Merge branch 'dev' into feature/create-bam-parameter

Author: grst

CHANGELOG.md

@@ -5,7 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-- Add --create-bam parameter to cellranger count and multi pipelines ([#384](https://github.com/nf-core/scrnaseq/issues/384))
+- Add `--save_align_intermeds` parameter that publishes BAM files to the output directory (for `starsolo`, `cellranger` and `cellranger multi`) ([#384](https://github.com/nf-core/scrnaseq/issues/384))
+- Added support for pre-built indexes in `genomes.config` file for `cellranger`, `cellranger-arc`, `simpleaf` and `simpleaf txp2gene` ([#371](https://github.com/nf-core/scrnaseq/issues/371))
 
 ## v2.7.1 - 2024-08-13
 

workflows/scrnaseq.nf

@@ -37,9 +37,20 @@ workflow SCRNASEQ {
         error "Only cellranger supports `protocol = 'auto'`. Please specify the protocol manually!"
     }
 
-    params.fasta = getGenomeAttribute('fasta')
-    params.gtf = getGenomeAttribute('gtf')
-    params.star_index = getGenomeAttribute('star')
+    // collect paths from genome attributes file (e.g. iGenomes.config; optional)
+    params.fasta            = getGenomeAttribute('fasta')
+    params.gtf              = getGenomeAttribute('gtf')
+    params.star_index       = getGenomeAttribute('star')
+    params.salmon_index     = getGenomeAttribute('simpleaf')
+    params.txp2gene         = getGenomeAttribute('simpleaf_tx2pgene')
+
+    // Make cellranger or cellranger-arc index conditional
+    if (params.aligner in ["cellranger", "cellrangermulti"]){
+        params.cellranger_index = getGenomeAttribute('cellranger')
+    }
+    else if (params.aligner == "cellrangerarc") {
+        params.cellranger_index = getGenomeAttribute('cellrangerarc')
+    }
 
     ch_genome_fasta = params.fasta ? file(params.fasta, checkIfExists: true) : []
     ch_gtf = params.gtf ? file(params.gtf, checkIfExists: true) : []