nf_modules: fix paired-single end handling

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}

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} \

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} \

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 \

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]}
   """

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 \

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]} \