Fix nf-core#432

main.nf

@@ -223,22 +223,21 @@ if ( params.fasta && !params.skipAlignment  ){
             .ifEmpty { exit 1, "Genome Fasta file not found: ${params.fasta}" }
             .set { ch_genome_fasta }
     }
-  }
-  else {
+  } else {
     if (hasExtension(params.fasta, "gz")){
       Channel.fromPath(params.fasta, checkIfExists: true)
           .ifEmpty { exit 1, "Genome fasta file not found: ${params.fasta}" }
           .set { genome_fasta_gz }
     } else {
       Channel.fromPath(params.fasta)
            .ifEmpty { exit 1, "Genome Fasta file not found: ${params.fasta}" }
-           .into { ch_fasta_for_star_index; ch_fasta_for_hisat_index}}
-}
-}
-else if (params.skipAlignment) {
+           .into { ch_fasta_for_star_index; ch_fasta_for_hisat_index;
+                   ch_fasta_for_rsem_reference }
+    }
+  }
+} else if (params.skipAlignment) {
   println "Skipping alignment ..."
-}
-else {
+} else {
     exit 1, "No reference genome files specified!"
 }
 
@@ -541,7 +540,7 @@ process get_software_versions {
 compressedReference = (hasExtension(params.fasta, 'gz') || 
     hasExtension(params.transcript_fasta, 'gz') || hasExtension(params.star_index, 'gz') || 
     hasExtension(params.hisat2_index, 'gz') || hasExtension(params.additional_fasta, "gz" ))
-     
+
 if (compressedReference) {
   // This complex logic is to prevent accessing the genome_fasta_gz variable if
   // necessary indices for STAR, HiSAT2, Salmon already exist, or if
@@ -1017,6 +1016,7 @@ if (params.with_umi) {
     process umi_tools_extract {
         tag "$name"
         label "low_memory"
+        cpus 1
         publishDir "${params.outdir}/umitools/extract", mode: "${params.publish_dir_mode}",
             saveAs: {filename ->
                 if (filename.endsWith('.log')) filename
@@ -1041,7 +1041,7 @@ if (params.with_umi) {
                 -I $reads \
                 -S ${name}_umi_extracted.fq.gz \
                 --extract-method=${params.umitools_extract_method} \
-                --bc-pattern=${params.umitools_bc_pattern} \
+                --bc-pattern="${params.umitools_bc_pattern}" \
                 ${params.umitools_extract_extra} > ${name}_umi_extract.log
             """
         }  else {
@@ -1052,7 +1052,7 @@ if (params.with_umi) {
                 -S ${name}_umi_extracted_R1.fq.gz \
                 --read2-out=${name}_umi_extracted_R2.fq.gz \
                 --extract-method=${params.umitools_extract_method} \
-                --bc-pattern=${params.umitools_bc_pattern} \
+                --bc-pattern="${params.umitools_bc_pattern}" \
                 ${params.umitools_extract_extra} > ${name}_umi_extract.log
             """
         }