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Deploy for release 0.6.0 from 84672a4 
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‎CHANGELOG.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
# openpipeline 0.5.2
1+
# openpipeline 0.6.0
22

33
## NEW FUNCTIONALITY
44

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "leiden"
33
namespace: "cluster"
4-
version: "0.5.2"
4+
version: "0.6.0"
55
authors:
66
- name: "Dries De Maeyer"
77
email: "[email protected]"
@@ -182,5 +182,5 @@ info:
182182
output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden"
183183
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden"
184184
viash_version: "0.6.7"
185-
git_commit: "8a1eaa5b5bb627077c0829c76d456032432a400e"
185+
git_commit: "84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
186186
git_remote: "https://github.com/openpipelines-bio/openpipeline"

‎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 0.5.2
3+
# leiden 0.6.0
44
#
55
# This wrapper script is auto-generated by viash 0.6.7 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -158,7 +158,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
158158

159159
# ViashHelp: Display helpful explanation about this executable
160160
function ViashHelp {
161-
echo "leiden 0.5.2"
161+
echo "leiden 0.6.0"
162162
echo ""
163163
echo "Cluster cells using the Leiden algorithm [Traag18] implemented in the Scanpy"
164164
echo "framework [Wolf18]."
@@ -433,10 +433,10 @@ RUN pip install --upgrade pip && \
433433
434434
LABEL org.opencontainers.image.authors="Dries De Maeyer"
435435
LABEL org.opencontainers.image.description="Companion container for running component cluster leiden"
436-
LABEL org.opencontainers.image.created="2022-12-21T10:58:43Z"
436+
LABEL org.opencontainers.image.created="2022-12-21T12:20:50Z"
437437
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
438-
LABEL org.opencontainers.image.revision="8a1eaa5b5bb627077c0829c76d456032432a400e"
439-
LABEL org.opencontainers.image.version="0.5.2"
438+
LABEL org.opencontainers.image.revision="84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
439+
LABEL org.opencontainers.image.version="0.6.0"
440440
VIASHDOCKER
441441
}
442442

@@ -585,7 +585,7 @@ while [[ $# -gt 0 ]]; do
585585
shift 1
586586
;;
587587
--version)
588-
echo "leiden 0.5.2"
588+
echo "leiden 0.6.0"
589589
exit
590590
;;
591591
--input)
@@ -730,14 +730,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
730730
ViashDockerInstallationCheck
731731

732732
if [ $VIASH_MODE == "docker_setup" ]; then
733-
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:0.5.2' "$VIASH_DOCKER_SETUP_STRATEGY"
733+
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:0.6.0' "$VIASH_DOCKER_SETUP_STRATEGY"
734734
exit 0
735735
fi
736-
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:0.5.2' ifneedbepullelsecachedbuild
736+
ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:0.6.0' ifneedbepullelsecachedbuild
737737

738738
if [ $VIASH_MODE == "docker_debug" ]; then
739-
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:0.5.2'"
740-
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:0.5.2'
739+
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:0.6.0'"
740+
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:0.6.0'
741741
exit 0
742742
fi
743743

@@ -923,7 +923,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
923923
function ViashPerformChown {
924924
if (( ${#VIASH_CHOWN_VARS[@]} )); then
925925
set +e
926-
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster_leiden:0.5.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
926+
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster_leiden:0.6.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
927927
set -e
928928
fi
929929
}
@@ -938,8 +938,8 @@ if [ ! -z "$VIASH_META_CPUS" ]; then
938938
VIASH_EXTRA_DOCKER_ARGS="$VIASH_EXTRA_DOCKER_ARGS --cpus=${VIASH_META_CPUS}"
939939
fi
940940

941-
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:0.5.2)"
942-
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:0.5.2
941+
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:0.6.0)"
942+
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:0.6.0
943943
set -e
944944
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-leiden-XXXXXX").py
945945
function clean_up {

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "tar_extract"
33
namespace: "compression"
4-
version: "0.5.2"
4+
version: "0.6.0"
55
authors: []
66
inputs: []
77
outputs: []
@@ -106,5 +106,5 @@ info:
106106
output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract"
107107
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract/tar_extract"
108108
viash_version: "0.6.7"
109-
git_commit: "8a1eaa5b5bb627077c0829c76d456032432a400e"
109+
git_commit: "84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
110110
git_remote: "https://github.com/openpipelines-bio/openpipeline"

‎target/docker/compression/tar_extract/tar_extract‎

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-
# tar_extract 0.5.2
3+
# tar_extract 0.6.0
44
#
55
# This wrapper script is auto-generated by viash 0.6.7 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -155,7 +155,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
155155

156156
# ViashHelp: Display helpful explanation about this executable
157157
function ViashHelp {
158-
echo "tar_extract 0.5.2"
158+
echo "tar_extract 0.6.0"
159159
echo ""
160160
echo "Extract files from a tar archive"
161161
echo ""
@@ -403,10 +403,10 @@ FROM ubuntu:latest
403403
404404
RUN :
405405
LABEL org.opencontainers.image.description="Companion container for running component compression tar_extract"
406-
LABEL org.opencontainers.image.created="2022-12-21T10:58:40Z"
406+
LABEL org.opencontainers.image.created="2022-12-21T12:20:47Z"
407407
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
408-
LABEL org.opencontainers.image.revision="8a1eaa5b5bb627077c0829c76d456032432a400e"
409-
LABEL org.opencontainers.image.version="0.5.2"
408+
LABEL org.opencontainers.image.revision="84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
409+
LABEL org.opencontainers.image.version="0.6.0"
410410
VIASHDOCKER
411411
}
412412

@@ -555,7 +555,7 @@ while [[ $# -gt 0 ]]; do
555555
shift 1
556556
;;
557557
--version)
558-
echo "tar_extract 0.5.2"
558+
echo "tar_extract 0.6.0"
559559
exit
560560
;;
561561
--input)
@@ -690,14 +690,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
690690
ViashDockerInstallationCheck
691691

692692
if [ $VIASH_MODE == "docker_setup" ]; then
693-
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2' "$VIASH_DOCKER_SETUP_STRATEGY"
693+
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0' "$VIASH_DOCKER_SETUP_STRATEGY"
694694
exit 0
695695
fi
696-
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2' ifneedbepullelsecachedbuild
696+
ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0' ifneedbepullelsecachedbuild
697697

698698
if [ $VIASH_MODE == "docker_debug" ]; then
699-
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2'"
700-
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2'
699+
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0'"
700+
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0'
701701
exit 0
702702
fi
703703

@@ -869,7 +869,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
869869
function ViashPerformChown {
870870
if (( ${#VIASH_CHOWN_VARS[@]} )); then
871871
set +e
872-
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
872+
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
873873
set -e
874874
fi
875875
}
@@ -884,8 +884,8 @@ if [ ! -z "$VIASH_META_CPUS" ]; then
884884
VIASH_EXTRA_DOCKER_ARGS="$VIASH_EXTRA_DOCKER_ARGS --cpus=${VIASH_META_CPUS}"
885885
fi
886886

887-
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2)"
888-
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_tar_extract:0.5.2
887+
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0)"
888+
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_tar_extract:0.6.0
889889
set -e
890890
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-tar_extract-XXXXXX").sh
891891
function clean_up {

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "from_10xh5_to_h5mu"
33
namespace: "convert"
4-
version: "0.5.2"
4+
version: "0.6.0"
55
authors:
66
- name: "Robrecht Cannoodt"
77
email: "[email protected]"
@@ -231,5 +231,5 @@ info:
231231
output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu"
232232
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu"
233233
viash_version: "0.6.7"
234-
git_commit: "8a1eaa5b5bb627077c0829c76d456032432a400e"
234+
git_commit: "84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
235235
git_remote: "https://github.com/openpipelines-bio/openpipeline"

‎target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_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-
# from_10xh5_to_h5mu 0.5.2
3+
# from_10xh5_to_h5mu 0.6.0
44
#
55
# This wrapper script is auto-generated by viash 0.6.7 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -159,7 +159,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
159159

160160
# ViashHelp: Display helpful explanation about this executable
161161
function ViashHelp {
162-
echo "from_10xh5_to_h5mu 0.5.2"
162+
echo "from_10xh5_to_h5mu 0.6.0"
163163
echo ""
164164
echo "Converts a 10x h5 into an h5mu file."
165165
echo ""
@@ -419,10 +419,10 @@ RUN pip install --upgrade pip && \
419419
420420
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
421421
LABEL org.opencontainers.image.description="Companion container for running component convert from_10xh5_to_h5mu"
422-
LABEL org.opencontainers.image.created="2022-12-21T10:58:33Z"
422+
LABEL org.opencontainers.image.created="2022-12-21T12:20:40Z"
423423
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
424-
LABEL org.opencontainers.image.revision="8a1eaa5b5bb627077c0829c76d456032432a400e"
425-
LABEL org.opencontainers.image.version="0.5.2"
424+
LABEL org.opencontainers.image.revision="84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
425+
LABEL org.opencontainers.image.version="0.6.0"
426426
VIASHDOCKER
427427
}
428428

@@ -571,7 +571,7 @@ while [[ $# -gt 0 ]]; do
571571
shift 1
572572
;;
573573
--version)
574-
echo "from_10xh5_to_h5mu 0.5.2"
574+
echo "from_10xh5_to_h5mu 0.6.0"
575575
exit
576576
;;
577577
--input)
@@ -716,14 +716,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
716716
ViashDockerInstallationCheck
717717

718718
if [ $VIASH_MODE == "docker_setup" ]; then
719-
ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2' "$VIASH_DOCKER_SETUP_STRATEGY"
719+
ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0' "$VIASH_DOCKER_SETUP_STRATEGY"
720720
exit 0
721721
fi
722-
ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2' ifneedbepullelsecachedbuild
722+
ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0' ifneedbepullelsecachedbuild
723723

724724
if [ $VIASH_MODE == "docker_debug" ]; then
725-
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2'"
726-
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2'
725+
ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0'"
726+
docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0'
727727
exit 0
728728
fi
729729

@@ -910,7 +910,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
910910
function ViashPerformChown {
911911
if (( ${#VIASH_CHOWN_VARS[@]} )); then
912912
set +e
913-
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
913+
eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
914914
set -e
915915
fi
916916
}
@@ -925,8 +925,8 @@ if [ ! -z "$VIASH_META_CPUS" ]; then
925925
VIASH_EXTRA_DOCKER_ARGS="$VIASH_EXTRA_DOCKER_ARGS --cpus=${VIASH_META_CPUS}"
926926
fi
927927

928-
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2)"
929-
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.5.2
928+
ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0)"
929+
cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xh5_to_h5mu:0.6.0
930930
set -e
931931
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-from_10xh5_to_h5mu-XXXXXX").py
932932
function clean_up {

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
functionality:
22
name: "from_10xmtx_to_h5mu"
33
namespace: "convert"
4-
version: "0.5.2"
4+
version: "0.6.0"
55
authors:
66
- name: "Robrecht Cannoodt"
77
email: "[email protected]"
@@ -117,5 +117,5 @@ info:
117117
output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu"
118118
executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu"
119119
viash_version: "0.6.7"
120-
git_commit: "8a1eaa5b5bb627077c0829c76d456032432a400e"
120+
git_commit: "84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
121121
git_remote: "https://github.com/openpipelines-bio/openpipeline"

‎target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_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-
# from_10xmtx_to_h5mu 0.5.2
3+
# from_10xmtx_to_h5mu 0.6.0
44
#
55
# This wrapper script is auto-generated by viash 0.6.7 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -159,7 +159,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
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# ViashHelp: Display helpful explanation about this executable
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function ViashHelp {
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echo "from_10xmtx_to_h5mu 0.5.2"
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echo "from_10xmtx_to_h5mu 0.6.0"
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echo ""
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echo "Converts a 10x mtx into an h5mu file."
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echo ""
@@ -397,10 +397,10 @@ RUN pip install --upgrade pip && \
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LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
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LABEL org.opencontainers.image.description="Companion container for running component convert from_10xmtx_to_h5mu"
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LABEL org.opencontainers.image.created="2022-12-21T10:58:42Z"
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LABEL org.opencontainers.image.created="2022-12-21T12:20:49Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="8a1eaa5b5bb627077c0829c76d456032432a400e"
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LABEL org.opencontainers.image.version="0.5.2"
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LABEL org.opencontainers.image.revision="84672a470c637ce3ae7be923b7e4a8ff5ad9bf19"
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LABEL org.opencontainers.image.version="0.6.0"
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VIASHDOCKER
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}
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@@ -549,7 +549,7 @@ while [[ $# -gt 0 ]]; do
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shift 1
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;;
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--version)
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echo "from_10xmtx_to_h5mu 0.5.2"
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echo "from_10xmtx_to_h5mu 0.6.0"
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exit
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;;
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--input)
@@ -650,14 +650,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
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ViashDockerInstallationCheck
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if [ $VIASH_MODE == "docker_setup" ]; then
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ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2' "$VIASH_DOCKER_SETUP_STRATEGY"
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ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0' "$VIASH_DOCKER_SETUP_STRATEGY"
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exit 0
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fi
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ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2' ifneedbepullelsecachedbuild
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ViashDockerSetup 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0' ifneedbepullelsecachedbuild
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if [ $VIASH_MODE == "docker_debug" ]; then
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ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2'"
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docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2'
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ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0'"
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docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0'
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exit 0
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fi
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@@ -819,7 +819,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
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function ViashPerformChown {
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if (( ${#VIASH_CHOWN_VARS[@]} )); then
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set +e
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eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
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eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
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set -e
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fi
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}
@@ -834,8 +834,8 @@ if [ ! -z "$VIASH_META_CPUS" ]; then
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VIASH_EXTRA_DOCKER_ARGS="$VIASH_EXTRA_DOCKER_ARGS --cpus=${VIASH_META_CPUS}"
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fi
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ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2)"
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cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.5.2
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ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0)"
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cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/convert_from_10xmtx_to_h5mu:0.6.0
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set -e
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tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-from_10xmtx_to_h5mu-XXXXXX").py
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function clean_up {

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