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Backport #936 and #938 to 1.0.x (#939)
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‎CHANGELOG.md‎

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# openpipelines 1.0.4
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## BUG FIXES
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* `scvi_leiden` workflow: fix the input layer argument of the workflow not being passed to the scVI component (PR #939, backported from PR #936 and PR #938).
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# openpipelines 1.0.3
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## BUG FIXES
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* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR # , backported from PR #852).
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* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR #853 , backported from PR #852).
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# openpipelines 1.0.2
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‎src/workflows/integration/scvi_leiden/config.vsh.yaml‎

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description: Path to the sample.
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example: dataset.h5mu
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- name: "--layer"
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default: "log_normalized"
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type: string
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description: use specified layer for expression values instead of the .X object from the modality.
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required: false

‎src/workflows/integration/scvi_leiden/main.nf‎

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"lr_factor": state.lr_factor,
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"lr_patience": state.lr_patience,
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"output_model": state.output_model,
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"modality": state.modality
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"modality": state.modality,
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"input_layer": state.layer,
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]
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},
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// use map when viash 0.7.6 is released

‎src/workflows/integration/scvi_leiden/test.nf‎

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[
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id: "simple_execution_test",
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input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
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layer: "log_normalized",
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layer: null,
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obs_batch: "sample_id",
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max_epochs: 1,
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output_model: "simple_execution_test_model/"
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],
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[
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id: "no_leiden_resolutions_test",
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input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
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layer: "log_normalized",
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layer: null,
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obs_batch: "sample_id",
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output_model: "no_leiden_resolutions_test_model/",
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max_epochs: 1,

‎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: "1.0.3"
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version: "1.0.4"
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authors:
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- name: "Matthias Beyens"
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roles:
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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"
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viash_version: "0.8.6"
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git_commit: "36dc4369a0372420366dea16260f2bab2ea959e1"
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git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "1.0.2-4-g36dc4369a0"
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git_tag: "1.0.3-3-g74f972ebfd"

‎target/docker/annotate/popv/popv‎

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#!/usr/bin/env bash
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# popv 1.0.3
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# popv 1.0.4
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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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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# ViashHelp: Display helpful explanation about this executable
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function ViashHelp {
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echo "popv 1.0.3"
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echo "popv 1.0.4"
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echo ""
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echo "Performs popular major vote cell typing on single cell sequence data using"
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echo "multiple algorithms. Note that this is a one-shot version of PopV."
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LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
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LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
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LABEL org.opencontainers.image.created="2024-08-09T10:01:42Z"
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LABEL org.opencontainers.image.created="2024-12-17T13:15:07Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="36dc4369a0372420366dea16260f2bab2ea959e1"
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LABEL org.opencontainers.image.version="1.0.3"
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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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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 "popv 1.0.3"
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echo "popv 1.0.4"
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exit
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;;
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--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: "1.0.3"
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version: "1.0.4"
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authors:
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- name: "Dries De Maeyer"
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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"
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viash_version: "0.8.6"
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git_commit: "36dc4369a0372420366dea16260f2bab2ea959e1"
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git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "1.0.2-4-g36dc4369a0"
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git_tag: "1.0.3-3-g74f972ebfd"

‎target/docker/cluster/leiden/leiden‎

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#!/usr/bin/env bash
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# leiden 1.0.3
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# leiden 1.0.4
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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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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# ViashHelp: Display helpful explanation about this executable
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function ViashHelp {
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echo "leiden 1.0.3"
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echo "leiden 1.0.4"
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echo ""
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echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy"
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echo "framework] [Wolf18]."
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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="2024-08-09T10:01:44Z"
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LABEL org.opencontainers.image.created="2024-12-17T13:15:07Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="36dc4369a0372420366dea16260f2bab2ea959e1"
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LABEL org.opencontainers.image.version="1.0.3"
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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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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 1.0.3"
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echo "leiden 1.0.4"
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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: "1.0.3"
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version: "1.0.4"
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authors:
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- name: "Dries Schaumont"
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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"
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viash_version: "0.8.6"
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git_commit: "36dc4369a0372420366dea16260f2bab2ea959e1"
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git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "1.0.2-4-g36dc4369a0"
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git_tag: "1.0.3-3-g74f972ebfd"

‎target/docker/compression/compress_h5mu/compress_h5mu‎

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#!/usr/bin/env bash
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# compress_h5mu 1.0.3
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# compress_h5mu 1.0.4
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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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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# ViashHelp: Display helpful explanation about this executable
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function ViashHelp {
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echo "compress_h5mu 1.0.4"
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echo ""
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echo "Compress a MuData file."
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echo ""
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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="2024-08-09T10:01:45Z"
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LABEL org.opencontainers.image.created="2024-12-17T13:15:04Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="36dc4369a0372420366dea16260f2bab2ea959e1"
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LABEL org.opencontainers.image.version="1.0.3"
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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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VIASHDOCKER
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}
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--version)
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echo "compress_h5mu 1.0.3"
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echo "compress_h5mu 1.0.4"
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exit
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;;
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--input)

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