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

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "popv"
33
namespace: "annotate"
4-
version: "1.0.0-rc6"
4+
version: "1.0.0"
55
authors:
66
- name: "Matthias Beyens"
77
roles:
@@ -253,7 +253,7 @@ platforms:
253253
image: "python:3.9-slim"
254254
target_organization: "openpipelines-bio"
255255
target_registry: "ghcr.io"
256-
target_tag: "1.0.0-rc6"
256+
target_tag: "1.0.0"
257257
namespace_separator: "/"
258258
resolve_volume: "Automatic"
259259
chown: true
@@ -352,6 +352,6 @@ info:
352352
output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv"
353353
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv"
354354
viash_version: "0.8.5"
355-
git_commit: "e56b8a4b8598953a6b92130a19681e9852ee4816"
355+
git_commit: "f6afb13a00da46b141b778b1770be7f1a382e109"
356356
git_remote: "https://github.com/openpipelines-bio/openpipeline"
357-
git_tag: "1.0.0-rc5"
357+
git_tag: "1.0.0-rc6"

‎target/docker/annotate/popv/popv‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# popv 1.0.0-rc6
3+
# popv 1.0.0
44
#
55
# This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
174174

175175
# ViashHelp: Display helpful explanation about this executable
176176
function ViashHelp {
177-
echo "popv 1.0.0-rc6"
177+
echo "popv 1.0.0"
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 && \
503503
504504
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="2024-06-10T08:53:22Z"
506+
LABEL org.opencontainers.image.created="2024-06-12T11:06:52Z"
507507
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
508-
LABEL org.opencontainers.image.revision="e56b8a4b8598953a6b92130a19681e9852ee4816"
509-
LABEL org.opencontainers.image.version="1.0.0-rc6"
508+
LABEL org.opencontainers.image.revision="f6afb13a00da46b141b778b1770be7f1a382e109"
509+
LABEL org.opencontainers.image.version="1.0.0"
510510
511511
VIASHDOCKER
512512
}
@@ -657,7 +657,7 @@ while [[ $# -gt 0 ]]; do
657657
shift 1
658658
;;
659659
--version)
660-
echo "popv 1.0.0-rc6"
660+
echo "popv 1.0.0"
661661
exit
662662
;;
663663
--input)
@@ -890,14 +890,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
890890
ViashDockerInstallationCheck
891891

892892
if [ $VIASH_MODE == "docker_setup" ]; then
893-
ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6' "$VIASH_DOCKER_SETUP_STRATEGY"
893+
ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0' "$VIASH_DOCKER_SETUP_STRATEGY"
894894
exit 0
895895
fi
896-
ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6' ifneedbepullelsecachedbuild
896+
ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0' ifneedbepullelsecachedbuild
897897

898898
if [ $VIASH_MODE == "docker_debug" ]; then
899-
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6'"
900-
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6'
899+
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0'"
900+
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0'
901901
exit 0
902902
fi
903903

@@ -1120,7 +1120,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
11201120
function ViashPerformChown {
11211121
if (( ${#VIASH_CHOWN_VARS[@]} )); then
11221122
set +e
1123-
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
1123+
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/annotate/popv:1.0.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
11241124
set -e
11251125
fi
11261126
}
@@ -1139,8 +1139,8 @@ fi
11391139
# set dependency paths
11401140

11411141

1142-
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6)"
1143-
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc6
1142+
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:1.0.0)"
1143+
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:1.0.0
11441144
set -e
11451145
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-popv-XXXXXX").py
11461146
function clean_up {

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

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "leiden"
33
namespace: "cluster"
4-
version: "1.0.0-rc6"
4+
version: "1.0.0"
55
authors:
66
- name: "Dries De Maeyer"
77
roles:
@@ -147,7 +147,7 @@ platforms:
147147
image: "python:3.11-slim"
148148
target_organization: "openpipelines-bio"
149149
target_registry: "ghcr.io"
150-
target_tag: "1.0.0-rc6"
150+
target_tag: "1.0.0"
151151
namespace_separator: "/"
152152
resolve_volume: "Automatic"
153153
chown: true
@@ -230,6 +230,6 @@ info:
230230
output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden"
231231
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden"
232232
viash_version: "0.8.5"
233-
git_commit: "e56b8a4b8598953a6b92130a19681e9852ee4816"
233+
git_commit: "f6afb13a00da46b141b778b1770be7f1a382e109"
234234
git_remote: "https://github.com/openpipelines-bio/openpipeline"
235-
git_tag: "1.0.0-rc5"
235+
git_tag: "1.0.0-rc6"

‎target/docker/cluster/leiden/leiden‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# leiden 1.0.0-rc6
3+
# leiden 1.0.0
44
#
55
# This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
173173

174174
# ViashHelp: Display helpful explanation about this executable
175175
function ViashHelp {
176-
echo "leiden 1.0.0-rc6"
176+
echo "leiden 1.0.0"
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 && \
460460
461461
LABEL org.opencontainers.image.authors="Dries De Maeyer"
462462
LABEL org.opencontainers.image.description="Companion container for running component cluster leiden"
463-
LABEL org.opencontainers.image.created="2024-06-10T08:53:25Z"
463+
LABEL org.opencontainers.image.created="2024-06-12T11:06:53Z"
464464
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
465-
LABEL org.opencontainers.image.revision="e56b8a4b8598953a6b92130a19681e9852ee4816"
466-
LABEL org.opencontainers.image.version="1.0.0-rc6"
465+
LABEL org.opencontainers.image.revision="f6afb13a00da46b141b778b1770be7f1a382e109"
466+
LABEL org.opencontainers.image.version="1.0.0"
467467
468468
VIASHDOCKER
469469
}
@@ -614,7 +614,7 @@ while [[ $# -gt 0 ]]; do
614614
shift 1
615615
;;
616616
--version)
617-
echo "leiden 1.0.0-rc6"
617+
echo "leiden 1.0.0"
618618
exit
619619
;;
620620
--input)
@@ -776,14 +776,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
776776
ViashDockerInstallationCheck
777777

778778
if [ $VIASH_MODE == "docker_setup" ]; then
779-
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6' "$VIASH_DOCKER_SETUP_STRATEGY"
779+
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0' "$VIASH_DOCKER_SETUP_STRATEGY"
780780
exit 0
781781
fi
782-
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6' ifneedbepullelsecachedbuild
782+
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0' ifneedbepullelsecachedbuild
783783

784784
if [ $VIASH_MODE == "docker_debug" ]; then
785-
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6'"
786-
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6'
785+
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0'"
786+
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0'
787787
exit 0
788788
fi
789789

@@ -990,7 +990,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
990990
function ViashPerformChown {
991991
if (( ${#VIASH_CHOWN_VARS[@]} )); then
992992
set +e
993-
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
993+
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster/leiden:1.0.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
994994
set -e
995995
fi
996996
}
@@ -1009,8 +1009,8 @@ fi
10091009
# set dependency paths
10101010

10111011

1012-
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6)"
1013-
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc6
1012+
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:1.0.0)"
1013+
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:1.0.0
10141014
set -e
10151015
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-leiden-XXXXXX").py
10161016
function clean_up {

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

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "compress_h5mu"
33
namespace: "compression"
4-
version: "1.0.0-rc6"
4+
version: "1.0.0"
55
authors:
66
- name: "Dries Schaumont"
77
roles:
@@ -89,7 +89,7 @@ platforms:
8989
image: "python:3.10-slim"
9090
target_organization: "openpipelines-bio"
9191
target_registry: "ghcr.io"
92-
target_tag: "1.0.0-rc6"
92+
target_tag: "1.0.0"
9393
namespace_separator: "/"
9494
resolve_volume: "Automatic"
9595
chown: true
@@ -171,6 +171,6 @@ info:
171171
output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu"
172172
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu/compress_h5mu"
173173
viash_version: "0.8.5"
174-
git_commit: "e56b8a4b8598953a6b92130a19681e9852ee4816"
174+
git_commit: "f6afb13a00da46b141b778b1770be7f1a382e109"
175175
git_remote: "https://github.com/openpipelines-bio/openpipeline"
176-
git_tag: "1.0.0-rc5"
176+
git_tag: "1.0.0-rc6"

‎target/docker/compression/compress_h5mu/compress_h5mu‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# compress_h5mu 1.0.0-rc6
3+
# compress_h5mu 1.0.0
44
#
55
# This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
173173

174174
# ViashHelp: Display helpful explanation about this executable
175175
function ViashHelp {
176-
echo "compress_h5mu 1.0.0-rc6"
176+
echo "compress_h5mu 1.0.0"
177177
echo ""
178178
echo "Compress a MuData file."
179179
echo ""
@@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \
423423
424424
LABEL org.opencontainers.image.authors="Dries Schaumont"
425425
LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu"
426-
LABEL org.opencontainers.image.created="2024-06-10T08:53:25Z"
426+
LABEL org.opencontainers.image.created="2024-06-12T11:06:55Z"
427427
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
428-
LABEL org.opencontainers.image.revision="e56b8a4b8598953a6b92130a19681e9852ee4816"
429-
LABEL org.opencontainers.image.version="1.0.0-rc6"
428+
LABEL org.opencontainers.image.revision="f6afb13a00da46b141b778b1770be7f1a382e109"
429+
LABEL org.opencontainers.image.version="1.0.0"
430430
431431
VIASHDOCKER
432432
}
@@ -577,7 +577,7 @@ while [[ $# -gt 0 ]]; do
577577
shift 1
578578
;;
579579
--version)
580-
echo "compress_h5mu 1.0.0-rc6"
580+
echo "compress_h5mu 1.0.0"
581581
exit
582582
;;
583583
--input)
@@ -683,14 +683,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
683683
ViashDockerInstallationCheck
684684

685685
if [ $VIASH_MODE == "docker_setup" ]; then
686-
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6' "$VIASH_DOCKER_SETUP_STRATEGY"
686+
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0' "$VIASH_DOCKER_SETUP_STRATEGY"
687687
exit 0
688688
fi
689-
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6' ifneedbepullelsecachedbuild
689+
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0' ifneedbepullelsecachedbuild
690690

691691
if [ $VIASH_MODE == "docker_debug" ]; then
692-
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6'"
693-
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6'
692+
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0'"
693+
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0'
694694
exit 0
695695
fi
696696

@@ -874,7 +874,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
874874
function ViashPerformChown {
875875
if (( ${#VIASH_CHOWN_VARS[@]} )); then
876876
set +e
877-
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
877+
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
878878
set -e
879879
fi
880880
}
@@ -893,8 +893,8 @@ fi
893893
# set dependency paths
894894

895895

896-
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6)"
897-
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc6
896+
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0)"
897+
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0
898898
set -e
899899
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-compress_h5mu-XXXXXX").py
900900
function clean_up {

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

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "tar_extract"
33
namespace: "compression"
4-
version: "1.0.0-rc6"
4+
version: "1.0.0"
55
arguments:
66
- type: "file"
77
name: "--input"
@@ -93,7 +93,7 @@ platforms:
9393
image: "ubuntu:latest"
9494
target_organization: "openpipelines-bio"
9595
target_registry: "ghcr.io"
96-
target_tag: "1.0.0-rc6"
96+
target_tag: "1.0.0"
9797
namespace_separator: "/"
9898
resolve_volume: "Automatic"
9999
chown: true
@@ -107,6 +107,6 @@ info:
107107
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"
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viash_version: "0.8.5"
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git_commit: "e56b8a4b8598953a6b92130a19681e9852ee4816"
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git_commit: "f6afb13a00da46b141b778b1770be7f1a382e109"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "1.0.0-rc5"
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git_tag: "1.0.0-rc6"

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