example: `variants.vcf`. Ignore variants in this vcf file for source quality computation",
"help_text": "Type: `file`, example: `variants.vcf`. Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas.\n"
}
,
"def_nm_q": {
"type":
"integer",
"description": "Type: `integer`, example: `-1`. If \u003e= 0, then replace non-match base qualities with this default value",
"help_text": "Type: `integer`, example: `-1`. If \u003e= 0, then replace non-match base qualities with this default value. Default: -1.\n"
}
,
"sig": {
"type":
"number",
"description": "Type: `double`, example: `0.01`. P-Value cutoff / significance level",
"help_text": "Type: `double`, example: `0.01`. P-Value cutoff / significance level. Default: 0.010000.\n"
}
,
"bonf": {
"type":
"string",
"description": "Type: `string`, example: `dynamic`. Bonferroni factor",
"help_text": "Type: `string`, example: `dynamic`. Bonferroni factor. \u0027dynamic\u0027 (increase per actually performed test) or INT. Default: Dynamic.\n"
}
,
"min_cov": {
"type":
"integer",
"description": "Type: `integer`, example: `1`. Test only positions having at least this coverage",
"help_text": "Type: `integer`, example: `1`. Test only positions having at least this coverage. Default: 1.\n(note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done).\n"
}
,
"max_depth": {
"type":
"integer",
"description": "Type: `integer`, example: `1000000`. Cap coverage at this depth",
"help_text": "Type: `integer`, example: `1000000`. Cap coverage at this depth. Default: 1000000.\n"
}
,
"illumina_13": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Assume the quality is Illumina-1",
"help_text": "Type: `boolean_true`, default: `false`. Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.\n"
,
"default": "False"
}
,
"use_orphan": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Count anomalous read pairs (i",
"help_text": "Type: `boolean_true`, default: `false`. Count anomalous read pairs (i.e. where mate is not aligned properly).\n"
,
"default": "False"
}
,
"plp_summary_only": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. No variant calling",
"help_text": "Type: `boolean_true`, default: `false`. No variant calling. Just output pileup summary per column.\n"
,
"default": "False"
}
,
"no_default_filter": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Don\u0027t run default \u0027lofreq filter\u0027 automatically after calling variants",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t run default \u0027lofreq filter\u0027 automatically after calling variants.\n"
,
"default": "False"
}
,
"force_overwrite": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Overwrite any existing output",
"help_text": "Type: `boolean_true`, default: `false`. Overwrite any existing output.\n"
,
"default": "False"
}
,
"verbose": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Be verbose",
"help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n"
,
"default": "False"
}
,
"debug": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Enable debugging",
"help_text": "Type: `boolean_true`, default: `false`. Enable debugging.\n"
,
"default": "False"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/inputs"
},
{
"$ref": "#/definitions/outputs"
},
{
"$ref": "#/definitions/arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

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

@@ -197,7 +197,7 @@ build_info:
output: "target/nextflow/lofreq/lofreq_indelqual"
executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/lofreq/lofreq_indelqual/main.nf
View File

@@ -3019,7 +3019,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/lofreq/lofreq_indelqual",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

71
target/nextflow/seqtk/seqtk_sample/nextflow_schema.json → target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json
View File

@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "seqtk_sample",
"description": "Subsamples sequences from FASTA/Q files.",
"title": "lofreq_indelqual",
"description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\u0027s BQSR (\u003e=2) If that\u0027s not possible, use this subcommand.\nThe command has two modes: \u0027uniform\u0027 and \u0027dindel\u0027:\n- \u0027uniform\u0027 will assign a given value uniformly, whereas\n- \u0027dindel\u0027 will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n",
"type": "object",
"definitions": {
@@ -17,8 +17,18 @@
"input": {
"type":
"string",
"description": "Type: `file`, required. The input FASTA/Q file",
"help_text": "Type: `file`, required. The input FASTA/Q file."
"description": "Type: `file`, required, example: `normal.bam`. Input BAM file",
"help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n"
}
,
"ref": {
"type":
"string",
"description": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel)",
"help_text": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel).\n"
}
@@ -34,13 +44,13 @@
"properties": {
"output": {
"out": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.output`. The output FASTA/Q file",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. The output FASTA/Q file."
"description": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file",
"help_text": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file.\n"
,
"default": "$id.$key.output.output"
"default": "$id.$key.out.bam"
}
@@ -48,40 +58,39 @@
},
"options" : {
"title": "Options",
"arguments" : {
"title": "Arguments",
"type": "object",
"description": "No description",
"properties": {
"seed": {
"uniform": {
"type":
"integer",
"description": "Type: `integer`, default: `42`. Seed for random generator",
"help_text": "Type: `integer`, default: `42`. Seed for random generator."
,
"default": "42"
"string",
"description": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases",
"help_text": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel).\n"
}
,
"fraction_number": {
"type":
"number",
"description": "Type: `double`, default: `0.1`. Fraction or number of sequences to sample",
"help_text": "Type: `double`, default: `0.1`. Fraction or number of sequences to sample."
,
"default": "0.1"
}
,
"two_pass_mode": {
"dindel": {
"type":
"boolean",
"description": "Type: `boolean`, default: `false`. twice as slow but with much reduced memory",
"help_text": "Type: `boolean`, default: `false`. twice as slow but with much reduced memory"
"description": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref)",
"help_text": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref).\n"
,
"default": "False"
}
,
"verbose": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Be verbose",
"help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n"
,
"default": "False"
}
@@ -132,7 +141,7 @@
},
{
"$ref": "#/definitions/options"
"$ref": "#/definitions/arguments"
},
{

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

@@ -438,7 +438,7 @@ build_info:
output: "target/nextflow/multiqc"
executable: "target/nextflow/multiqc/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/multiqc/main.nf
View File

@@ -3310,7 +3310,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/multiqc",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -380,7 +380,7 @@ build_info:
output: "target/nextflow/pear"
executable: "target/nextflow/pear/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/pear/main.nf
View File

@@ -3201,7 +3201,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/pear",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -263,7 +263,7 @@ build_info:
output: "target/nextflow/salmon/salmon_index"
executable: "target/nextflow/salmon/salmon_index/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/salmon/salmon_index/main.nf
View File

@@ -3077,7 +3077,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_index",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -1153,7 +1153,7 @@ build_info:
output: "target/nextflow/salmon/salmon_quant"
executable: "target/nextflow/salmon/salmon_quant/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/salmon/salmon_quant/main.nf
View File

@@ -3906,7 +3906,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_quant",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -250,7 +250,7 @@ build_info:
output: "target/nextflow/samtools/samtools_collate"
executable: "target/nextflow/samtools/samtools_collate/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/samtools/samtools_collate/main.nf
View File

@@ -3088,7 +3088,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_collate",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -229,7 +229,7 @@ build_info:
output: "target/nextflow/samtools/samtools_faidx"
executable: "target/nextflow/samtools/samtools_faidx/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/samtools/samtools_faidx/main.nf
View File

@@ -3060,7 +3060,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_faidx",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

196
target/nextflow/samtools/samtools_faidx/nextflow_schema.json Normal file
View File

@@ -0,0 +1,196 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "samtools_faidx",
"description": "Indexes FASTA files to enable random access to fasta and fastq files.",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: `file`. FASTA input file",
"help_text": "Type: `file`. FASTA input file.\n"
}
,
"length": {
"type":
"integer",
"description": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping",
"help_text": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping. If zero, this means do not\nline wrap. Defaults to the line length in the input file.\n"
,
"default": "60"
}
,
"region_file": {
"type":
"string",
"description": "Type: `file`. File of regions",
"help_text": "Type: `file`. File of regions. Format is chr:from-to. One per line.\nMust be used with --output to avoid sending output to stdout.\n"
}
}
},
"outputs" : {
"title": "Outputs",
"type": "object",
"description": "No description",
"properties": {
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file",
"help_text": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file.\n"
,
"default": "$id.$key.output.fasta"
}
,
"mark_strand": {
"type":
"string",
"description": "Type: `string`, default: `rc`. Add strand indicator to sequence name",
"help_text": "Type: `string`, default: `rc`. Add strand indicator to sequence name. Options are:\n[ rc, no, sign, custom,\u003cpos\u003e,\u003cneg\u003e ]\n"
,
"default": "rc"
}
,
"fai_idx": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file",
"help_text": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file.fa.fai).\n"
,
"default": "$id.$key.fai_idx.fai"
}
,
"gzi_idx": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with ",
"help_text": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n"
,
"default": "$id.$key.gzi_idx.gzi"
}
,
"fastq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format",
"help_text": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format. Same as using samtools fqidx.\n"
,
"default": "False"
}
}
},
"options" : {
"title": "Options",
"type": "object",
"description": "No description",
"properties": {
"continue": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested",
"help_text": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested.\n"
,
"default": "False"
}
,
"reverse_complement": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Reverse complement sequences",
"help_text": "Type: `boolean_true`, default: `false`. Reverse complement sequences.\n"
,
"default": "False"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/inputs"
},
{
"$ref": "#/definitions/outputs"
},
{
"$ref": "#/definitions/options"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

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

@@ -417,7 +417,7 @@ build_info:
output: "target/nextflow/samtools/samtools_fastq"
executable: "target/nextflow/samtools/samtools_fastq/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/samtools/samtools_fastq/main.nf
View File

@@ -3252,7 +3252,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_fastq",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

355
target/nextflow/samtools/samtools_fastq/nextflow_schema.json
View File

@@ -1,355 +0,0 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "samtools_fastq",
"description": "Converts a SAM, BAM or CRAM to FASTQ format.",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: `file`, required. input SAM/BAM/CRAM file",
"help_text": "Type: `file`, required. input SAM/BAM/CRAM file"
}
}
},
"outputs" : {
"title": "Outputs",
"type": "object",
"description": "No description",
"properties": {
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file"
,
"default": "$id.$key.output.output"
}
}
},
"options" : {
"title": "Options",
"type": "object",
"description": "No description",
"properties": {
"no_suffix": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set",
"help_text": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.\n"
,
"default": "False"
}
,
"suffix": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files",
"help_text": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files.\n"
,
"default": "False"
}
,
"use_oq": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available",
"help_text": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available.\n"
,
"default": "False"
}
,
"singleton": {
"type":
"string",
"description": "Type: `file`. write singleton reads to FILE",
"help_text": "Type: `file`. write singleton reads to FILE."
}
,
"copy_tags": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist",
"help_text": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist.\n"
,
"default": "False"
}
,
"copy_tags_list": {
"type":
"string",
"description": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist",
"help_text": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. \nTAGLIST can be blank or * to indicate all tags should be copied to the output. If using *, \nbe careful to quote it to avoid unwanted shell expansion.\n"
}
,
"read1": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them",
"help_text": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n"
,
"default": "$id.$key.read1.read1"
}
,
"read2": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them",
"help_text": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n"
,
"default": "$id.$key.read2.read2"
}
,
"output_reads": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout",
"help_text": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n"
,
"default": "$id.$key.output_reads.output_reads"
}
,
"output_reads_both": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them",
"help_text": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n"
,
"default": "$id.$key.output_reads_both.output_reads_both"
}
,
"filter_flags": {
"type":
"integer",
"description": "Type: `integer`, default: `0`. Only output alignments with all bits set in INT present in the FLAG field",
"help_text": "Type: `integer`, default: `0`. Only output alignments with all bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/).\n"
,
"default": "0"
}
,
"excl_flags": {
"type":
"string",
"description": "Type: `string`, default: `2304`. Do not output alignments with any bits set in INT present in the FLAG field",
"help_text": "Type: `string`, default: `2304`. Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and \nsupplementary alignments.\n"
,
"default": "2304"
}
,
"incl_flags": {
"type":
"string",
"description": "Type: `string`, default: `0`. Only output alignments with any bits set in INT present in the FLAG field",
"help_text": "Type: `string`, default: `0`. Only output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated list of \nflag names.\n"
,
"default": "0"
}
,
"excl_flags_all": {
"type":
"integer",
"description": "Type: `integer`, default: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field",
"help_text": "Type: `integer`, default: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0\u0027 \n(i.e. /^0[0-7]+/).\n"
,
"default": "0"
}
,
"aux_tag": {
"type":
"string",
"description": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL",
"help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is comparable to the method used in samtools view --tag. The option may be specified \nmultiple times and is equivalent to using the --aux_tag_file option.\n"
}
,
"aux_tag_file": {
"type":
"string",
"description": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE",
"help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. \nThe format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.\n"
}
,
"casava": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. add Illumina Casava 1",
"help_text": "Type: `boolean_true`, default: `false`. add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
,
"default": "False"
}
,
"compression": {
"type":
"integer",
"description": "Type: `integer`, default: `0`. set compression level when writing gz or bgzf fastq files",
"help_text": "Type: `integer`, default: `0`. set compression level when writing gz or bgzf fastq files."
,
"default": "0"
}
,
"index1": {
"type":
"string",
"description": "Type: `file`. write first index reads to FILE",
"help_text": "Type: `file`. write first index reads to FILE."
}
,
"index2": {
"type":
"string",
"description": "Type: `file`. write second index reads to FILE",
"help_text": "Type: `file`. write second index reads to FILE."
}
,
"barcode_tag": {
"type":
"string",
"description": "Type: `string`, default: `BC`. Auxiliary tag to find index reads in",
"help_text": "Type: `string`, default: `BC`. Auxiliary tag to find index reads in."
,
"default": "BC"
}
,
"quality_tag": {
"type":
"string",
"description": "Type: `string`, default: `QT`. Auxiliary tag to find index quality in",
"help_text": "Type: `string`, default: `QT`. Auxiliary tag to find index quality in."
,
"default": "QT"
}
,
"index_format": {
"type":
"string",
"description": "Type: `string`. string to describe how to parse the barcode and quality tags",
"help_text": "Type: `string`. string to describe how to parse the barcode and quality tags. For example:\n[i14i8]: the first 14 characters are index 1, the next 8 characters are index 2.\n[n8i14]: ignore the first 8 characters, and use the next 14 characters for index 1.\nIf the tag contains a separator, then the numeric part can be replaced with \u0027*\u0027 to mean \n\u0027read until the separator or end of tag\u0027, for example: [n*i*].\n"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/inputs"
},
{
"$ref": "#/definitions/outputs"
},
{
"$ref": "#/definitions/options"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

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

@@ -159,7 +159,7 @@ build_info:
output: "target/nextflow/samtools/samtools_flagstat"
executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "0edf4d8d6700495424c4910e0c5047693d015b63"
git_commit: "796c3bcdbb5f5fa578686cd33c28817d83f04427"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/samtools/samtools_flagstat/main.nf
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@@ -2976,7 +2976,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_flagstat",
"viash_version" : "0.9.0-RC6",
"git_commit" : "0edf4d8d6700495424c4910e0c5047693d015b63",
"git_commit" : "796c3bcdbb5f5fa578686cd33c28817d83f04427",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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