minor changes on bwa mem and samtools view+sort of Nextflow modules

structuralvariants/nextflow/modules/bwa_mem_paired.nf

 process BWA_MEM_PAIRED {
-  tag { "bwa-mem paired" }
+  tag { "bwa mem" }
   container 'quay.io/biocontainers/bwa:0.7.17--h84994c4_5'
 
   input:

structuralvariants/nextflow/modules/bwa_mem_unpaired.nf

 process BWA_MEM_UNPAIRED {
-  tag { "bwa-mem unpaired" }
+  tag { "bwa mem" }
   container 'quay.io/biocontainers/bwa:0.7.17--h84994c4_5'
 
   input:

structuralvariants/nextflow/modules/samtools_view.nf

@@ -4,10 +4,10 @@ process SAMTOOLS_VIEW {
 
     input:
       path input
-    
+
     output:
       path '*.filtered.bam', emit: output
-    
+
     script:
     def min_mapping_qualityArgument = params.min_mapping_quality ? "-q $params.min_mapping_quality" : ''
     def bits_setArgument = params.bits_set ? "-F $params.bits_set" : ''
@@ -18,4 +18,4 @@ process SAMTOOLS_VIEW {
 
     samtools view $threadsArgument $min_mapping_qualityArgument $bits_setArgument $input -o \$outputName.filtered.bam
     """
-}
\ No newline at end of file
+}

structuralvariants/nextflow/subworkflows/bwa_mem.nf

@@ -2,7 +2,7 @@
  * Include for bwa_mem
 */
 include {
-    BWA_MEM_PAIRED as BWA_MEM_READS
+    BWA_MEM_PAIRED as BWA_MEM_PAIRED
 } from "../modules/bwa_mem_paired"
 include {
     BWA_MEM_UNPAIRED as BWA_MEM_UNPAIRED1
@@ -27,12 +27,12 @@ workflow SUB_BWA_MEM {
     unpaired1 = reads.map{it[3]}
     unpaired2 = reads.map{it[4]}
 
-    BWA_MEM_READS(srr_id, paired1, paired2, indexFiles)
+    BWA_MEM_PAIRED(srr_id, paired1, paired2, indexFiles)
     BWA_MEM_UNPAIRED1(srr_id, unpaired1, indexFiles)
     BWA_MEM_UNPAIRED2(srr_id, unpaired2, indexFiles)
 
   emit:
-    output_paired = BWA_MEM_READS.out
-    output_unpairedR1 = BWA_MEM_UNPAIRED1.out
-    output_unpairedR2 = BWA_MEM_UNPAIRED2.out
+    paired = BWA_MEM_PAIRED.out
+    unpairedR1 = BWA_MEM_UNPAIRED1.out
+    unpairedR2 = BWA_MEM_UNPAIRED2.out
 }

structuralvariants/nextflow/subworkflows/samtools_sort.nf

@@ -29,4 +29,4 @@ workflow SUB_SAMTOOLS_SORT {
     paired = SAMTOOLS_SORT_PAIRED.out
     unpairedR1 = SAMTOOLS_SORT_UNPAIRED_R1.out
     unpairedR2 = SAMTOOLS_SORT_UNPAIRED_R2.out
-}
\ No newline at end of file
+}

structuralvariants/nextflow/subworkflows/samtools_view_sam2bam.nf

 /*
- * Include for samtools_view_sam2bam 
+ * Include for samtools_view_sam2bam
 */
 include {
-    SAMTOOLS_VIEW_SAM2BAM as SAMTOOLS_VIEW_SAM2BAM_READS
+    SAMTOOLS_VIEW_SAM2BAM as SAMTOOLS_VIEW_SAM2BAM_PAIRED
 } from "../modules/samtools_view_sam2bam"
 include {
     SAMTOOLS_VIEW_SAM2BAM as SAMTOOLS_VIEW_SAM2BAM_UNPAIRED1
@@ -22,12 +22,12 @@ workflow SUB_SAMTOOLS_VIEW_SAM2BAM {
     unpairedR2
 
   main:
-    SAMTOOLS_VIEW_SAM2BAM_READS(paired)
+    SAMTOOLS_VIEW_SAM2BAM_PAIRED(paired)
     SAMTOOLS_VIEW_SAM2BAM_UNPAIRED1(unpairedR1)
     SAMTOOLS_VIEW_SAM2BAM_UNPAIRED2(unpairedR2)
 
   emit:
-    reads = SAMTOOLS_VIEW_SAM2BAM_READS.out
+    paired = SAMTOOLS_VIEW_SAM2BAM_PAIRED.out
     unpairedR1 = SAMTOOLS_VIEW_SAM2BAM_UNPAIRED1.out
     unpairedR2 = SAMTOOLS_VIEW_SAM2BAM_UNPAIRED2.out
-}
\ No newline at end of file
+}