Merge remote-tracking branch 'origin/main' into release

Author: rcannood

CHANGELOG.md

@@ -30,9 +30,6 @@ on each modality instead of on the whole `MuData` object.
 
 * `interactive/run_cellxgene`: Updated container to ubuntu:focal because it contains python3.6 but cellxgene dropped python3.6 support.
 
-* `download/download_file`: Switch base container from `ubuntu:22.04` to `bash:5.1` because `ubuntu:22.04`
-  was causing some edge case issues.
-
 * `mapping/bd_rhapsody_wta`: Set `--parallel` to true by default.
 
 * `mapping/bd_rhapsody_wta`: Translate Bash script into Python.
@@ -47,6 +44,10 @@ on each modality instead of on the whole `MuData` object.
 
 * Various `config.vsh.yaml`s: Renamed `values:` to `choices:`.
 
+* `download/download_file` and `transfer/publish`: Switch base container from `bash:5.1` to `python:3.10`.
+
+* `mapping/bd_rhapsody_wta`: Make sure procps is installed.
+
 ## BUG FIXES
 
 * `mapping/bd_rhapsody_wta`: Use a smaller test dataset to reduce test time and make sure that the Github Action runners do not run out of disk space.

bin/build_release.md

@@ -26,6 +26,9 @@ bin/viash_build -m release -t $TAG
 # run unit tests (when done right, these should all pass)
 bin/viash_test -m release -t $TAG
 
+# rebuild readme
+quarto render README.qmd
+
 # push docker containers to docker hub
 bin/viash_push -m release -t $TAG
 

src/download/download_file/config.vsh.yaml

@@ -37,9 +37,6 @@ functionality:
       path: run_test.sh
 platforms:
   - type: docker
-    image: "bash:5.1"
-    setup:
-      - type: apk
-        packages: [ wget ]
+    image: "python:3.10"
   - type: nextflow
     variant: vdsl3

src/mapping/bd_rhapsody_wta/config.vsh.yaml

@@ -118,7 +118,7 @@ platforms:
       - type: docker
         run: apt-get --allow-releaseinfo-change update
       - type: apt
-        packages: cwltool
+        packages: [ cwltool, procps ]
   - type: nextflow
     variant: vdsl3
     directives:

src/mapping/bd_rhapsody_wta_1_10/config.novsh.yaml

@@ -132,7 +132,7 @@ platforms:
     image: bdgenomics/rhapsody:1.10
     setup:
       - type: apt
-        packages: cwltool
+        packages: [ cwltool, procps ]
   - type: nextflow
     variant: vdsl3
     directives:

src/mapping/bd_rhapsody_wta_1_10_1/config.novsh.yaml

@@ -132,7 +132,7 @@ platforms:
     image: bdgenomics/rhapsody:1.10.1
     setup:
       - type: apt
-        packages: cwltool
+        packages: [ cwltool, procps ]
   - type: nextflow
     variant: vdsl3
     directives:

src/transfer/publish/config.vsh.yaml

@@ -27,6 +27,6 @@ functionality:
       path: run_test.sh
 platforms:
   - type: docker
-    image: bash:5.1
+    image: python:3.10
   - type: nextflow
     variant: vdsl3

workflows/1_ingestion/bd_rhapsody_wta/main.nf

@@ -148,7 +148,7 @@ workflow run_wf {
     | groupTuple()
 
     // Step 4: convert to h5ad
-    | map { id, input -> [ id, input, params ]}
+    | map { id, input -> [ id, [input: input ], params ]}
     | view { "converting_to_h5ad: [$it]" }
     | from_bdrhap_to_h5ad
 

workflows/1_ingestion/bd_rhapsody_wta/test/integration_test.sh

@@ -13,7 +13,8 @@ bin/nextflow \
   -main-script workflows/1_ingestion/bd_rhapsody_wta/main.nf \
   -entry test_wf \
   -resume \
-  -with-docker
+  -with-docker \
+  -with-trace work/trace.txt
 
 # -c workflows/1_ingestion/bd_rhapsody_wta/nextflow.config \
 

workflows/1_ingestion/cellranger_demux/test/integration_test.sh

@@ -13,4 +13,5 @@ bin/nextflow \
   -main-script workflows/1_ingestion/cellranger_demux/main.nf \
   -entry test_wf \
   -resume \
-  -with-docker
+  -with-docker \
+  -with-trace work/trace.txt