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Build branch feat/disable_cutadapt_demultiplexing with version feat-disable_cutadapt_demultiplexing (bca3e47)

Browse Source 
Build pipeline: vsh-ci-template-tbkbq

Source commit: bca3e47bdf

Source message: Cutadapt: fix --par_quality_cutoff_r2
This commit is contained in:
CI
2024-07-01 15:15:32 +00:00
parent 8025fea736
commit d9f14fcb41
115 changed files with 160 additions and 145 deletions
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13
CHANGELOG.md
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@@ -1,4 +1,14 @@
# biobox unreleased
# biobox x.x.x
## BUG FIXES
* `pear`: fix component not exiting with the correct exitcode when PEAR fails.
* `cutadapt`: fix `--par_quality_cutoff_r2` argument.
* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
# biobox 0.1.0
## BREAKING CHANGES
@@ -6,7 +16,6 @@
Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
splitting up certain file paths.
* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
## NEW FEATURES

2
src/cutadapt/script.sh
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@@ -127,7 +127,7 @@ mod_args=$(echo \
${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \
${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \
${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \
${par_quality_cutoff_r2:+--quality-cutoff_r2 "${par_quality_cutoff_r2}"} \
${par_quality_cutoff_r2:+-Q "${par_quality_cutoff_r2}"} \
${par_quality_base:+--quality-base "${par_quality_base}"} \
${par_poly_a:+--poly-a} \
${par_length:+--length "${par_length}"} \

2
src/pear/script.sh
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@@ -1,5 +1,7 @@
#!/bin/bash
set -eo pipefail
## VIASH START
## VIASH END

2
target/executable/arriba/.config.vsh.yaml
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@@ -688,7 +688,7 @@ build_info:
output: "target/executable/arriba"
executable: "target/executable/arriba/arriba"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/arriba/arriba
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@@ -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="2024-07-01T09:28:57Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:43Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bcl_convert/bcl_convert
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@@ -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="2024-07-01T09:28:56Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:41Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
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@@ -217,7 +217,7 @@ build_info:
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
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@@ -521,9 +521,9 @@ RUN apt-get update && \
RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2024-07-01T09:28:56Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:41Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/busco/busco_download_datasets/.config.vsh.yaml
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@@ -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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/busco/busco_download_datasets/busco_download_datasets
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@@ -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="2024-07-01T09:28:51Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:36Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/busco/busco_list_datasets/.config.vsh.yaml
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@@ -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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/busco/busco_list_datasets/busco_list_datasets
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@@ -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="2024-07-01T09:28:51Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:36Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/busco/busco_run/.config.vsh.yaml
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@@ -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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/busco/busco_run/busco_run
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@@ -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="2024-07-01T09:28:52Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:37Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/cutadapt/.config.vsh.yaml
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@@ -727,7 +727,7 @@ build_info:
output: "target/executable/cutadapt"
executable: "target/executable/cutadapt/cutadapt"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

6
target/executable/cutadapt/cutadapt
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@@ -826,9 +826,9 @@ RUN pip install --upgrade pip && \
RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
LABEL org.opencontainers.image.created="2024-07-01T09:28:48Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:34Z"
LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER
@@ -2585,7 +2585,7 @@ mod_args=\$(echo \\
\${par_cut_r2:+--cut_r2 "\${par_cut_r2}"} \\
\${par_nextseq_trim:+--nextseq-trim "\${par_nextseq_trim}"} \\
\${par_quality_cutoff:+--quality-cutoff "\${par_quality_cutoff}"} \\
\${par_quality_cutoff_r2:+--quality-cutoff_r2 "\${par_quality_cutoff_r2}"} \\
\${par_quality_cutoff_r2:+-Q "\${par_quality_cutoff_r2}"} \\
\${par_quality_base:+--quality-base "\${par_quality_base}"} \\
\${par_poly_a:+--poly-a} \\
\${par_length:+--length "\${par_length}"} \\

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

@@ -304,7 +304,7 @@ build_info:
output: "target/executable/falco"
executable: "target/executable/falco/falco"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:48Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:33Z"
LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/fastp/.config.vsh.yaml
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@@ -1065,7 +1065,7 @@ build_info:
output: "target/executable/fastp"
executable: "target/executable/fastp/fastp"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/fastp/fastp
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@@ -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="2024-07-01T09:28:49Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:34Z"
LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/featurecounts/.config.vsh.yaml
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@@ -631,7 +631,7 @@ build_info:
output: "target/executable/featurecounts"
executable: "target/executable/featurecounts/featurecounts"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/featurecounts/featurecounts
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@@ -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="2024-07-01T09:28:58Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:43Z"
LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/gffread/gffread
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@@ -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="2024-07-01T09:28:49Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:34Z"
LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:52Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
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@@ -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="2024-07-01T09:28:52Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/multiqc/.config.vsh.yaml
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@@ -438,7 +438,7 @@ build_info:
output: "target/executable/multiqc"
executable: "target/executable/multiqc/multiqc"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:47Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:33Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

2
target/executable/pear/.config.vsh.yaml
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@@ -380,7 +380,7 @@ build_info:
output: "target/executable/pear"
executable: "target/executable/pear/pear"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

6
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="2024-07-01T09:28:56Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:41Z"
LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER
@@ -1504,6 +1504,8 @@ trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash
set -eo pipefail
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_FORWARD_FASTQ+x} ]; then echo "${VIASH_PAR_FORWARD_FASTQ}" | sed "s#'#'\"'\"'#g;s#.*#par_forward_fastq='&'#" ; else echo "# par_forward_fastq="; fi )

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:57Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:42Z"
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

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

@@ -1159,7 +1159,7 @@ build_info:
output: "target/executable/salmon/salmon_quant"
executable: "target/executable/salmon/salmon_quant/salmon_quant"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -1163,9 +1163,9 @@ ENTRYPOINT []
RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
LABEL org.opencontainers.image.created="2024-07-01T09:28:57Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:42Z"
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:54Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:39Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:55Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:53Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:39Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:55Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:54Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:53Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:38Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:55Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:40Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:54Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:39Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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="2024-07-01T09:28:53Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:38Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

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

@@ -2108,7 +2108,7 @@ build_info:
output: "target/executable/star/star_align_reads"
executable: "target/executable/star/star_align_reads/star_align_reads"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -1665,9 +1665,9 @@ RUN apt-get update && \
RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
LABEL org.opencontainers.image.created="2024-07-01T09:28:50Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:35Z"
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
VIASHDOCKER

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

@@ -319,7 +319,7 @@ build_info:
output: "target/executable/star/star_genome_generate"
executable: "target/executable/star/star_genome_generate/star_genome_generate"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -572,9 +572,9 @@ RUN apt-get update && \
RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
LABEL org.opencontainers.image.created="2024-07-01T09:28:50Z"
LABEL org.opencontainers.image.created="2024-07-01T14:59:35Z"
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
LABEL org.opencontainers.image.revision="d95b3721d5e175d323b41232c045364d60d38d1d"
LABEL org.opencontainers.image.revision="bca3e47bdf43f5c4703569354a924fe550bfef7f"
LABEL org.opencontainers.image.version="feat-disable_cutadapt_demultiplexing"
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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -217,7 +217,7 @@ build_info:
output: "target/nextflow/bedtools/bedtools_getfasta"
executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

2
target/nextflow/bedtools/bedtools_getfasta/main.nf
View File

@@ -3033,7 +3033,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/bedtools/bedtools_getfasta",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -727,7 +727,7 @@ build_info:
output: "target/nextflow/cutadapt"
executable: "target/nextflow/cutadapt/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/nextflow/cutadapt/main.nf
View File

@@ -3568,7 +3568,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/cutadapt",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {
@@ -3805,7 +3805,7 @@ mod_args=\\$(echo \\\\
\\${par_cut_r2:+--cut_r2 "\\${par_cut_r2}"} \\\\
\\${par_nextseq_trim:+--nextseq-trim "\\${par_nextseq_trim}"} \\\\
\\${par_quality_cutoff:+--quality-cutoff "\\${par_quality_cutoff}"} \\\\
\\${par_quality_cutoff_r2:+--quality-cutoff_r2 "\\${par_quality_cutoff_r2}"} \\\\
\\${par_quality_cutoff_r2:+-Q "\\${par_quality_cutoff_r2}"} \\\\
\\${par_quality_base:+--quality-base "\\${par_quality_base}"} \\\\
\\${par_poly_a:+--poly-a} \\\\
\\${par_length:+--length "\\${par_length}"} \\\\

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -1065,7 +1065,7 @@ build_info:
output: "target/nextflow/fastp"
executable: "target/nextflow/fastp/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -671,7 +671,7 @@ build_info:
output: "target/nextflow/gffread"
executable: "target/nextflow/gffread/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {
@@ -3243,6 +3243,8 @@ tempscript=".viash_script.sh"
cat > "$tempscript" << VIASHMAIN
#!/bin/bash
set -eo pipefail
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_FORWARD_FASTQ+x} ]; then echo "${VIASH_PAR_FORWARD_FASTQ}" | sed "s#'#'\\"'\\"'#g;s#.*#par_forward_fastq='&'#" ; else echo "# par_forward_fastq="; fi )

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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

@@ -1159,7 +1159,7 @@ build_info:
output: "target/nextflow/salmon/salmon_quant"
executable: "target/nextflow/salmon/salmon_quant/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -3912,7 +3912,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_quant",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
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" : "d95b3721d5e175d323b41232c045364d60d38d1d",
"git_commit" : "bca3e47bdf43f5c4703569354a924fe550bfef7f",
"git_remote" : "https://github.com/viash-hub/biobox"
},
"package_config" : {

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: "d95b3721d5e175d323b41232c045364d60d38d1d"
git_commit: "bca3e47bdf43f5c4703569354a924fe550bfef7f"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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