Allow no fasta during param checks

Author: pinin4fjords

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf

@@ -180,8 +180,14 @@ def validateInputParameters() {
 
     genomeExistsError()
 
-    if (!params.fasta) {
-        error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")
+    if (
+        !params.fasta &&
+        (
+            ! params.skip_alignment ||  // Alignment needs fasta
+            ! params.transcript_fasta // Dynamically making a transcript fasta needs the fasta
+        )
+    ) {
+        error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file. You must supply a genome FASTA file or use --skip_alignment and provide your own transcript fasta using --transcript_fasta for use in quantification.")
     }
 
     if (!params.gtf && !params.gff) {