Merge pull request #416 from nictru/anndata-concatenation

Fix anndata concatenation
nf-core · Jan 15, 2025 · 582c8a7 · 582c8a7
2 parents 52bbe2f + d99d05c
commit 582c8a7
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Showing 24 changed files with 457 additions and 151 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -38,7 +38,7 @@ process {
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
-        withName: 'ADATA_BARCODES' {
+        withName: 'ANNDATA_BARCODES' {
             ext.prefix = { "${meta.id}_${meta.input_type}_matrix" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/mtx_conversions/${meta.id}" },

diff --git a/modules.json b/modules.json
@@ -5,10 +5,15 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "anndata/barcodes": {
+                        "branch": "master",
+                        "git_sha": "05e4d643e8a9cd600fdce51dccdfc68cf9a72489",
+                        "installed_by": ["h5ad_removebackground_barcodes_cellbender_anndata"]
+                    },
                     "cellbender/removebackground": {
                         "branch": "master",
                         "git_sha": "e01435f46b46adff59546d6a4b4002e31f6c4457",
-                        "installed_by": ["modules"]
+                        "installed_by": ["h5ad_removebackground_barcodes_cellbender_anndata", "modules"]
                     },
                     "cellranger/count": {
                         "branch": "master",
@@ -94,6 +99,11 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "h5ad_removebackground_barcodes_cellbender_anndata": {
+                        "branch": "master",
+                        "git_sha": "23600f6cd1c7fc4da79709bb531e5ba3cd5e840e",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",

diff --git a/modules/local/adata_barcodes.nf b/modules/local/adata_barcodes.nf
diff --git a/modules/local/templates/concat_h5ad.py b/modules/local/templates/concat_h5ad.py
@@ -62,9 +62,9 @@ def dump_versions():
 
     # merge with data.frame, on sample information
     adata.obs = adata.obs.join(df_samplesheet, on="sample", how="left").astype(str)
-    adata.write_h5ad("combined_${meta.input_type}_matrix.h5ad")
+    adata.write_h5ad("${meta.id}_${meta.input_type}_matrix.h5ad")
 
-    print("Wrote h5ad file to {}".format("combined_${meta.input_type}_matrix.h5ad"))
+    print("Wrote h5ad file to {}".format("${meta.id}_${meta.input_type}_matrix.h5ad"))
 
     # dump versions
     dump_versions()
diff --git a/modules/nf-core/anndata/barcodes/environment.yml b/modules/nf-core/anndata/barcodes/environment.yml
diff --git a/modules/nf-core/anndata/barcodes/main.nf b/modules/nf-core/anndata/barcodes/main.nf
diff --git a/modules/nf-core/anndata/barcodes/meta.yml b/modules/nf-core/anndata/barcodes/meta.yml
diff --git a/modules/local/templates/barcodes.py → ...re/anndata/barcodes/templates/barcodes.py b/modules/local/templates/barcodes.py → ...re/anndata/barcodes/templates/barcodes.py
diff --git a/modules/nf-core/anndata/barcodes/tests/main.nf.test b/modules/nf-core/anndata/barcodes/tests/main.nf.test
diff --git a/modules/nf-core/anndata/barcodes/tests/main.nf.test.snap b/modules/nf-core/anndata/barcodes/tests/main.nf.test.snap
diff --git a/modules/nf-core/anndata/barcodes/tests/tags.yml b/modules/nf-core/anndata/barcodes/tests/tags.yml