Fix #802

Author: drpatelh

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - [[#791](https://github.com/nf-core/rnaseq/issues/791)] - Add outputs for umitools dedup summary stats
 - [[#798](https://github.com/nf-core/rnaseq/issues/798)] - Decompress transcript fasta error
+- [[#802](https://github.com/nf-core/rnaseq/issues/802)] - `--bam_csi_index` error generated if `--skip_alignment` specified
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 
 ### Parameters

workflows/rnaseq.nf

@@ -167,10 +167,12 @@ workflow RNASEQ {
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     // Check if contigs in genome fasta file > 512 Mbp
-    PREPARE_GENOME
-        .out
-        .fai
-        .map { WorkflowRnaseq.checkMaxContigSize(it, log) }
+    if (!params.skip_alignment) {
+        PREPARE_GENOME
+            .out
+            .fai
+            .map { WorkflowRnaseq.checkMaxContigSize(it, log) }
+    }
 
     //
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files