From 7b667fec7f9e2c92a817fd5bf4157f296e92880b Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 12 Feb 2025 09:42:08 +0000
Subject: [PATCH] Prepare new release

---
 CHANGELOG.md                       |  3 +++
 modules/processes/GSAlign/main.nf  |  9 ---------
 modules/processes/blat/main.nf     | 21 +++++++--------------
 modules/processes/lastz/main.nf    | 11 +----------
 modules/processes/minimap2/main.nf |  7 +------
 modules/subworkflows/GSAlign.nf    | 11 +++++++++++
 modules/subworkflows/blat.nf       |  9 +++++++++
 modules/subworkflows/minimap2.nf   | 10 ++++++++++
 nextflow.config                    |  2 +-
 9 files changed, 43 insertions(+), 40 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e53a3f9..5ddba75 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,7 @@
 # Changelog
+## [v1.8.6]
+- Fix bugs originated after the workflow simplification.
+
 ## [v1.8.5]
 - Upkeep release.
 
diff --git a/modules/processes/GSAlign/main.nf b/modules/processes/GSAlign/main.nf
index 63122c9..07ca48e 100644
--- a/modules/processes/GSAlign/main.nf
+++ b/modules/processes/GSAlign/main.nf
@@ -23,17 +23,8 @@ process gsalign{
         command = "GSAlign -i ${srcname} -q ${tgtfile} -sen -t ${task.cpus} -idy 75 -no_vcf -o ${srcname}.${tgtname}.tmp"
     } else if (params.distance == 'far') {
         command = "GSAlign -i ${srcname} -q ${tgtfile} -sen -t ${task.cpus} -idy 70 -no_vcf -o ${srcname}.${tgtname}.tmp"
-    } else if (params.distance == 'same') {
-        command = "GSAlign -i ${srcname} -q ${tgtfile} -sen -t ${task.cpus} -no_vcf -o ${srcname}.${tgtname}.tmp"
     } else {
         command = "GSAlign -i ${srcname} -q ${tgtfile} -sen -t ${task.cpus} -no_vcf -o ${srcname}.${tgtname}.tmp"
-        log.info"""Preset ${params.distance} not available for GSAlign"""   
-        log.info"""The software will use the same instead."""   
-        log.info"""If it is not ok for you, re-run selecting among the following options:"""   
-        log.info""" 1 - near"""   
-        log.info""" 2 - medium"""   
-        log.info""" 3 - far"""   
-        log.info""" 4 - same"""   
     }
     """
     ${command}
diff --git a/modules/processes/blat/main.nf b/modules/processes/blat/main.nf
index e8f83dc..19605e6 100644
--- a/modules/processes/blat/main.nf
+++ b/modules/processes/blat/main.nf
@@ -15,29 +15,22 @@ process blat {
         tuple val(srcname), val(tgtname), file("${srcname}.${tgtname}.psl"), emit: al_files_ch
 
     script:
-    def blat_args = "-fastMap -tileSize=12 -minIdentity=98"
+    def blat_args = "-fastMap -tileSize=12 -minIdentity=98 -ooc=${ooc12}"
     if (params.custom) {
         blat_args = params.custom
     } else if (params.distance == 'near'){
-        blat_args = "-t=dna -q=dna -fastMap -noHead -tileSize=11 -minScore=100 -minIdentity=98"
+        blat_args = "-t=dna -q=dna -fastMap -noHead -tileSize=11 -minScore=100 -minIdentity=98 -ooc=${ooc11}"
     } else if (params.distance == 'medium'){
-        blat_args = "-t=dna -q=dna -fastMap -noHead -tileSize=11 -stepSize=11 -oneOff=0 -minMatch=2 -minScore=30 -minIdentity=90 -maxGap=2 -maxIntron=75000"
+        blat_args = "-t=dna -q=dna -fastMap -noHead -tileSize=11 -stepSize=11 -oneOff=0 -minMatch=2 -minScore=30 -minIdentity=90 -maxGap=2 -maxIntron=75000 -ooc=${ooc11}"
     } else if (params.distance == 'far') {
-        blat_args = "-t=dna -q=dna -fastMap -noHead -tileSize=12 -oneOff=1 -minMatch=1 -minScore=30 -minIdentity=80 -maxGap=3 -maxIntron=75000"
+        blat_args = "-t=dna -q=dna -fastMap -noHead -tileSize=12 -oneOff=1 -minMatch=1 -minScore=30 -minIdentity=80 -maxGap=3 -maxIntron=75000 -ooc=${ooc12}"
     } else if (params.distance == 'balanced') {
-        blat_args = "-fastMap -tileSize=12 -minIdentity=98"
+        blat_args = "-fastMap -tileSize=12 -minIdentity=98 -ooc=${ooc12}"
     } else {
-        blat_args = "-fastMap -tileSize=12 -minIdentity=98"
-        log.info"""Preset ${params.distance} not available for blat"""   
-        log.info"""The software will use the balanced instead."""   
-        log.info"""If it is not ok for you, re-run selecting among the following options:"""   
-        log.info""" 1 - near"""   
-        log.info""" 2 - medium"""   
-        log.info""" 3 - far"""   
-        log.info""" 4 - balanced"""   
+        blat_args = "-fastMap -tileSize=12 -minIdentity=98 -ooc=${ooc12}"
     }
     """
-    blat ${srcfile} ${tgtfile} ${blat_args} -ooc=${ooc12} -out=psl tmp.psl 
+    blat ${srcfile} ${tgtfile} ${blat_args} -out=psl tmp.psl 
     liftUp -type=.psl stdout $srclift warn tmp.psl |
         liftUp -type=.psl -pslQ ${srcname}.${tgtname}.psl $tgtlift warn stdin 
     """
diff --git a/modules/processes/lastz/main.nf b/modules/processes/lastz/main.nf
index 4a6c783..04f5d50 100644
--- a/modules/processes/lastz/main.nf
+++ b/modules/processes/lastz/main.nf
@@ -62,17 +62,8 @@ process lastz{
         lastz_args = "B=0 C=0 E=30 H=2000 K=2200 L=6000 M=50 O=400 T=2 Y=3400"
     } else if (params.distance == 'primate') {
         lastz_args = "E=30 H=3000 K=5000 L=5000 M=10 O=400 T=1 ‑‑allocate:traceback=2048.0M"
-    } else if (params.distance == 'general') {
-        lastz_args = "E=30 H=2200 K=3000 L=3000 O=400 T=1 ‑‑allocate:traceback=2048.0M"
     } else {
-        log.info"""Preset ${params.distance} not available for lastz"""   
-        log.info"""The software will use general instead."""   
-        log.info"""If it is not ok for you, re-run selecting among the following options:"""   
-        log.info""" 1 - near"""   
-        log.info""" 2 - medium"""   
-        log.info""" 3 - far"""   
-        log.info""" 4 - primate"""   
-        log.info""" 5 - general"""   
+        lastz_args = "E=30 H=2200 K=3000 L=3000 O=400 T=1 ‑‑allocate:traceback=2048.0M"
     }
     def qscores = qmatrix.simpleName != "OPTIONAL_FILE" ? "Q=${qmatrix}" : ""
     """
diff --git a/modules/processes/minimap2/main.nf b/modules/processes/minimap2/main.nf
index d62432e..763bbb6 100644
--- a/modules/processes/minimap2/main.nf
+++ b/modules/processes/minimap2/main.nf
@@ -22,12 +22,7 @@ process minimap2 {
     } else if (params.distance == 'far') {
         mm2_args = "-cx asm20"
     } else {
-        log.info"""Preset ${params.distance} not available for minimap2"""   
-        log.info"""The software will use the medium instead."""   
-        log.info"""If it is not ok for you, re-run selecting among the following options:"""   
-        log.info""" 1 - near"""   
-        log.info""" 2 - medium"""   
-        log.info""" 3 - far"""   
+        mm2_args = "-cx asm10"
     }
     """
     minimap2 -t ${task.cpus} ${mm2_args} --cap-kalloc 100m --cap-sw-mem 50m --cs=long ${srcfile} ${tgtfile} | 
diff --git a/modules/subworkflows/GSAlign.nf b/modules/subworkflows/GSAlign.nf
index 5f7c7aa..a68a0e1 100644
--- a/modules/subworkflows/GSAlign.nf
+++ b/modules/subworkflows/GSAlign.nf
@@ -18,6 +18,17 @@ workflow GSALIGN {
         twoBitTN  
 
     main:
+        // Log if the preset is not available
+        if (params.distance != "near" && params.distance != "medium" && params.distance != "far" && params.distance != "same" && params.distance != "custom"){
+            log.info"""Preset ${params.distance} not available for GSAlign"""
+            log.info"""The software will use the same instead."""
+            log.info"""If it is not ok for you, re-run selecting among the following options:"""
+            log.info""" 1 - near"""
+            log.info""" 2 - medium"""
+            log.info""" 3 - far"""
+            log.info""" 4 - same"""
+        }
+
         // make index
         bwt_index( pairspath_ch.groupTuple(by: [0, 1] ).unique() )
 
diff --git a/modules/subworkflows/blat.nf b/modules/subworkflows/blat.nf
index c3ce8cf..addff51 100644
--- a/modules/subworkflows/blat.nf
+++ b/modules/subworkflows/blat.nf
@@ -20,6 +20,15 @@ workflow BLAT {
 
     main:
         // Check that preset is among the available ones
+        if (params.distance != "near" && params.distance != "medium" && params.distance != "far" && params.distance != "balanced" && params.distance != "custom"){
+            log.info"""Preset ${params.distance} not available for blat"""
+            log.info"""The software will use the balanced instead."""
+            log.info"""If it is not ok for you, re-run selecting among the following options:"""
+            log.info""" 1 - near"""
+            log.info""" 2 - medium"""
+            log.info""" 3 - far"""
+            log.info""" 4 - balanced"""
+        }
 
 
         // Prepare Ooc files
diff --git a/modules/subworkflows/minimap2.nf b/modules/subworkflows/minimap2.nf
index 0eadbfd..f612e52 100644
--- a/modules/subworkflows/minimap2.nf
+++ b/modules/subworkflows/minimap2.nf
@@ -18,6 +18,16 @@ workflow MINIMAP2 {
         twoBitTN  
 
     main:
+        // Log if the preset is not available
+        if (params.distance != "near" && params.distance != "medium" && params.distance != "far" && params.distance != "custom"){
+            log.info"""Preset ${params.distance} not available for minimap2"""
+            log.info"""The software will use the medium instead."""
+            log.info"""If it is not ok for you, re-run selecting among the following options:"""
+            log.info""" 1 - near"""
+            log.info""" 2 - medium"""
+            log.info""" 3 - far"""
+        }
+
         // Run minimap2
         minimap2(pairspath_ch, tgt_lift, src_lift)  
         axtChain( minimap2.out.al_files_ch, twoBitS, twoBitT)   
diff --git a/nextflow.config b/nextflow.config
index e3155ac..891b0cc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -187,5 +187,5 @@ manifest {
   mainScript      = 'main.nf'
   nextflowVersion = '>=21.10.0'
   defaultBranch   = 'main'
-  version         = '1.8.5'
+  version         = '1.8.6'
 }