Fix workflow ID error and bump to v0.2.3

viash-io · Feb 8, 2024 · e51a8b3 · e51a8b3
1 parent 82b49c3
commit e51a8b3
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Showing 21 changed files with 141 additions and 118 deletions.
diff --git a/_viash.yaml b/_viash.yaml
@@ -4,7 +4,7 @@ source: src
 target: target
 
 config_mods: |
-  .functionality.version := '0.2.2'
+  .functionality.version := '0.2.3'
   .platforms[.type == 'docker'].target_registry := 'ghcr.io'
   .platforms[.type == 'docker'].target_organization := 'viash-io/viash_project_template'
   .platforms[.type == 'docker'].target_image_source := 'https://github.com/viash-io/viash_project_template'

diff --git a/src/template/combine_columns/config.vsh.yaml b/src/template/combine_columns/config.vsh.yaml
@@ -18,4 +18,8 @@ functionality:
 platforms:
   - type: docker
     image: eddelbuettel/r2u:22.04
+    setup:
+      - type: r
+        packages:
+          - bit64
   - type: nextflow
diff --git a/src/template/workflow/main.nf b/src/template/workflow/main.nf
@@ -30,8 +30,12 @@ workflow run_wf {
         // its output list into a channel item that can be used
         // directly with downstream components.
         | vsh_toList.run(
-            args: [ id: "combined" ],
-            fromState: [ input: "output" ],
+            fromState: { id, state ->
+              [
+                id: id,
+                input: state.output
+              ]
+            },
             toState: [ output: "output" ]
           )
 
@@ -40,12 +44,7 @@ workflow run_wf {
         | combine_columns.run(
             auto: [ publish: true ],
             fromState: [ input: "output" ],
-            toState: { id, result, state ->
-              [
-                output: result.output,
-                _meta: [ join_id: "1" ]
-              ]
-            }
+            toState: { id, result, state -> result }
           )
 
   emit:

diff --git a/target/docker/template/combine_columns/.config.vsh.yaml b/target/docker/template/combine_columns/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "combine_columns"
   namespace: "template"
-  version: "0.2.2"
+  version: "0.2.3"
   arguments:
   - type: "file"
     name: "--input"
@@ -45,6 +45,11 @@ platforms:
   chown: true
   setup_strategy: "ifneedbepullelsecachedbuild"
   target_image_source: "https://github.com/viash-io/viash_project_template"
+  setup:
+  - type: "r"
+    packages:
+    - "bit64"
+    bioc_force_install: false
   entrypoint: []
   cmd: null
 - type: "nextflow"
@@ -96,6 +101,6 @@ info:
   output: "/Users/toni/code/projects/viash/viash_project_template/target/docker/template/combine_columns"
   executable: "/Users/toni/code/projects/viash/viash_project_template/target/docker/template/combine_columns/combine_columns"
   viash_version: "0.8.4"
-  git_commit: "11b6278597bf22afbfb56a8e83065a55553c9dd0"
+  git_commit: "82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
   git_remote: "https://github.com/viash-io/viash_project_template"
-  git_tag: "v0.2.1"
+  git_tag: "v0.2.2"
diff --git a/target/docker/template/combine_columns/combine_columns b/target/docker/template/combine_columns/combine_columns
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# combine_columns 0.2.2
+# combine_columns 0.2.3
 # 
 # This wrapper script is auto-generated by viash 0.8.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "combine_columns 0.2.2"
+  echo "combine_columns 0.2.3"
   echo ""
   echo "Arguments:"
   echo "    -i, --input"
@@ -400,12 +400,14 @@ FROM eddelbuettel/r2u:22.04
 ENTRYPOINT []
 
  
-RUN :
+RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
+  Rscript -e 'remotes::install_cran(c("bit64"), repos = "https://cran.rstudio.com")'
+
 LABEL org.opencontainers.image.description="Companion container for running component template combine_columns"
-LABEL org.opencontainers.image.created="2024-01-16T14:48:43+01:00"
+LABEL org.opencontainers.image.created="2024-02-08T14:48:54+01:00"
 LABEL org.opencontainers.image.source="https://github.com/viash-io/viash_project_template"
-LABEL org.opencontainers.image.revision="11b6278597bf22afbfb56a8e83065a55553c9dd0"
-LABEL org.opencontainers.image.version="0.2.2"
+LABEL org.opencontainers.image.revision="82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
+LABEL org.opencontainers.image.version="0.2.3"
 
 VIASHDOCKER
 }
@@ -556,7 +558,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "combine_columns 0.2.2"
+            echo "combine_columns 0.2.3"
             exit
             ;;
         --input)
@@ -666,14 +668,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3'
   exit 0
 fi
 
@@ -854,7 +856,7 @@ 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 ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -873,8 +875,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.2
+ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/combine_columns:0.2.3
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-combine_columns-XXXXXX").R
 function clean_up {

diff --git a/target/docker/template/remove_comments/.config.vsh.yaml b/target/docker/template/remove_comments/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "remove_comments"
   namespace: "template"
-  version: "0.2.2"
+  version: "0.2.3"
   arguments:
   - type: "file"
     name: "--input"
@@ -104,6 +104,6 @@ info:
   output: "/Users/toni/code/projects/viash/viash_project_template/target/docker/template/remove_comments"
   executable: "/Users/toni/code/projects/viash/viash_project_template/target/docker/template/remove_comments/remove_comments"
   viash_version: "0.8.4"
-  git_commit: "11b6278597bf22afbfb56a8e83065a55553c9dd0"
+  git_commit: "82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
   git_remote: "https://github.com/viash-io/viash_project_template"
-  git_tag: "v0.2.1"
+  git_tag: "v0.2.2"
diff --git a/target/docker/template/remove_comments/remove_comments b/target/docker/template/remove_comments/remove_comments
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# remove_comments 0.2.2
+# remove_comments 0.2.3
 # 
 # This wrapper script is auto-generated by viash 0.8.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "remove_comments 0.2.2"
+  echo "remove_comments 0.2.3"
   echo ""
   echo "Arguments:"
   echo "    -i, --input"
@@ -404,10 +404,10 @@ ENTRYPOINT []
  
 RUN :
 LABEL org.opencontainers.image.description="Companion container for running component template remove_comments"
-LABEL org.opencontainers.image.created="2024-01-16T14:48:39+01:00"
+LABEL org.opencontainers.image.created="2024-02-08T14:48:49+01:00"
 LABEL org.opencontainers.image.source="https://github.com/viash-io/viash_project_template"
-LABEL org.opencontainers.image.revision="11b6278597bf22afbfb56a8e83065a55553c9dd0"
-LABEL org.opencontainers.image.version="0.2.2"
+LABEL org.opencontainers.image.revision="82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
+LABEL org.opencontainers.image.version="0.2.3"
 
 VIASHDOCKER
 }
@@ -558,7 +558,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "remove_comments 0.2.2"
+            echo "remove_comments 0.2.3"
             exit
             ;;
         --input)
@@ -659,14 +659,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3'
   exit 0
 fi
 
@@ -832,7 +832,7 @@ 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 ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -851,8 +851,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.2
+ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/remove_comments:0.2.3
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-remove_comments-XXXXXX").sh
 function clean_up {

diff --git a/target/docker/template/take_column/.config.vsh.yaml b/target/docker/template/take_column/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "take_column"
   namespace: "template"
-  version: "0.2.2"
+  version: "0.2.3"
   arguments:
   - type: "file"
     name: "--input"
@@ -116,6 +116,6 @@ info:
   output: "/Users/toni/code/projects/viash/viash_project_template/target/docker/template/take_column"
   executable: "/Users/toni/code/projects/viash/viash_project_template/target/docker/template/take_column/take_column"
   viash_version: "0.8.4"
-  git_commit: "11b6278597bf22afbfb56a8e83065a55553c9dd0"
+  git_commit: "82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
   git_remote: "https://github.com/viash-io/viash_project_template"
-  git_tag: "v0.2.1"
+  git_tag: "v0.2.2"
diff --git a/target/docker/template/take_column/take_column b/target/docker/template/take_column/take_column
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# take_column 0.2.2
+# take_column 0.2.3
 # 
 # This wrapper script is auto-generated by viash 0.8.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "take_column 0.2.2"
+  echo "take_column 0.2.3"
   echo ""
   echo "Arguments:"
   echo "    -i, --input"
@@ -412,10 +412,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component template take_column"
-LABEL org.opencontainers.image.created="2024-01-16T14:48:47+01:00"
+LABEL org.opencontainers.image.created="2024-02-08T14:49:14+01:00"
 LABEL org.opencontainers.image.source="https://github.com/viash-io/viash_project_template"
-LABEL org.opencontainers.image.revision="11b6278597bf22afbfb56a8e83065a55553c9dd0"
-LABEL org.opencontainers.image.version="0.2.2"
+LABEL org.opencontainers.image.revision="82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
+LABEL org.opencontainers.image.version="0.2.3"
 
 VIASHDOCKER
 }
@@ -566,7 +566,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "take_column 0.2.2"
+            echo "take_column 0.2.3"
             exit
             ;;
         --input)
@@ -678,14 +678,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3'
   exit 0
 fi
 
@@ -862,7 +862,7 @@ 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 ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -881,8 +881,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/take_column:0.2.2
+ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/viash-io/viash_project_template/template/take_column:0.2.3
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-take_column-XXXXXX").py
 function clean_up {

diff --git a/target/nextflow/template/combine_columns/.config.vsh.yaml b/target/nextflow/template/combine_columns/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "combine_columns"
   namespace: "template"
-  version: "0.2.2"
+  version: "0.2.3"
   arguments:
   - type: "file"
     name: "--input"
@@ -45,6 +45,11 @@ platforms:
   chown: true
   setup_strategy: "ifneedbepullelsecachedbuild"
   target_image_source: "https://github.com/viash-io/viash_project_template"
+  setup:
+  - type: "r"
+    packages:
+    - "bit64"
+    bioc_force_install: false
   entrypoint: []
   cmd: null
 - type: "nextflow"
@@ -96,6 +101,6 @@ info:
   output: "/Users/toni/code/projects/viash/viash_project_template/target/nextflow/template/combine_columns"
   executable: "/Users/toni/code/projects/viash/viash_project_template/target/nextflow/template/combine_columns/combine_columns"
   viash_version: "0.8.4"
-  git_commit: "11b6278597bf22afbfb56a8e83065a55553c9dd0"
+  git_commit: "82b49c3c35b4fd813b4c585e921a5b0885b25cc3"
   git_remote: "https://github.com/viash-io/viash_project_template"
-  git_tag: "v0.2.1"
+  git_tag: "v0.2.2"