Merge pull request #127 from nf-core/seqera-containers

Replace `erikfas/spatialvi` with Seqera image

Author: cavenel

CHANGELOG.md

@@ -18,6 +18,7 @@ compatible with further downstream analyses and/or exploration in _e.g._
 
 ### `Added`
 
+- Make the main spatial Docker image work with Seqera Containers [[#127](https://github.com/nf-core/spatialvi/pull/127)]
 - Fix 'dir' handling for cloud file systems [[#122](https://github.com/nf-core/spatialvi/pull/122)]
 - Follow the new Nextflow strict syntax for local (sub-) workflows [[#115](https://github.com/nf-core/spatialvi/pull/115)]
 - Add ability to use unknown slides for Space Ranger-based analyses [[#99](https://github.com/nf-core/spatialvi/issues/99) and [#109](https://github.com/nf-core/spatialvi/pull/109)]

bin/clustering.qmd

@@ -44,7 +44,7 @@ sample_id = "".join(
 sdata = spatialdata.read_zarr(input_sdata, ["images", "tables", "shapes"])
 adata = to_legacy_anndata(
     sdata,
-    coordinate_system="downscaled_hires",
+    coordinate_system=f"{sample_id}_downscaled_hires",
     table_name=f"{sample_id}_table",
     include_images=True
 )

bin/quality_controls.qmd

@@ -64,7 +64,7 @@ sample_id = "".join(
 sdata = spatialdata.read_zarr(input_sdata, ["images", "tables", "shapes"])
 adata = to_legacy_anndata(
     sdata,
-    coordinate_system="downscaled_hires",
+    coordinate_system=f"{sample_id}_downscaled_hires",
     table_name=f"{sample_id}_table",
     include_images=True
 )

bin/spatially_variable_genes.qmd

@@ -41,7 +41,7 @@ sample_id = "".join(
 sdata = spatialdata.read_zarr(input_sdata, ["images", "tables", "shapes"])
 adata = to_legacy_anndata(
     sdata,
-    coordinate_system="downscaled_hires",
+    coordinate_system=f"{sample_id}_downscaled_hires",
     table_name=f"{sample_id}_table",
     include_images=True
 )

conf/modules.config

@@ -62,10 +62,13 @@ process {
         container = 'docker.io/multiqc/multiqc:v1.29'
     }
 
+    // The Seqera image used in multiple modules of this pipeline contains many
+    // different packages, the build information for which you can find here:
+    // https://wave.seqera.io/view/builds/bd-95f731fde0b9ddef_1.
     withName: 'READ_DATA|QUALITY_CONTROLS|CLUSTERING|SPATIALLY_VARIABLE_GENES' {
         ext.prefix = { "${notebook.baseName}" }
         ext.args = { "--metadata subtitle:'Sample: ${meta.id}'" }
-        container = 'docker.io/erikfas/spatialvi'
+        container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef'
         publishDir = [
             [
                 path: { "${params.outdir}/${meta.id}/reports" },
@@ -115,7 +118,7 @@ process {
 
     withName: 'INTEGRATE_SDATA' {
         ext.prefix = { "${notebook.baseName}" }
-        container = 'docker.io/erikfas/spatialvi'
+        container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef'
         publishDir = [
             [
                 path: { "${params.outdir}/aggregation/reports"},

env/.dockerignore

@@ -4,7 +4,7 @@
 process MERGE_SDATA {
 
     label 'process_low'
-    container "docker.io/erikfas/spatialvi"
+    container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef"
 
     input:
     path(sdata, stageAs: "?/*")

env/Dockerfile

@@ -6,7 +6,7 @@ process READ_DATA {
     tag "${meta.id}"
     label 'process_low'
 
-    container "docker.io/erikfas/spatialvi"
+    container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef"
 
     input:
     tuple val(meta), path("${meta.id}")