diff --git a/src/nf_modules/bowtie/main.nf b/src/nf_modules/bowtie/main.nf
index 67887887526339e5578f5cdfccbfd120982ac563..a841fc36195dabcf2bb238431680f9e0677aa701 100644
--- a/src/nf_modules/bowtie/main.nf
+++ b/src/nf_modules/bowtie/main.nf
@@ -77,7 +77,7 @@ process mapping_fastq {
   tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
     ${file_id}_bowtie_mapping_report.txt
   """
-  else if (reads.size() == 1)
+  else
   """
   bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
     ${params.mapping_fastq}
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 1dc0780d52dc6b5118022a91fdf2b5c9c9f73e59..2b0cf96320902da5aa8c78004c06f5db7de25939 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -78,7 +78,7 @@ process mapping_fastq {
   tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
     ${file_prefix}_bowtie2_mapping_report.txt
   """
-  else if (reads.size() == 1)
+  else
   """
   bowtie2 ${params.mapping_fastq} \
     -p ${task.cpus} \
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 2f47c2393a800ffbe64dc8b03c2fbc8823b961da..07bf30d31c71e71b4f0372840145290787b76905 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -70,7 +70,7 @@ ${index_id} ${reads[0]} ${reads[1]} 2> \
   ${file_prefix}_bwa_report.txt | \
   samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
 """
-  else if (reads.size() == 1)
+  else
 """
 bwa mem -t ${task.cpus} \
 ${params.mapping_fastq} \
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index b0b31c624e08f0cbb7ff3d94b4ff398ba0a5ec91..7b5d9b56f012d57f6a7a4fb36efb2aa358c83d87 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -64,7 +64,7 @@ process fastp_default {
     --json ${file_prefix}_fastp.json \
     --report_title ${file_prefix}
   """
-  else if (reads.size() == 1)
+  else
   """
   fastp --thread ${task.cpus} \
     --qualified_quality_phred 20 \
@@ -128,7 +128,7 @@ process fastp_accel_1splus {
       --json ${file_prefix}_fastp.json \
       --report_title ${file_prefix}
   """
-  else if (reads.size() == 1)
+  else
   """
   fastp --thread ${task.cpus} \
     --disable_quality_filtering \
diff --git a/src/nf_modules/fastqc/main.nf b/src/nf_modules/fastqc/main.nf
index 4501b02685a39d653847130055fdd147b8b88927..da0c7bc7c952a7c4161751eef34fcfcf1882d2bd 100644
--- a/src/nf_modules/fastqc/main.nf
+++ b/src/nf_modules/fastqc/main.nf
@@ -24,7 +24,7 @@ process fastqc_fastq {
     ${params.fastqc_fastq} \
     ${reads[0]} ${reads[1]}
   """
-  else if (reads.size() == 1)
+  else
   """
     fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${params.fastqc_fastq} ${reads[0]}
   """
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 2a9adcbc172307aa6ce9c6738eaec8e901f4f6d7..67570e2d4739f025a646388407430cf7200dc705 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -57,7 +57,7 @@ process mapping_fastq {
   ${params.mapping_fastq} -o ${file_prefix} \
   ${reads[0]} ${reads[1]} &> ${file_prefix}_kallisto_mapping_report.txt
   """
-  else if (reads.size() == 1)
+  else
   """
   mkdir ${file_prefix}
   kallisto quant -i ${index} -t ${task.cpus} --single \
diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf
index 94279df885615b280b90fab8926453b4fd470021..b91afb74ccad107e7accd76ead32ea9945dda8b1 100644
--- a/src/nf_modules/urqt/main.nf
+++ b/src/nf_modules/urqt/main.nf
@@ -29,7 +29,7 @@ UrQt ${params.trimming} --m ${task.cpus} --gz \
   --out ${file_prefix}_trim_R1.fastq.gz --outpair ${file_prefix}_trim_R2.fastq.gz \
   > ${pair_id}_trimming_report.txt
 """
-  else if (reads.size() == 1)
+  else
 """
 UrQt ${params.trimming} --m ${task.cpus} --gz \
   --in ${reads[0]} \