fix(readmapping): use more strict mapping parameter

default/fullPipelineAggregate.yml

@@ -34,7 +34,7 @@ steps:
      # Just using relative abundance makes it difficult to tell if a genome is part of a dataset.
      # Thats why it makes sense to set at leat a low min covered fraction parameter.
     coverm:
-      additionalParams: " --min-covered-fraction 30 "
+      additionalParams: " --min-covered-fraction 80  --min-read-percent-identity 95 --min-read-aligned-percent 95 "
     minimap:
       additionalParams:
         minimap_index: ""

default/fullPipeline_illumina_nanpore.yml

@@ -71,9 +71,9 @@ steps:
         # samtools flags are used to filter resulting bam file
         samtoolsView: " -F 3584 " 
     contigsCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     genomeCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     # Primary binning tool
     metabat:
       # Set --seed positive numbers to reproduce the result exactly. Otherwise, random seed will be set each time.
@@ -86,9 +86,9 @@ steps:
         # samtools flags are used to filter resulting bam file
         samtoolsView: " -F 3584 " 
     contigsCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     genomeCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     metabat:
       additionalParams: " --seed 234234  "
   magAttributes:
@@ -118,7 +118,7 @@ steps:
         bwa2: "  "
         # We demand that matches should be at least 70 percent to restrict the
         # search space. We further restrict all found matches in 'coveredBasesCutoff' parameter.
-        coverm: " --min-covered-fraction 70 "
+        coverm: " --min-covered-fraction 70  --min-read-percent-identity 95 --min-read-aligned-percent 95 "
         minimap: "   "
         samtoolsViewBwa2: " -F 3584 " 
         samtoolsViewMinimap: " " 
@@ -159,7 +159,7 @@ steps:
      # Just using relative abundance makes it difficult to tell if a genome is part of a dataset.
      # Thats why it makes sense to set at leat a low min covered fraction parameter.
     coverm:
-      additionalParams: " --min-covered-fraction 30 "
+      additionalParams: " --min-covered-fraction 80  --min-read-percent-identity 95 --min-read-aligned-percent 95 "
     minimap:
       additionalParams:
         minimap_index: ""
@@ -180,7 +180,7 @@ steps:
       additionalParams:
         bwa2: "  "
         SCAPP: "  "
-        coverm: " --min-covered-fraction 0 "
+        coverm: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
         minimap: " "
         samtoolsViewBwa2: " -F 3584 " 
         samtoolsViewMinimap: " " 

default/fullPipeline_illumina_nanpore_without_aggregate.yml

@@ -71,9 +71,9 @@ steps:
         # samtools flags are used to filter resulting bam file
         samtoolsView: " -F 3584 " 
     contigsCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     genomeCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     # Primary binning tool
     metabat:
       # Set --seed positive numbers to reproduce the result exactly. Otherwise, random seed will be set each time.
@@ -86,9 +86,9 @@ steps:
         # samtools flags are used to filter resulting bam file
         samtoolsView: " -F 3584 " 
     contigsCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0  --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     genomeCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0  --min-read-percent-identity 100 --min-read-aligned-percent 100 "
     metabat:
       additionalParams: " --seed 234234  "
   magAttributes:
@@ -118,7 +118,7 @@ steps:
         bwa2: "  "
         # We demand that matches should be at least 70 percent to restrict the
         # search space. We further restrict all found matches in 'coveredBasesCutoff' parameter.
-        coverm: " --min-covered-fraction 70 "
+        coverm: " --min-covered-fraction 70 --min-read-percent-identity 95 --min-read-aligned-percent 95  "
         minimap: "   "
         samtoolsViewBwa2: " -F 3584 " 
         samtoolsViewMinimap: " " 
@@ -131,9 +131,9 @@ steps:
     # For final reporting of the covered fraction, the --min-covered-fraction parameter is set to the same value as 
     # in the binning and other sections
     genomeCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 95 --min-read-aligned-percent 95 "
     contigsCoverage:
-      additionalParams: " --min-covered-fraction 0 "
+      additionalParams: " --min-covered-fraction 0 --min-read-percent-identity 95 --min-read-aligned-percent 95 "
   annotation:
     prokka:
       defaultKingdom: false
@@ -215,7 +215,7 @@ steps:
       additionalParams:
         bwa2: "  "
         SCAPP: "  "
-        coverm: " --min-covered-fraction 0 "
+        coverm: " --min-covered-fraction 0 --min-read-percent-identity 100 --min-read-aligned-percent 100 "
         minimap: " "
         samtoolsViewBwa2: " -F 3584 " 
         samtoolsViewMinimap: " "