From c701d6c597fc6a9b15b1e38ea4c96c7ad2c78a66 Mon Sep 17 00:00:00 2001
From: "Davi Marcon (@mxrcon)" <davijosuemarcon@gmail.com>
Date: Fri, 28 Oct 2022 23:40:42 -0300
Subject: [PATCH] base work on modules

---
 modules/local/call2plink/bedify.nf        | 16 ++++++++++++++++
 modules/local/call2plink/combineBed.nf    | 19 +++++++++++++++++++
 modules/local/call2plink/fillinbam.nf     | 10 ++++++++++
 modules/local/call2plink/illumina2lgen.nf | 15 +++++++++++++++
 4 files changed, 60 insertions(+)
 create mode 100644 modules/local/call2plink/bedify.nf
 create mode 100644 modules/local/call2plink/combineBed.nf
 create mode 100644 modules/local/call2plink/fillinbam.nf
 create mode 100644 modules/local/call2plink/illumina2lgen.nf

diff --git a/modules/local/call2plink/bedify.nf b/modules/local/call2plink/bedify.nf
new file mode 100644
index 0000000..75e2147
--- /dev/null
+++ b/modules/local/call2plink/bedify.nf
@@ -0,0 +1,16 @@
+process bedify {
+    
+   input:
+     set file(ped), file(map)
+   output:
+     file("${base}.bed"), emit: bed_ch
+     file ("${base}.bim"), emit: bim_ch
+     file("${base}.fam"), emit: fam_ch
+   script:
+      def base = ped.baseName
+      """
+      echo $base
+
+      plink --file $base --no-fid --make-bed --out $base
+      """
+  }
diff --git a/modules/local/call2plink/combineBed.nf b/modules/local/call2plink/combineBed.nf
new file mode 100644
index 0000000..9432629
--- /dev/null
+++ b/modules/local/call2plink/combineBed.nf
@@ -0,0 +1,19 @@
+// Combine  all plinks and possibly remove errprs
+ process combineBed {
+   input:
+     file(bed) 
+     file(bim) 
+     file(fam)
+   output:
+     tuple file("raw.bed"), file("raw.fam"), file("raw.log"), emit: plink_src
+     file("rawraw.bim"), emit: fill_in_bim_ch
+   script:
+    """
+    ls *.bed | sort > beds
+    ls *.bim | sort >  bims
+    ls *.fam | sort >  fams
+    paste beds bims fams >  mergelist
+    plink --merge-list mergelist  --make-bed --out raw
+    mv raw.bim rawraw.bim
+    """
+ } 
diff --git a/modules/local/call2plink/fillinbam.nf b/modules/local/call2plink/fillinbam.nf
new file mode 100644
index 0000000..c4f0a9d
--- /dev/null
+++ b/modules/local/call2plink/fillinbam.nf
@@ -0,0 +1,10 @@
+process fillInBim {  //  Deals with monomorphic or non-called SNPs
+    input:
+     file(inbim)
+     file(strand)
+     file(manifest)
+    output:
+     file("raw.bim"), emit: filled_bim_ch
+    script:
+       "fill_in_bim.py ${params.output_align} $strand $manifest $inbim  raw.bim"
+  }
diff --git a/modules/local/call2plink/illumina2lgen.nf b/modules/local/call2plink/illumina2lgen.nf
new file mode 100644
index 0000000..4a23f28
--- /dev/null
+++ b/modules/local/call2plink/illumina2lgen.nf
@@ -0,0 +1,15 @@
+process illumina2lgen {
+    input:
+    set file(report), file(array)
+
+    output:
+    tuple file("${output}.ped"), file("${output}.map"), emit: ped_ch
+    script:
+        def samplesize = params.samplesize
+	def idpat      = params.idpat
+        def output = report.baseName
+        """
+        hostname
+        topbottom.py $array $report $samplesize '$idpat' $output
+        """
+ }