From 773c470426daac6f648929f3a9710efc37ed1d7c Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 24 Mar 2021 11:58:44 +0100
Subject: [PATCH 1/3] set a path height to show path names

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 67afce9f..0d680d66 100644
--- a/main.nf
+++ b/main.nf
@@ -231,7 +231,7 @@ process odgiViz {
   odgi viz \
     -i $graph \
     -o ${graph}.viz_mqc.png \
-    -x 1500 -y 500 -P 5
+    -x 1500 -y 500 -P 10
   """
 }
 

From c02f24663a551aed8ba8393afd67a321ae0cf699 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 24 Mar 2021 17:00:47 +0100
Subject: [PATCH 2/3] remove consensus paths for downstream analyses

---
 main.nf | 34 +++++++++++++++++++++++++++-------
 1 file changed, 27 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 0d680d66..72865696 100644
--- a/main.nf
+++ b/main.nf
@@ -190,6 +190,21 @@ process smoothxg {
     """
 }
 
+process removeConsensusPaths {
+    publishDir "${params.outdir}/smoothxg", mode: "${params.publish_dir_mode}"
+
+    input:
+        path(graph)
+
+    output:
+        path("${graph}.no_cons.gfa"), emit: gfa_smooth_no_cons
+
+    script:
+        """
+        grep "Consensus_" "$graph" -v > "${graph}.no_cons.gfa"
+        """
+}
+
 process odgiBuild {
   publishDir "${params.outdir}/odgi_build", mode: "${params.publish_dir_mode}"
 
@@ -227,12 +242,13 @@ process odgiViz {
   output:
     path("${graph}.viz_mqc.png")
 
-  """
-  odgi viz \
+  script:
+    """
+    odgi viz \
     -i $graph \
     -o ${graph}.viz_mqc.png \
     -x 1500 -y 500 -P 10
-  """
+    """
 }
 
 process odgiChop {
@@ -325,16 +341,20 @@ workflow {
       seqwish(fasta, wfmash.out.collect{it[1]})
     }
     smoothxg(seqwish.out)
+
+    removeConsensusPaths(smoothxg.out.gfa_smooth)
     if (params.do_stats) {
-      odgiBuild(seqwish.out.collect{it[1]}.mix(smoothxg.out.gfa_smooth, smoothxg.out.consensus_smooth.flatten()))
-      odgiStats(odgiBuild.out)
+        odgiBuild(seqwish.out.collect{it[1]}.mix(removeConsensusPaths.out, smoothxg.out.consensus_smooth.flatten()))
+        odgiStats(odgiBuild.out)
     }
     else {
-      odgiBuild(smoothxg.out.gfa_smooth)
+        odgiBuild(seqwish.out.collect{it[1]}.mix(removeConsensusPaths.out, smoothxg.out.gfa_smooth))
     }
+
     odgiVizOut = Channel.empty()
+    removeConsensusPathsOut = Channel.empty()
     if (params.do_viz) {
-      odgiVizOut = odgiViz(odgiBuild.out.filter(~".*smooth.*"))
+        odgiVizOut = odgiViz(odgiBuild.out)
     }
     odgiDrawOut = Channel.empty()
     if (params.do_layout) {

From 8f6d87d5de035910ddc2e495f7e57ce8e8f5d8d4 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 24 Mar 2021 17:04:25 +0100
Subject: [PATCH 3/3] update odgi draw parameter

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 72865696..d7a14f82 100644
--- a/main.nf
+++ b/main.nf
@@ -293,8 +293,8 @@ process odgiDraw {
     -c $layoutGraph \
     -p ${layoutGraph}.draw_mqc.png \
     -C \
-    -w 50 \
-    -H 1000 -t ${task.cpus}
+    -w 20 \
+    -H 1500 -t ${task.cpus}
   """
 }