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

Author: DriesSchaumont

CHANGELOG.md

@@ -1,8 +1,14 @@
+# openpipelines 1.0.4
+
+## BUG FIXES
+
+* `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). 
+
 # openpipelines 1.0.3
 
 ## BUG FIXES
 
-* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR # , backported from PR #852).
+* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR #853 , backported from PR #852).
 
 # openpipelines 1.0.2
 

src/workflows/integration/scvi_leiden/config.vsh.yaml

@@ -19,7 +19,6 @@ functionality:
           description: Path to the sample.
           example: dataset.h5mu
         - name: "--layer"
-          default: "log_normalized"
           type: string
           description: use specified layer for expression values instead of the .X object from the modality.
           required: false

src/workflows/integration/scvi_leiden/main.nf

@@ -24,7 +24,8 @@ workflow run_wf {
           "lr_factor": state.lr_factor,
           "lr_patience": state.lr_patience,
           "output_model": state.output_model,
-          "modality": state.modality
+          "modality": state.modality,
+          "input_layer": state.layer,
        ]
       },
     // use map when viash 0.7.6 is released

src/workflows/integration/scvi_leiden/test.nf

@@ -10,15 +10,15 @@ workflow test_wf {
       [
         id: "simple_execution_test",
         input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
-        layer: "log_normalized",
+        layer: null,
         obs_batch: "sample_id",
         max_epochs: 1,
         output_model: "simple_execution_test_model/"
       ],
       [
         id: "no_leiden_resolutions_test",
         input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
-        layer: "log_normalized",
+        layer: null,
         obs_batch: "sample_id",
         output_model: "no_leiden_resolutions_test_model/",
         max_epochs: 1,

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

@@ -1,7 +1,7 @@
 functionality:
   name: "popv"
   namespace: "annotate"
-  version: "1.0.3"
+  version: "1.0.4"
   authors:
   - name: "Matthias Beyens"
     roles:
@@ -352,6 +352,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv"
   viash_version: "0.8.6"
-  git_commit: "36dc4369a0372420366dea16260f2bab2ea959e1"
+  git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.2-4-g36dc4369a0"
+  git_tag: "1.0.3-3-g74f972ebfd"

target/docker/annotate/popv/popv

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# popv 1.0.3
+# popv 1.0.4
 # 
 # This wrapper script is auto-generated by viash 0.8.6 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 1.0.3"
+  echo "popv 1.0.4"
   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="2024-08-09T10:01:42Z"
+LABEL org.opencontainers.image.created="2024-12-17T13:15:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="36dc4369a0372420366dea16260f2bab2ea959e1"
-LABEL org.opencontainers.image.version="1.0.3"
+LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
+LABEL org.opencontainers.image.version="1.0.4"
 
 VIASHDOCKER
 }
@@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "popv 1.0.3"
+            echo "popv 1.0.4"
             exit
             ;;
         --input)

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

@@ -1,7 +1,7 @@
 functionality:
   name: "leiden"
   namespace: "cluster"
-  version: "1.0.3"
+  version: "1.0.4"
   authors:
   - name: "Dries De Maeyer"
     roles:
@@ -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: "0.8.6"
-  git_commit: "36dc4369a0372420366dea16260f2bab2ea959e1"
+  git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.2-4-g36dc4369a0"
+  git_tag: "1.0.3-3-g74f972ebfd"

target/docker/cluster/leiden/leiden

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# leiden 1.0.3
+# leiden 1.0.4
 # 
 # This wrapper script is auto-generated by viash 0.8.6 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 1.0.3"
+  echo "leiden 1.0.4"
   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="2024-08-09T10:01:44Z"
+LABEL org.opencontainers.image.created="2024-12-17T13:15:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="36dc4369a0372420366dea16260f2bab2ea959e1"
-LABEL org.opencontainers.image.version="1.0.3"
+LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
+LABEL org.opencontainers.image.version="1.0.4"
 
 VIASHDOCKER
 }
@@ -618,7 +618,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "leiden 1.0.3"
+            echo "leiden 1.0.4"
             exit
             ;;
         --input)

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

@@ -1,7 +1,7 @@
 functionality:
   name: "compress_h5mu"
   namespace: "compression"
-  version: "1.0.3"
+  version: "1.0.4"
   authors:
   - name: "Dries Schaumont"
     roles:
@@ -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: "0.8.6"
-  git_commit: "36dc4369a0372420366dea16260f2bab2ea959e1"
+  git_commit: "74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.2-4-g36dc4369a0"
+  git_tag: "1.0.3-3-g74f972ebfd"

target/docker/compression/compress_h5mu/compress_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# compress_h5mu 1.0.3
+# compress_h5mu 1.0.4
 # 
 # This wrapper script is auto-generated by viash 0.8.6 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 1.0.3"
+  echo "compress_h5mu 1.0.4"
   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="2024-08-09T10:01:45Z"
+LABEL org.opencontainers.image.created="2024-12-17T13:15:04Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="36dc4369a0372420366dea16260f2bab2ea959e1"
-LABEL org.opencontainers.image.version="1.0.3"
+LABEL org.opencontainers.image.revision="74f972ebfd45203c74b6d58897e1f5d5b80afe0f"
+LABEL org.opencontainers.image.version="1.0.4"
 
 VIASHDOCKER
 }
@@ -581,7 +581,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "compress_h5mu 1.0.3"
+            echo "compress_h5mu 1.0.4"
             exit
             ;;
         --input)