reorganize star modules

nf-core · Sep 30, 2024 · e366396 · e366396
1 parent 7fc32f0
commit e366396
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Showing 4 changed files with 10 additions and 42 deletions.
diff --git a/modules/local/star/mtx_to_h5ad.nf b/modules/local/star/mtx_to_h5ad.nf
diff --git a/modules/local/star/star_align.nf → modules/local/star_align.nf b/modules/local/star/star_align.nf → modules/local/star_align.nf
diff --git a/modules/local/star/templates/mtx_to_h5ad.py → modules/local/templates/mtx_to_h5ad_star.py b/modules/local/star/templates/mtx_to_h5ad.py → modules/local/templates/mtx_to_h5ad_star.py
@@ -82,11 +82,11 @@ def input_to_adata(
 #
 
 # create the directory with the sample name
-os.makedirs("${meta2.id}", exist_ok=True)
+os.makedirs("${meta.id}", exist_ok=True)
 
 # input_type comes from NF module
 adata = input_to_adata(
-    input_data="${meta2.input_type}",
-    output="${meta2.id}/${meta2.id}_${meta2.input_type}_matrix.h5ad",
-    sample="${meta2.id}"
+    input_data="${meta.input_type}",
+    output="${meta.id}/${meta.id}_${meta.input_type}_matrix.h5ad",
+    sample="${meta.id}"
 )
diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf
@@ -1,6 +1,6 @@
 /* --    IMPORT LOCAL MODULES/SUBWORKFLOWS     -- */
-include { STAR_ALIGN  } from '../../modules/local/star/star_align'
-include { MTX_TO_H5AD } from '../../modules/local/star/mtx_to_h5ad'
+include { STAR_ALIGN  } from '../../modules/local/star_align'
+include { MTX_TO_H5AD } from '../../modules/local/mtx_to_h5ad'
 
 /* --    IMPORT NF-CORE MODULES/SUBWORKFLOWS   -- */
 include { GUNZIP }                      from '../../modules/nf-core/gunzip/main'
@@ -58,7 +58,10 @@ workflow STARSOLO {
     * Perform h5ad conversion
     */
     MTX_TO_H5AD (
-        STAR_ALIGN.out.raw_counts.mix( STAR_ALIGN.out.filtered_counts ),
+        STAR_ALIGN.out.raw_counts
+            .map{ meta, files -> [meta + [input_type: 'raw'], files] }
+            .mix( STAR_ALIGN.out.filtered_counts.map{ meta, files -> [meta + [input_type: 'filtered'], files] } ),
+        [],
         star_index.map{ meta, index -> index }
     )
     ch_versions = ch_versions.mix(MTX_TO_H5AD.out.versions.first())