Add in options for chrM and tn5 shift.

astrocyte_pkg.yml

@@ -108,6 +108,34 @@ workflow_parameters:
       read length, and then starts another round of reading from the opposite
       end of the fragment.
 
+  - id: chrM
+    type: select
+    required: true
+    choices:
+      - [ 'true', 'True']
+      - [ 'false', 'False']
+    description: |
+      In ATAC-seq and DNase-seq, mitochondrial reads are overrepresented.
+      We recomend filtering these reads out for further downstream analysis.
+
+  - id: tn5
+    type: select
+    required: true
+    choices:
+      - [ 'true', 'True']
+      - [ 'false', 'False']
+    description: |
+      ATAC-seq leverages the hyperactive Tn5 transposase,
+      preloaded with sequencing adaptors, to simultaneously
+      fragment transposase-accessible DNA and tag the
+      fragmented DNA with the sequencing adaptors, a
+      process called tagmentation. The Tn5 transposase has been shown to function as a
+      dimer and inserts the two sequencing adaptors into
+      target regions separated by 9 bp. For downstream
+      analysis, such as peak-calling and footprint analysis,
+      coordinates of all read alignments in the filtered
+      BAM file thus need to be shifted.
+
   - id: design
     type: file
     required: true

workflow/main.nf

@@ -6,6 +6,8 @@
 // Define Input variables
 params.reads = "$baseDir/../test_data/*.fastq.gz"
 params.pairedEnd = false
+params.chrM = true
+params.tn5 = true
 params.designFile = "$baseDir/../test_data/design_ENCSR265ZXX_SE.txt"
 params.genome = 'GRCm38'
 params.genomes = []
@@ -32,6 +34,8 @@ readsList = Channel
 
 // Define regular variables
 pairedEnd = params.pairedEnd
+chrM = params.chrM
+tn5 = params.tn5
 designFile = params.designFile
 genomeSize = params.genomeSize
 chromSizes = params.chromSizes
@@ -218,14 +222,48 @@ process convertReads {
   script:
 
   if (pairedEnd) {
-    """
-    python3 $baseDir/scripts/convert_reads.py -b $deduped -p
-    """
+    if (tn5 && chrM){
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -p -m -t
+      """
+    }
+    else if (tn5){
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -p -t
+      """
+    }
+    else if (chrM){
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -p -m
+      """
+    }
+    else{
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -p
+      """
+    }
   }
   else {
-    """
-    python3 $baseDir/scripts/convert_reads.py -b $deduped
-    """
+    if (tn5 && chrM){
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -m -t
+      """
+    }
+    else if (tn5){
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -t
+      """
+    }
+    else if (chrM){
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped -m
+      """
+    }
+    else{
+      """
+      python3 $baseDir/scripts/convert_reads.py -b $deduped
+      """
+    }
   }
 
 }

workflow/scripts/convert_reads.py

@@ -45,10 +45,10 @@ def get_args():
                         default=True,
                         action='store_true')
 
-     parser.add_argument('-t', '--tn5'
-                        help='Enable TN5 shifting for ATAC-Seq.'
-                        default=True,
-                        action='store_true')
+    parser.add_argument('-t', '--tn5'
+                    help='Enable TN5 shifting for ATAC-Seq.'
+                    default=True,
+                    action='store_true')
 
     args = parser.parse_args()
     return args