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DriesSchaumontDriesSchaumont
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Bump viash for 1.0.x (#1008)
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‎CHANGELOG.md

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# openpipeline 1.0.5
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## BUG FIXES
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* Add support for nextflow versions starting major version 25.01 (PR #1008).
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* Fix an issue where an interger being passed to a argument with `type: double` would causes an error (PR #1008).
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# openpipelines 1.0.4
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## BUG FIXES

‎_viash.yaml

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viash_version: 0.8.6
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viash_version: 0.8.8
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source: src
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target: target

‎target/docker/annotate/popv/.config.vsh.yaml

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functionality:
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name: "popv"
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namespace: "annotate"
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version: "1.0.4"
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version: "1.0.5"
55
authors:
66
- name: "Matthias Beyens"
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roles:
@@ -351,7 +351,7 @@ info:
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platform: "docker"
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output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv"
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executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv"
354-
viash_version: "0.8.6"
355-
git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
354+
viash_version: "0.8.8"
355+
git_commit: "bfe311bb5542f97dfe80b20a3e47a02800708f43"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
357-
git_tag: "1.0.3-3-g74f972ebfd"
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git_tag: "1.0.4-3-gbfe311bb554"

‎target/docker/annotate/popv/popv

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#!/usr/bin/env bash
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# popv 1.0.4
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# popv 1.0.5
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#
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# This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative
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# This wrapper script is auto-generated by viash 0.8.8 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
88
#
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
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# ViashHelp: Display helpful explanation about this executable
176176
function ViashHelp {
177-
echo "popv 1.0.4"
177+
echo "popv 1.0.5"
178178
echo ""
179179
echo "Performs popular major vote cell typing on single cell sequence data using"
180180
echo "multiple algorithms. Note that this is a one-shot version of PopV."
@@ -503,10 +503,10 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \
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LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
505505
LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
506-
LABEL org.opencontainers.image.created="2024-12-17T13:15:07Z"
506+
LABEL org.opencontainers.image.created="2025-04-24T13:19:35Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
509-
LABEL org.opencontainers.image.version="1.0.4"
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LABEL org.opencontainers.image.revision="bfe311bb5542f97dfe80b20a3e47a02800708f43"
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LABEL org.opencontainers.image.version="1.0.5"
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VIASHDOCKER
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}
@@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do
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shift 1
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;;
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--version)
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echo "popv 1.0.4"
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echo "popv 1.0.5"
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exit
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;;
667667
--input)

‎target/docker/cluster/leiden/.config.vsh.yaml

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functionality:
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name: "leiden"
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namespace: "cluster"
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version: "1.0.4"
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version: "1.0.5"
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authors:
66
- name: "Dries De Maeyer"
77
roles:
@@ -229,7 +229,7 @@ info:
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platform: "docker"
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output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden"
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executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden"
232-
viash_version: "0.8.6"
233-
git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
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viash_version: "0.8.8"
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git_commit: "bfe311bb5542f97dfe80b20a3e47a02800708f43"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "1.0.3-3-g74f972ebfd"
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git_tag: "1.0.4-3-gbfe311bb554"

‎target/docker/cluster/leiden/leiden

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#!/usr/bin/env bash
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# leiden 1.0.4
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# leiden 1.0.5
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#
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# This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative
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# This wrapper script is auto-generated by viash 0.8.8 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
88
#
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
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174174
# ViashHelp: Display helpful explanation about this executable
175175
function ViashHelp {
176-
echo "leiden 1.0.4"
176+
echo "leiden 1.0.5"
177177
echo ""
178178
echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy"
179179
echo "framework] [Wolf18]."
@@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \
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LABEL org.opencontainers.image.authors="Dries De Maeyer"
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LABEL org.opencontainers.image.description="Companion container for running component cluster leiden"
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LABEL org.opencontainers.image.created="2024-12-17T13:15:07Z"
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LABEL org.opencontainers.image.created="2025-04-24T13:19:36Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
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LABEL org.opencontainers.image.version="1.0.4"
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LABEL org.opencontainers.image.revision="bfe311bb5542f97dfe80b20a3e47a02800708f43"
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LABEL org.opencontainers.image.version="1.0.5"
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VIASHDOCKER
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}
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shift 1
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;;
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--version)
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echo "leiden 1.0.4"
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echo "leiden 1.0.5"
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exit
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;;
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--input)

‎target/docker/compression/compress_h5mu/.config.vsh.yaml

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functionality:
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name: "compress_h5mu"
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namespace: "compression"
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version: "1.0.4"
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version: "1.0.5"
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authors:
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- name: "Dries Schaumont"
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roles:
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platform: "docker"
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output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu"
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executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu/compress_h5mu"
173-
viash_version: "0.8.6"
174-
git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
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viash_version: "0.8.8"
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git_commit: "bfe311bb5542f97dfe80b20a3e47a02800708f43"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "1.0.3-3-g74f972ebfd"
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git_tag: "1.0.4-3-gbfe311bb554"

‎target/docker/compression/compress_h5mu/compress_h5mu

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#!/usr/bin/env bash
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# compress_h5mu 1.0.4
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# compress_h5mu 1.0.5
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#
5-
# This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative
5+
# This wrapper script is auto-generated by viash 0.8.8 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
88
#
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174174
# ViashHelp: Display helpful explanation about this executable
175175
function ViashHelp {
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echo "compress_h5mu 1.0.4"
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echo "compress_h5mu 1.0.5"
177177
echo ""
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echo "Compress a MuData file."
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echo ""
@@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \
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LABEL org.opencontainers.image.authors="Dries Schaumont"
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LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu"
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LABEL org.opencontainers.image.created="2024-12-17T13:15:04Z"
426+
LABEL org.opencontainers.image.created="2025-04-24T13:19:33Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
429-
LABEL org.opencontainers.image.version="1.0.4"
428+
LABEL org.opencontainers.image.revision="bfe311bb5542f97dfe80b20a3e47a02800708f43"
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LABEL org.opencontainers.image.version="1.0.5"
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VIASHDOCKER
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}
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shift 1
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;;
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--version)
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echo "compress_h5mu 1.0.4"
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echo "compress_h5mu 1.0.5"
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exit
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;;
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--input)

‎target/docker/compression/tar_extract/.config.vsh.yaml

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functionality:
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name: "tar_extract"
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namespace: "compression"
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version: "1.0.4"
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version: "1.0.5"
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arguments:
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- type: "file"
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name: "--input"
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platform: "docker"
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output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract"
108108
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract/tar_extract"
109-
viash_version: "0.8.6"
110-
git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
109+
viash_version: "0.8.8"
110+
git_commit: "bfe311bb5542f97dfe80b20a3e47a02800708f43"
111111
git_remote: "https://github.com/openpipelines-bio/openpipeline"
112-
git_tag: "1.0.3-3-g74f972ebfd"
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git_tag: "1.0.4-3-gbfe311bb554"

‎target/docker/compression/tar_extract/tar_extract

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#!/usr/bin/env bash
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# tar_extract 1.0.4
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# tar_extract 1.0.5
44
#
5-
# This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative
5+
# This wrapper script is auto-generated by viash 0.8.8 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
77
# Intuitive.
88
#
@@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
170170

171171
# ViashHelp: Display helpful explanation about this executable
172172
function ViashHelp {
173-
echo "tar_extract 1.0.4"
173+
echo "tar_extract 1.0.5"
174174
echo ""
175175
echo "Extract files from a tar archive"
176176
echo ""
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421421
422422
RUN :
423423
LABEL org.opencontainers.image.description="Companion container for running component compression tar_extract"
424-
LABEL org.opencontainers.image.created="2024-12-17T13:15:04Z"
424+
LABEL org.opencontainers.image.created="2025-04-24T13:19:33Z"
425425
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
426-
LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
427-
LABEL org.opencontainers.image.version="1.0.4"
426+
LABEL org.opencontainers.image.revision="bfe311bb5542f97dfe80b20a3e47a02800708f43"
427+
LABEL org.opencontainers.image.version="1.0.5"
428428
429429
VIASHDOCKER
430430
}
@@ -579,7 +579,7 @@ while [[ $# -gt 0 ]]; do
579579
shift 1
580580
;;
581581
--version)
582-
echo "tar_extract 1.0.4"
582+
echo "tar_extract 1.0.5"
583583
exit
584584
;;
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--input)

‎target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml

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functionality:
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name: "from_10xh5_to_h5mu"
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namespace: "convert"
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version: "1.0.4"
4+
version: "1.0.5"
55
authors:
66
- name: "Robrecht Cannoodt"
77
roles:
@@ -276,7 +276,7 @@ info:
276276
platform: "docker"
277277
output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu"
278278
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu"
279-
viash_version: "0.8.6"
280-
git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
279+
viash_version: "0.8.8"
280+
git_commit: "bfe311bb5542f97dfe80b20a3e47a02800708f43"
281281
git_remote: "https://github.com/openpipelines-bio/openpipeline"
282-
git_tag: "1.0.3-3-g74f972ebfd"
282+
git_tag: "1.0.4-3-gbfe311bb554"

‎target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu

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#!/usr/bin/env bash
22

3-
# from_10xh5_to_h5mu 1.0.4
3+
# from_10xh5_to_h5mu 1.0.5
44
#
5-
# This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative
5+
# This wrapper script is auto-generated by viash 0.8.8 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
77
# Intuitive.
88
#
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
173173

174174
# ViashHelp: Display helpful explanation about this executable
175175
function ViashHelp {
176-
echo "from_10xh5_to_h5mu 1.0.4"
176+
echo "from_10xh5_to_h5mu 1.0.5"
177177
echo ""
178178
echo "Converts a 10x h5 into an h5mu file."
179179
echo ""
@@ -445,10 +445,10 @@ RUN pip install --upgrade pip && \
445445
446446
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
447447
LABEL org.opencontainers.image.description="Companion container for running component convert from_10xh5_to_h5mu"
448-
LABEL org.opencontainers.image.created="2024-12-17T13:15:02Z"
448+
LABEL org.opencontainers.image.created="2025-04-24T13:19:39Z"
449449
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
450-
LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
451-
LABEL org.opencontainers.image.version="1.0.4"
450+
LABEL org.opencontainers.image.revision="bfe311bb5542f97dfe80b20a3e47a02800708f43"
451+
LABEL org.opencontainers.image.version="1.0.5"
452452
453453
VIASHDOCKER
454454
}
@@ -603,7 +603,7 @@ while [[ $# -gt 0 ]]; do
603603
shift 1
604604
;;
605605
--version)
606-
echo "from_10xh5_to_h5mu 1.0.4"
606+
echo "from_10xh5_to_h5mu 1.0.5"
607607
exit
608608
;;
609609
--input)

‎target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml

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functionality:
22
name: "from_10xmtx_to_h5mu"
33
namespace: "convert"
4-
version: "1.0.4"
4+
version: "1.0.5"
55
authors:
66
- name: "Robrecht Cannoodt"
77
roles:
@@ -170,7 +170,7 @@ info:
170170
platform: "docker"
171171
output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu"
172172
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu"
173-
viash_version: "0.8.6"
174-
git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
173+
viash_version: "0.8.8"
174+
git_commit: "bfe311bb5542f97dfe80b20a3e47a02800708f43"
175175
git_remote: "https://github.com/openpipelines-bio/openpipeline"
176-
git_tag: "1.0.3-3-g74f972ebfd"
176+
git_tag: "1.0.4-3-gbfe311bb554"

‎target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
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#!/usr/bin/env bash
22

3-
# from_10xmtx_to_h5mu 1.0.4
3+
# from_10xmtx_to_h5mu 1.0.5
44
#
5-
# This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative
5+
# This wrapper script is auto-generated by viash 0.8.8 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
77
# Intuitive.
88
#
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
173173

174174
# ViashHelp: Display helpful explanation about this executable
175175
function ViashHelp {
176-
echo "from_10xmtx_to_h5mu 1.0.4"
176+
echo "from_10xmtx_to_h5mu 1.0.5"
177177
echo ""
178178
echo "Converts a 10x mtx into an h5mu file."
179179
echo ""
@@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \
423423
424424
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
425425
LABEL org.opencontainers.image.description="Companion container for running component convert from_10xmtx_to_h5mu"
426-
LABEL org.opencontainers.image.created="2024-12-17T13:15:01Z"
426+
LABEL org.opencontainers.image.created="2025-04-24T13:19:39Z"
427427
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
428-
LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
429-
LABEL org.opencontainers.image.version="1.0.4"
428+
LABEL org.opencontainers.image.revision="bfe311bb5542f97dfe80b20a3e47a02800708f43"
429+
LABEL org.opencontainers.image.version="1.0.5"
430430
431431
VIASHDOCKER
432432
}
@@ -581,7 +581,7 @@ while [[ $# -gt 0 ]]; do
581581
shift 1
582582
;;
583583
--version)
584-
echo "from_10xmtx_to_h5mu 1.0.4"
584+
echo "from_10xmtx_to_h5mu 1.0.5"
585585
exit
586586
;;
587587
--input)

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