make hdf5

Gregor-Mendel-Institute · Aug 8, 2018 · 71742b7 · 71742b7
1 parent 04e4365
commit 71742b7
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diff --git a/main.nf b/main.nf
@@ -494,6 +494,25 @@ if(params.aligner == 'methylpy'){
 
 }
 
+/*
+Make hdf5 files for the allc
+*/
+process make_hdf5 {
+  tag { "$name" }
+  publishDir "${params.outdir}/hdf5", mode: 'copy'
+
+  input:
+  set val(name), file(allc) from allc
+
+  output:
+  set val(name), file("*hdf5") into hdf5_out
+
+  script:
+  """
+  bshap methylation_percentage -i $allc -a new -b Chr1,1,100 -o temp -v
+  """
+}
+
 /*
 SNP calling from the methylpy
 */

diff --git a/methylpyDiffGenomes.nf b/methylpyDiffGenomes.nf
@@ -392,6 +392,22 @@ process bam_index {
   """
 }
 
+process make_hdf5 {
+  tag { "${accID}_$allc" }
+  publishDir "${params.outdir}/hdf5", mode: 'copy'
+
+  input:
+  set val(accID), file(allc) from allc
+
+  output:
+  set val(accID), file("*hdf5") into hdf5_out
+
+  script:
+  """
+  bshap methylation_percentage -i $allc -a new -b Chr1,1,100 -o temp -v
+  """
+}
+
 /*
  * STEP 8 - Qualimap
 process qualimap {