final corrections to SE pipeline

src/RNAseq_sen1D_bowtie2_SE.nf

@@ -254,29 +254,29 @@ multiqc -f .
 /*                      bams sorting                                    */
 
 process sort_bam {
-  tag "$reads.baseName"
+  tag "$bam.baseName"
   cpus 4
   publishDir "results/mapping_SE/bams/", mode: 'copy'
   input:
-    set pair_id, file(bam) from bam_files
+    file bam from bam_files
 
   output:
-    set pair_id, "*_sorted.bam" into sorted_bam_files
+    file "*_sorted.bam" into sorted_bam_files
 
   script:
 """
-samtools sort -@ ${task.cpus} -O BAM -o ${pair_id}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
 """
 }
 /*                      bams indexing                                     */
 
 process index_bam {
-  tag "$reads.baseName"
+  tag "$bam.baseName"
   publishDir "results/mapping_SE/bams/", mode: 'copy'
   input:
-    set pair_id, file(bam) from sorted_bam_files
+    file bam from sorted_bam_files
   output:
-    set pair_id, "*bam*" into indexed_bam_file
+    file "*bam*" into indexed_bam_file
   script:
 """
 samtools index ${bam}