Merge pull request #5 from platforma-open/use-software-package

use software packages for STAR and subread
platforma-open · Nov 15, 2024 · a07f0c0 · a07f0c0
2 parents b8cad40 + aa4d10c
commit a07f0c0
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Showing 6 changed files with 43 additions and 17 deletions.
diff --git a/.github/workflows/build-genome-assets.yaml b/.github/workflows/build-genome-assets.yaml
@@ -5,14 +5,14 @@ on:
     branches:
       - "main"
     paths:
-      - "genomeFiles/**"
+      - "genomeFiles/package.json"
       - ".github/workflows/build-genome-assets.yaml"
 
   push:
     branches:
       - "main"
     paths:
-      - "genomeFiles/**"
+      - "genomeFiles/package.json"
       - ".github/workflows/build-genome-assets.yaml"
 
   workflow_dispatch: {}

diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml
@@ -16,7 +16,9 @@ catalog:
   '@milaboratories/graph-maker': ^1.0.21
   '@milaboratories/software-pframes-conv': ^1.6.4
   '@platforma-open/milaboratories.software-small-binaries': ^1.13.1
-  '@platforma-open/milaboratories.star-read-mapping.genome-asset': ^1.0.5
+  '@platforma-open/milaboratories.software-subread': ^1.0.0
+  '@platforma-open/milaboratories.software-star': ^1.0.1
+  '@platforma-open/milaboratories.star-read-mapping.genome-asset': ^1.1.2
 
   '@ag-grid-community/core': ^32.2.2
   '@ag-grid-community/client-side-row-model': ^32.2.2

diff --git a/workflow/package.json b/workflow/package.json
@@ -11,6 +11,8 @@
     "@platforma-sdk/workflow-tengo": "catalog:",
     "@milaboratories/software-pframes-conv": "catalog:",
     "@platforma-open/milaboratories.software-small-binaries": "catalog:",
+    "@platforma-open/milaboratories.software-star": "catalog:",
+    "@platforma-open/milaboratories.software-subread": "catalog:",
     "@platforma-open/milaboratories.star-read-mapping.genome-asset": "catalog:"
   }
-}
+}
diff --git a/workflow/src/genomeAssets.lib.tengo b/workflow/src/genomeAssets.lib.tengo
@@ -4,7 +4,7 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
 getGenomeAsset := func(species) {
     yeastAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:saccharomyces-cerevisiae")
     // humanAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:homo-sapiens")
-    // mouseAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:mus-musculus")
+    mouseAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:mus-musculus")
     // ratAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:rattus-norvegicus")
     // zebrafishAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:danio-rerio")
     // fruitFlyAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:drosophila-melanogaster")
@@ -14,10 +14,10 @@ getGenomeAsset := func(species) {
     // cowAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:bos-taurus")
     // pigAssets := assets.importAsset("@platforma-open/milaboratories.star-read-mapping.genome-asset:sus_scrofa")
 
-    GenomeAssetsMap := {
-        "saccharomyces-cerevisiae": yeastAssets//,
+    GenomeAssetsMap := ll.toStrict({
+        "saccharomyces-cerevisiae": yeastAssets,
         // "homo-sapiens": humanAssets,
-        // "mus-musculus": mouseAssets,
+        "mus-musculus": mouseAssets//,
         // "rattus-norvegicus": ratAssets,
         // "danio-rerio": zebrafishAssets,
         // "drosophila-melanogaster": fruitFlyAssets,
@@ -26,7 +26,7 @@ getGenomeAsset := func(species) {
         // "gallus-gallus": chickenAssets,
         // "bos-taurus": cowAssets,
         // "sus_scrofa": pigAssets
-    }
+    })
 
     genomeAssets := GenomeAssetsMap[species]
 

diff --git a/workflow/src/star-alignment.tpl.tengo b/workflow/src/star-alignment.tpl.tengo
@@ -32,7 +32,7 @@ self.body(func(inputs) {
 genomeAssets := genomeAssetsLib.getGenomeAsset(species)
 
 	star:= exec.builder().
-			cmd("STAR").
+			software(assets.importSoftware("@platforma-open/milaboratories.software-star:star")).
 			mkDir("genomeIndex").
 			addAsset(genomeAssets, "genomeIndex", ["chrLength.txt"]).
 			addAsset(genomeAssets, "genomeIndex", ["chrName.txt"]).
@@ -92,7 +92,7 @@ genomeAssets := genomeAssetsLib.getGenomeAsset(species)
 
 	// Calculate counts from BAM file
 	featureCounts:= exec.builder().
-					cmd("featureCounts").
+					software(assets.importSoftware("@platforma-open/milaboratories.software-subread:featureCounts")).
 					addFile("sample_Aligned.sortedByCoord.out.bam", bamFile).
 					addAsset(genomeAssets, ".", ["annotations.gtf"]).
 					arg("-t").arg("exon").