deploy: 84b5f87

Author: DriesSchaumont

CHANGELOG.md

@@ -1,4 +1,4 @@
-# openpipelines 1.0.0rc2
+# openpipelines 1.0.0-rc2
 
 ## BUG FIXES
 

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

@@ -1,7 +1,7 @@
 functionality:
   name: "popv"
   namespace: "annotate"
-  version: "1.0.0rc2"
+  version: "1.0.0-rc2"
   authors:
   - name: "Matthias Beyens"
     roles:
@@ -253,7 +253,7 @@ platforms:
   image: "python:3.9-slim"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "1.0.0rc2"
+  target_tag: "1.0.0-rc2"
   namespace_separator: "_"
   resolve_volume: "Automatic"
   chown: true
@@ -351,6 +351,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv"
   viash_version: "0.8.5"
-  git_commit: "ac02e9747ee677373b09256e2f648537b9d80692"
+  git_commit: "4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0rc1"
+  git_tag: "1.0.0rc1-1-g4c219ba08e"

target/docker/annotate/popv/popv

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# popv 1.0.0rc2
+# popv 1.0.0-rc2
 # 
 # This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "popv 1.0.0rc2"
+  echo "popv 1.0.0-rc2"
   echo ""
   echo "Performs popular major vote cell typing on single cell sequence data using"
   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 && \
 
 LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
-LABEL org.opencontainers.image.created="2024-03-11T14:02:52Z"
+LABEL org.opencontainers.image.created="2024-03-11T16:07:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="ac02e9747ee677373b09256e2f648537b9d80692"
-LABEL org.opencontainers.image.version="1.0.0rc2"
+LABEL org.opencontainers.image.revision="4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
+LABEL org.opencontainers.image.version="1.0.0-rc2"
 
 VIASHDOCKER
 }
@@ -657,7 +657,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "popv 1.0.0rc2"
+            echo "popv 1.0.0-rc2"
             exit
             ;;
         --input)
@@ -890,14 +890,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0-rc2' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0-rc2' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0-rc2'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate_popv:1.0.0-rc2'
   exit 0
 fi
 
@@ -1120,7 +1120,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
 function ViashPerformChown {
   if (( ${#VIASH_CHOWN_VARS[@]} )); then
     set +e
-    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/annotate_popv:1.0.0-rc2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -1139,8 +1139,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate_popv:1.0.0rc2
+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-rc2)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate_popv:1.0.0-rc2
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-popv-XXXXXX").py
 function clean_up {

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

@@ -1,7 +1,7 @@
 functionality:
   name: "leiden"
   namespace: "cluster"
-  version: "1.0.0rc2"
+  version: "1.0.0-rc2"
   authors:
   - name: "Dries De Maeyer"
     roles:
@@ -147,7 +147,7 @@ platforms:
   image: "python:3.11-slim"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "1.0.0rc2"
+  target_tag: "1.0.0-rc2"
   namespace_separator: "_"
   resolve_volume: "Automatic"
   chown: true
@@ -230,6 +230,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden"
   viash_version: "0.8.5"
-  git_commit: "ac02e9747ee677373b09256e2f648537b9d80692"
+  git_commit: "4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0rc1"
+  git_tag: "1.0.0rc1-1-g4c219ba08e"

target/docker/cluster/leiden/leiden

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# leiden 1.0.0rc2
+# leiden 1.0.0-rc2
 # 
 # This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "leiden 1.0.0rc2"
+  echo "leiden 1.0.0-rc2"
   echo ""
   echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy"
   echo "framework] [Wolf18]."
@@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component cluster leiden"
-LABEL org.opencontainers.image.created="2024-03-11T14:02:52Z"
+LABEL org.opencontainers.image.created="2024-03-11T16:07:32Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="ac02e9747ee677373b09256e2f648537b9d80692"
-LABEL org.opencontainers.image.version="1.0.0rc2"
+LABEL org.opencontainers.image.revision="4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
+LABEL org.opencontainers.image.version="1.0.0-rc2"
 
 VIASHDOCKER
 }
@@ -614,7 +614,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "leiden 1.0.0rc2"
+            echo "leiden 1.0.0-rc2"
             exit
             ;;
         --input)
@@ -776,14 +776,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0-rc2' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0-rc2' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0-rc2'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster_leiden:1.0.0-rc2'
   exit 0
 fi
 
@@ -990,7 +990,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
 function ViashPerformChown {
   if (( ${#VIASH_CHOWN_VARS[@]} )); then
     set +e
-    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster_leiden:1.0.0-rc2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -1009,8 +1009,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:1.0.0rc2
+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-rc2)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster_leiden:1.0.0-rc2
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-leiden-XXXXXX").py
 function clean_up {

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

@@ -1,7 +1,7 @@
 functionality:
   name: "compress_h5mu"
   namespace: "compression"
-  version: "1.0.0rc2"
+  version: "1.0.0-rc2"
   authors:
   - name: "Dries Schaumont"
     roles:
@@ -89,7 +89,7 @@ platforms:
   image: "python:3.10-slim"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "1.0.0rc2"
+  target_tag: "1.0.0-rc2"
   namespace_separator: "_"
   resolve_volume: "Automatic"
   chown: true
@@ -171,6 +171,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu/compress_h5mu"
   viash_version: "0.8.5"
-  git_commit: "ac02e9747ee677373b09256e2f648537b9d80692"
+  git_commit: "4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0rc1"
+  git_tag: "1.0.0rc1-1-g4c219ba08e"

target/docker/compression/compress_h5mu/compress_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# compress_h5mu 1.0.0rc2
+# compress_h5mu 1.0.0-rc2
 # 
 # This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "compress_h5mu 1.0.0rc2"
+  echo "compress_h5mu 1.0.0-rc2"
   echo ""
   echo "Compress a MuData file."
   echo ""
@@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu"
-LABEL org.opencontainers.image.created="2024-03-11T14:02:52Z"
+LABEL org.opencontainers.image.created="2024-03-11T16:07:31Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="ac02e9747ee677373b09256e2f648537b9d80692"
-LABEL org.opencontainers.image.version="1.0.0rc2"
+LABEL org.opencontainers.image.revision="4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
+LABEL org.opencontainers.image.version="1.0.0-rc2"
 
 VIASHDOCKER
 }
@@ -577,7 +577,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "compress_h5mu 1.0.0rc2"
+            echo "compress_h5mu 1.0.0-rc2"
             exit
             ;;
         --input)
@@ -683,14 +683,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0-rc2' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0-rc2' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0-rc2'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0-rc2'
   exit 0
 fi
 
@@ -874,7 +874,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
 function ViashPerformChown {
   if (( ${#VIASH_CHOWN_VARS[@]} )); then
     set +e
-    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0-rc2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -893,8 +893,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0rc2
+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-rc2)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression_compress_h5mu:1.0.0-rc2
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-compress_h5mu-XXXXXX").py
 function clean_up {

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

@@ -1,7 +1,7 @@
 functionality:
   name: "tar_extract"
   namespace: "compression"
-  version: "1.0.0rc2"
+  version: "1.0.0-rc2"
   arguments:
   - type: "file"
     name: "--input"
@@ -93,7 +93,7 @@ platforms:
   image: "ubuntu:latest"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "1.0.0rc2"
+  target_tag: "1.0.0-rc2"
   namespace_separator: "_"
   resolve_volume: "Automatic"
   chown: true
@@ -107,6 +107,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract/tar_extract"
   viash_version: "0.8.5"
-  git_commit: "ac02e9747ee677373b09256e2f648537b9d80692"
+  git_commit: "4c219ba08e8bfeff5bb53ec177f992ce5c8ce20e"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0rc1"
+  git_tag: "1.0.0rc1-1-g4c219ba08e"