From 7100f9ebc23880af9458d4ef81c9bf497fc35370 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 2 Apr 2025 10:57:13 +0100
Subject: [PATCH 01/12] Update release version, changelog and docs

---
 CHANGELOG.md                         |  5 ++++
 conf/base.config                     |  4 +--
 conf/eddie.config                    |  3 +--
 conf/eddie_conda.config              |  3 +--
 conf/params.config                   | 38 ----------------------------
 docs/changelog.md                    | 11 ++++++++
 modules/processes/preprocess/main.nf | 22 ++++++----------
 nextflow.config                      |  8 +++---
 nextflow_schema.json                 | 26 ++++++++++++++-----
 9 files changed, 53 insertions(+), 67 deletions(-)
 delete mode 100644 conf/params.config

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5ddba75..b83c25d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,9 @@
 # Changelog
+## [v1.8.6]
+- Add options to tweak minimap2 and GSAlign memory (e.g. `--gsalign_memory 6.GB` or `--minimap2_memory 8.GB`).
+- Uniform minimap2 options by prefixing with `--minimap2_`
+- Remove unnecessary configurations
+
 ## [v1.8.6]
 - Fix bugs originated after the workflow simplification.
 
diff --git a/conf/base.config b/conf/base.config
index 1eac65e..db74a02 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -120,7 +120,7 @@ process {
       }
     }
     memory = {
-      def baseMem = 6.GB * task.attempt
+      def baseMem = params.gsalign_memory as nextflow.util.MemoryUnit * task.attempt
       if (params.max_memory){
         baseMem.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1 ? params.max_memory as nextflow.util.MemoryUnit : baseMem
       } else {
@@ -146,7 +146,7 @@ process {
       }
     }
     memory = {
-      def baseMem = 8.GB * task.attempt
+      def baseMem = params.mm2_memory as nextflow.util.MemoryUnit * task.attempt
       if (params.max_memory){
         baseMem.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1 ? params.max_memory as nextflow.util.MemoryUnit : baseMem
       } else {
diff --git a/conf/eddie.config b/conf/eddie.config
index 4e67945..c7d9549 100644
--- a/conf/eddie.config
+++ b/conf/eddie.config
@@ -19,7 +19,6 @@ params {
   max_time = 240.h
   scratch = false
   queue_size = 100
-  rl9 = true
   project = "uoe_baseline"
 }
  
@@ -29,7 +28,7 @@ executor {
 }
  
 process {
-  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus} -R y -l rl9=${params.rl9} -P ${params.project} ${params.extra_cluster_options}" : "-R y -l rl9=${params.rl9} -P ${params.project ?: ''} ${params.extra_cluster_options}" }
+  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus} -R y -P ${params.project} ${params.extra_cluster_options}" : "-R y -P ${params.project ?: ''} ${params.extra_cluster_options}" }
   scratch = params.scratch
   penv = { task.cpus > 1 ? "sharedmem" : null }
 
diff --git a/conf/eddie_conda.config b/conf/eddie_conda.config
index 7e77c0a..51b2691 100644
--- a/conf/eddie_conda.config
+++ b/conf/eddie_conda.config
@@ -19,7 +19,6 @@ params {
   max_time = 240.h
   scratch = false
   queue_size = 100
-  rl9 = true
   project = "uoe_baseline"
 }
  
@@ -29,7 +28,7 @@ executor {
 }
  
 process {
-  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus} -R y -l rl9=${params.rl9} -P ${params.project} ${params.extra_cluster_options}" : "-R y -l rl9=${params.rl9} -P ${params.project ?: ''} ${params.extra_cluster_options}" }
+  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus} -R y -P ${params.project} ${params.extra_cluster_options}" : "-R y -P ${params.project ?: ''} ${params.extra_cluster_options}" }
   scratch = params.scratch
   penv = { task.cpus > 1 ? "sharedmem" : null }
 
diff --git a/conf/params.config b/conf/params.config
deleted file mode 100644
index f051f43..0000000
--- a/conf/params.config
+++ /dev/null
@@ -1,38 +0,0 @@
-params {
-    source = null
-    target = null
-    ncbi_source = false
-    ncbi_target = false
-    igenomes_source = false
-    igenomes_target = false
-    distance = 'medium'
-    aligner = 'lastz'
-    srcSize = 20000000
-    tgtSize = 10000000
-    tgtOvlp = 100000
-    srcOvlp = 0
-    qscores = null
-    outdir = "${launchDir}/OUTPUTS" 
-    annotation = null
-    annotation_format = null
-    custom = null
-    chainCustom = null
-    chain_name = 'liftover'
-    liftover_algorithm = 'liftover'
-    maf_tgt_name = 'tgt'
-    igenomes_base = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore = false  
-    no_maf = false
-    no_netsynt = false
-    mafTools = null
-    reciprocal_best = false
-    minimap2_threads = 2
-    gsalign_threads = 2
-    help = false
-    mamba = false
-    publish_dir_mode = 'copy'
-    extra_cluster_options = null
-    custom_config_version = 'master'
-    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    my_config = null
-}
diff --git a/docs/changelog.md b/docs/changelog.md
index 6575586..b83c25d 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,4 +1,15 @@
 # Changelog
+## [v1.8.6]
+- Add options to tweak minimap2 and GSAlign memory (e.g. `--gsalign_memory 6.GB` or `--minimap2_memory 8.GB`).
+- Uniform minimap2 options by prefixing with `--minimap2_`
+- Remove unnecessary configurations
+
+## [v1.8.6]
+- Fix bugs originated after the workflow simplification.
+
+## [v1.8.5]
+- Upkeep release.
+
 ## [v1.8.4]
 - Fix broken anaconda environment creation due to wrong repository order 
 - Better schema file
diff --git a/modules/processes/preprocess/main.nf b/modules/processes/preprocess/main.nf
index 3a7e50e..66f8766 100644
--- a/modules/processes/preprocess/main.nf
+++ b/modules/processes/preprocess/main.nf
@@ -142,13 +142,11 @@ process splitsrc {
         if [ -z \$myvalue ]; then
             myvalue=`faSize -tab ${source} | awk '\$1=="baseCount" {print \$2}'`
         fi
-        mkdir ./SPLIT_src && chmod a+rw ./SPLIT_src
-        faSplit size -oneFile -lift=source.lift ${source} \$myvalue SPLIT_src/src
+        mkdir ./SPLIT_src && faSplit size -oneFile -lift=source.lift ${source} \$myvalue SPLIT_src/src
         """
     else 
         """
-        mkdir ./SPLIT_src && chmod a+rw ./SPLIT_src
-        faSplit size -lift=source.lift -extra=${params.srcOvlp} ${source} ${params.srcSize} SPLIT_src/
+        mkdir ./SPLIT_src && faSplit size -lift=source.lift -extra=${params.srcOvlp} ${source} ${params.srcSize} SPLIT_src/
         """
 
     stub:
@@ -236,31 +234,27 @@ process splittgt {
     script:
     if( params.aligner == "blat" )
         """
-        mkdir ./SPLIT_tgt && chmod a+rw ./SPLIT_tgt
-        faSplit size -oneFile -lift=target.lift -extra=500 ${target} 4500 SPLIT_tgt/tmp
+        mkdir ./SPLIT_tgt && faSplit size -oneFile -lift=target.lift -extra=500 ${target} 4500 SPLIT_tgt/tmp
         """
-    else if ( params.aligner.toLowerCase() == "gsalign" || (params.aligner == 'minimap2' && params.mm2_full_alignment) )
+    else if ( params.aligner.toLowerCase() == "gsalign" || (params.aligner == 'minimap2' && params.minimap2_full_alignment) )
         """
         myvalue=`faSize -tab ${target} | awk '\$1=="maxSize" {print \$2}'`
         if [ -z \$myvalue ]; then
             myvalue=`faSize -tab ${target} | awk '\$1=="baseCount" {print \$2}'`
         fi
-        mkdir ./SPLIT_tgt && chmod a+rw ./SPLIT_tgt
-        faSplit size -oneFile -lift=target.lift ${target} \$myvalue SPLIT_tgt/tgt
+        mkdir ./SPLIT_tgt && faSplit size -oneFile -lift=target.lift ${target} \$myvalue SPLIT_tgt/tgt
         """
-    else if ( params.aligner == "minimap2" && !params.mm2_full_alignment && !params.mm2_lowmem )
+    else if ( params.aligner == "minimap2" && !params.minimap2_full_alignment && !params.minimap2_lowmem )
         """
         myvalue=`faSize -tab ${target} | awk '\$1=="maxSize" {print \$2}'`
         if [ -z \$myvalue ]; then
             myvalue=`faSize -tab ${target} | awk '\$1=="baseCount" {print \$2}'`
         fi
-        mkdir ./SPLIT_tgt && chmod a+rw ./SPLIT_tgt
-        faSplit size -lift=target.lift ${target} \$myvalue SPLIT_tgt/tgt
+        mkdir ./SPLIT_tgt && faSplit size -lift=target.lift ${target} \$myvalue SPLIT_tgt/tgt
         """
     else
         """
-        mkdir SPLIT_tgt && chmod a+rw SPLIT_tgt
-        faSplit size -lift=target.lift -extra=${params.tgtOvlp} ${target} ${params.tgtSize} SPLIT_tgt/
+        mkdir SPLIT_tgt && faSplit size -lift=target.lift -extra=${params.tgtOvlp} ${target} ${params.tgtSize} SPLIT_tgt/
         """
 
     stub:
diff --git a/nextflow.config b/nextflow.config
index 891b0cc..f8c0ab4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -38,10 +38,12 @@ params {
     mafTools = null
     report = false
     reciprocal_best = false
-    mm2_full_alignment = false
-    mm2_lowmem = false
+    minimap2_full_alignment = false
+    minimap2_lowmem = false
+    minimap2_memory = "8.GB"
     minimap2_threads = 2
     gsalign_threads = 2
+    gsalign_memory = "6.GB"
     max_memory = (Runtime.runtime.maxMemory() as nextflow.util.MemoryUnit).toGiga().GB
     max_cpus = Runtime.runtime.availableProcessors() == 1 ? 1 : Runtime.runtime.availableProcessors() - 1
     max_time = '240.h'
@@ -187,5 +189,5 @@ manifest {
   mainScript      = 'main.nf'
   nextflowVersion = '>=21.10.0'
   defaultBranch   = 'main'
-  version         = '1.8.6'
+  version         = '1.8.7'
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 109b383..40d6609 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -109,23 +109,37 @@
                     "type": "string",
                     "description": "Alignment custom options"
                 },
-                "minimap2_threads": {
-                    "type": "integer",
-                    "default": 2,
-                    "description": "Threads for the minimap2 alignment"
+                "gsalign_memory": {
+                    "type": "string",
+                    "default": "8.GB",
+                    "description": "Memory for the GSAlign alignment",
+                    "fa_icon": "fas fa-memory",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$"
                 },
                 "gsalign_threads": {
                     "type": "integer",
                     "default": 2,
                     "description": "Threads for the GSAlign alignment"
                 },
-                "mm2_full_alignment": {
+                "minimap2_threads": {
+                    "type": "integer",
+                    "default": 2,
+                    "description": "Threads for the minimap2 alignment"
+                },
+                "minimap2_memory": {
+                    "type": "string",
+                    "default": "8.GB",
+                    "description": "Memory for the minimap2 alignment",
+                    "fa_icon": "fas fa-memory",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$"
+                },
+                "minimap2_full_alignment": {
                     "type": "boolean",
                     "default": false,
                     "hidden": true,
                     "description": "Full minimap2 alignment; faster, but requires more memory"
                 },
-                "mm2_lowmem": {
+                "minimap2_lowmem": {
                     "type": "boolean",
                     "default": false,
                     "hidden": true,

From 3e0047a5bf37c57b933de330cac7a0a9d22635d7 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 2 Apr 2025 10:58:11 +0100
Subject: [PATCH 02/12] Further docs updates

---
 docs/alignments.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/alignments.md b/docs/alignments.md
index 3ac77cb..2ff5f11 100644
--- a/docs/alignments.md
+++ b/docs/alignments.md
@@ -102,6 +102,6 @@ The workflow now minimizes the memory impact of `minimap2` by generating an `.mm
 
 The default `minimap2` behaviour is now to align each sequence from the target genome separately, using one task at the time. This should achieve a good balance of number of processes and low number of cores per process.
 
-If the user wishes to use a single process, as in the previous version of the workflow, they can do so by providing `--mm2_full_alignment`. This will perform a single genome-to-genome process. You might want to increase the number of cores provided to minimap2 with `--minimap2_threads`.
+If the user wishes to use a single process, as in the previous version of the workflow, they can do so by providing `--minimap2_full_alignment`. This will perform a single genome-to-genome process. You might want to increase the number of cores provided to minimap2 with `--minimap2_threads` and memory with e.g. `--minimap2_memory 8.GB`.
 
-If the user needs to perform the alignment in a particularly low-memory environment, they can provide `--mm2_lowmem`. This will perform the scattering of the target genome using `--tgtSize`, and with the overlap specified in `--tgtOvlp`.
+If the user needs to perform the alignment in a particularly low-memory environment, they can provide `--minimap2_lowmem`. This will perform the scattering of the target genome using `--tgtSize`, and with the overlap specified in `--tgtOvlp`.

From 50d6b35a226e934d1ab72e370588bbb15b8ec6fb Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 2 Apr 2025 10:58:51 +0100
Subject: [PATCH 03/12] Update readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 8466502..1b64478 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 # Updates
 See [CHANGELOG](#CHANGELOG.md) for more details.
 
-**UPDATE 05/2024**: The `--aligner minimap2` mode now runs in multiple processes, splitting the target genome in fragments of at least `--tgtSize` bases; individual contigs and scaffolds **will not be fragmented**, and each chunk will contain entire sequences, unless the `--mm2_lowmem` option is provided. The old approach is still accessible through the `--mm2_full_alignment` option. The anaconda recipe with the dependencies has been updated, so please ensure to re-create the container where needed. This optimization allows to perform a `minimap2` liftover of the panTro6 to the hg38 genomes on a 16-cores Ryzen 7 8700G 64G Ubuntu machine in under half an hour
+**UPDATE 05/2024**: The `--aligner minimap2` mode now runs in multiple processes, splitting the target genome in fragments of at least `--tgtSize` bases; individual contigs and scaffolds **will not be fragmented**, and each chunk will contain entire sequences, unless the `--minimap2_lowmem` option is provided. The old approach is still accessible through the `--minimap2_full_alignment` option. The anaconda recipe with the dependencies has been updated, so please ensure to re-create the container where needed. This optimization allows to perform a `minimap2` liftover of the panTro6 to the hg38 genomes on a 16-cores Ryzen 7 8700G 64G Ubuntu machine in under half an hour.
 
 **UPDATE 14/12/2022**: Now the NCBI/iGenomes accession have to be provided in the `--source`/`--target` field, and then use the appropriate `--igenomes_source`/`--ncbi_source` and `--igenomes_target`/`--ncbi_target` as a modifier.
 

From 97100b75db7a73f2140c58de03af3f488d9b765b Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 2 Apr 2025 11:00:51 +0100
Subject: [PATCH 04/12] Bop

---
 CHANGELOG.md      | 2 +-
 docs/changelog.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b83c25d..1a4baf3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,5 @@
 # Changelog
-## [v1.8.6]
+## [v1.8.7]
 - Add options to tweak minimap2 and GSAlign memory (e.g. `--gsalign_memory 6.GB` or `--minimap2_memory 8.GB`).
 - Uniform minimap2 options by prefixing with `--minimap2_`
 - Remove unnecessary configurations
diff --git a/docs/changelog.md b/docs/changelog.md
index b83c25d..1a4baf3 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,5 +1,5 @@
 # Changelog
-## [v1.8.6]
+## [v1.8.7]
 - Add options to tweak minimap2 and GSAlign memory (e.g. `--gsalign_memory 6.GB` or `--minimap2_memory 8.GB`).
 - Uniform minimap2 options by prefixing with `--minimap2_`
 - Remove unnecessary configurations

From 72d3996e1e9bc3b75bab7812ff06a712cf3f0671 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Fri, 4 Apr 2025 11:49:49 +0100
Subject: [PATCH 05/12] Refuse

---
 conf/base.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/base.config b/conf/base.config
index db74a02..c4c7974 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -146,7 +146,7 @@ process {
       }
     }
     memory = {
-      def baseMem = params.mm2_memory as nextflow.util.MemoryUnit * task.attempt
+      def baseMem = params.minimap2_memory as nextflow.util.MemoryUnit * task.attempt
       if (params.max_memory){
         baseMem.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1 ? params.max_memory as nextflow.util.MemoryUnit : baseMem
       } else {

From 87d291d340f24f4acd0192b958d8ce809f5dee21 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Fri, 4 Apr 2025 13:35:48 +0100
Subject: [PATCH 06/12] Further tweaks

---
 main.nf | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/main.nf b/main.nf
index a76f558..882412e 100644
--- a/main.nf
+++ b/main.nf
@@ -29,14 +29,11 @@ workflow {
                 exit 0
         }
 
-        // If params.custom is set, define that as distance
-        if ( params.custom != '' && params.distance == 'custom' ) { params.distance = 'custom' }
-
         // If params.custom is set, define that as distance
         if ( !params.source && !params.target ) { log.error "You did not provide a source and a target files."; exit 1 }
         if ( !params.source && params.target ) { log.error "You did not provide a source file."; exit 1 }
         if ( params.source && !params.target ) { log.error "You did not provide a target file."; exit 1 }
-        if ( params.mm2_full_alignment && params.mm2_lowmem ) { log.error "Incompatible options: --mm2_lowmem and --mm2_full_alignment."; exit 1 }
+        if ( params.minimap2_full_alignment && params.minimap2_lowmem ) { log.error "Incompatible options: --mm2_lowmem and --mm2_full_alignment."; exit 1 }
 
         // Print run informations
         log.info '''
@@ -93,11 +90,11 @@ no_maf          : $params.no_maf"""
         if (params.gsalign_threads && params.aligner == 'gsalign'){
                 log.info"""low memory (mm2): $params.gsalign_threads"""
         } 
-        if (params.mm2_lowmem){
-                log.info"""low memory (mm2): $params.mm2_lowmem"""
+        if (params.minimap2_lowmem){
+                log.info"""low memory (mm2): $params.minimap2_lowmem"""
         } 
-        if (params.mm2_full_alignment){
-                log.info"""full-alignment  : $params.mm2_full_alignment"""
+        if (params.minimap2_full_alignment){
+                log.info"""full-alignment  : $params.minimap2_full_alignment"""
         } 
         if (params.mafTools){
                 log.info"""mafTools        : $params.mafTools"""

From 2323d8536830738ffcdee68cb5c2e19e315cedcc Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Fri, 4 Apr 2025 13:59:33 +0100
Subject: [PATCH 07/12] Fix mmi generation to use multiple threads and minimap2
 configuration

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

diff --git a/modules/processes/preprocess/main.nf b/modules/processes/preprocess/main.nf
index 66f8766..9bf7b3a 100644
--- a/modules/processes/preprocess/main.nf
+++ b/modules/processes/preprocess/main.nf
@@ -441,7 +441,7 @@ process makeSizeT {
 
 process make_mmi {
     tag "mmi"
-    label 'medium'
+    label 'minimap2'
 
     input:
     path fasta
@@ -455,7 +455,7 @@ process make_mmi {
         minimap2_conf = params.custom
     }
     """
-    minimap2 ${minimap2_conf} -d ${fasta.baseName}.mmi ${fasta}
+    minimap2 -t ${task.cpus} ${minimap2_conf} -d ${fasta.baseName}.mmi ${fasta}
     """
 
     stub:

From 11a3bbb92944564b415217588b95f9b8d7bc6d17 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Tue, 17 Jun 2025 09:53:49 +0100
Subject: [PATCH 08/12] Fix old reference

---
 modules/subworkflows/preprocess.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/subworkflows/preprocess.nf b/modules/subworkflows/preprocess.nf
index 29ee5f8..acfff67 100644
--- a/modules/subworkflows/preprocess.nf
+++ b/modules/subworkflows/preprocess.nf
@@ -34,7 +34,7 @@ workflow PREPROC {
         // split and group target
         splittgt(ch_target)
         tgt_lift = splittgt.out.tgt_lift_ch
-        if ( params.aligner.toLowerCase() == 'gsalign'  || (params.aligner == 'minimap2' && params.mm2_full_alignment) ){
+        if ( params.aligner.toLowerCase() == 'gsalign'  || (params.aligner == 'minimap2' && params.minimap2_full_alignment) ){
             ch_fragm_tgt_out = splittgt.out.tgtsplit_ch
             ch_fragm_tgt_fa = splittgt.out.tgtfas_ch
                 .flatten()

From 59feb0281b931830d5d20caf8809010398a0417c Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Tue, 17 Jun 2025 09:56:19 +0100
Subject: [PATCH 09/12] Fix configuration

---
 conf/base.config | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index c4c7974..d6f5128 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,7 +10,7 @@ process {
     cpus =  {
       def baseCpu = 1
       if (params.max_cpus){
-        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseMem
+        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseCpu
       } else {
         baseCpu
       }
@@ -36,7 +36,7 @@ process {
     cpus =  {
       def baseCpu = 1
       if (params.max_cpus){
-        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseMem
+        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseCpu
       } else {
         baseCpu
       }
@@ -62,7 +62,7 @@ process {
     cpus =  {
       def baseCpu = 1
       if (params.max_cpus){
-        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseMem
+        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseCpu
       } else {
         baseCpu
       }
@@ -88,7 +88,7 @@ process {
     cpus =  {
       def baseCpu = 2 * task.attempt
       if (params.max_cpus){
-        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseMem
+        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseCpu
       } else {
         baseCpu
       }
@@ -114,7 +114,7 @@ process {
     cpus =  {
       def baseCpu = params.gsalign_threads ? params.gsalign_threads as int * task.attempt : 1 * task.attempt
       if (params.max_cpus){
-        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int : baseMem
+        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int : baseCpu
       } else {
         baseCpu
       }
@@ -140,7 +140,7 @@ process {
     cpus =  {
       def baseCpu = params.minimap2_threads ? params.minimap2_threads as int * task.attempt : 1 * task.attempt
       if (params.max_cpus){
-        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseMem
+        baseCpu.compareTo(params.max_cpus as int) == 1 ? params.max_cpus as int  : baseCpu
       } else {
         baseCpu
       }

From b0fd269d3a5f61800e07c60c0fda71d4c26f5dd6 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Tue, 17 Jun 2025 10:54:28 +0100
Subject: [PATCH 10/12] Multiple patches to the configurations

---
 conf/eddie.config       | 92 ++++++++++++++++++++++++-----------------
 conf/eddie_conda.config | 73 +++++++++++++++++---------------
 nextflow.config         | 14 ++++++-
 3 files changed, 105 insertions(+), 74 deletions(-)

diff --git a/conf/eddie.config b/conf/eddie.config
index c7d9549..4d10571 100644
--- a/conf/eddie.config
+++ b/conf/eddie.config
@@ -1,57 +1,71 @@
 /*
  * ------------------------------------------------------
- *  Based on the nf-core/rnaseq Nextflow base config file
+ *  Custom eddie (singularity/apptainer) config file
  * ------------------------------------------------------
  */
- //Profile config names for nf-core/configs
+// New parameters specific to customize eddie behaviour
 params {
-  // iGenomes reference base
-  saveReference = true
-  igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
   config_profile_description = 'University of Edinburgh (eddie) cluster profile using anaconda tweaked by nf-core/configs.'
-  config_profile_contact = 'Andrea Talenti (@RenzoTale88)'
-  config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'// Add parameter to specify extra flags for eddie
-  extra_cluster_options = ""
-  enable_conda = false
-  cache_dir = null
-  max_memory = 2048.GB
-  max_cpus = 64
-  max_time = 240.h
-  scratch = false
-  queue_size = 100
-  project = "uoe_baseline"
+  config_profile_contact     = 'Andrea Talenti (@RenzoTale88)'
+  config_profile_url         = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'// Add parameter to specify extra flags for eddie
+  extra_cluster_options      = ""
+  enable_conda               = false
+  singularity_cache_dir      = null
+  max_memory                 = 2048.GB
+  max_cpus                   = 64
+  max_time                   = 240.h
+  scratch                    = false
+  queue_size                 = 100
+  project                    = "uoe_baseline"
 }
- 
+
 executor {
-  name = "sge"
-  queueSize = "${params.queue_size}"
+  name                       = "sge"
+  queueSize                  = params.queue_size
 }
- 
+
 process {
-  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus} -R y -P ${params.project} ${params.extra_cluster_options}" : "-R y -P ${params.project ?: ''} ${params.extra_cluster_options}" }
-  scratch = params.scratch
-  penv = { task.cpus > 1 ? "sharedmem" : null }
+  stageInMode                = 'symlink'
+  scratch                    = 'false'
+  penv                       = { task.cpus > 1 ? "sharedmem" : null }
 
+  // This will override all jobs clusterOptions
+  // This is necessary to allow jobs to run on Eddie for many users
+  // For each job, we add an extra 8 Gb of memory.
+  // For example, the process asked 16 Gb of RAM (task.memory). The job will reserve 24 Gb of RAM.
+  // The process will still use 16 Gb (task.memory) leaving 8 Gb for other system processes.
+  // This is very useful any JAVA programs which allocate task.memory RAM for its Virtual Machine
+  // Also it leaves enough memory for singularity to unpack images.
   // common SGE error statuses
-  errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
-  maxErrors = '-1'
-  maxRetries = 3
- 
-  beforeScript =
-  """
-  . /etc/profile.d/modules.sh
-  module load singularity
-  export SINGULARITY_TMPDIR="\$TMPDIR"
-  """
+  errorStrategy              = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
+  maxErrors                  = '-1'
+  maxRetries                 = 3
+
+  clusterOptions           = { 
+    def tot_memory = task.memory.toMega() + 8192
+    def memory_per_core = tot_memory / task.cpus
+    "-l h_vmem=${memory_per_core}M -R y -P ${params.project} ${params.extra_cluster_options}"
+  }
+  beforeScript             =
+    """
+    . /etc/profile.d/modules.sh
+    module load igmm/apps/singularity/3
+    export SINGULARITY_TMPDIR="\$TMPDIR"
+    export CUDA_VISIBLE_DEVICES=-1
+    """
 }
 
 env {
-  MALLOC_ARENA_MAX=1
+    MALLOC_ARENA_MAX=1
 }
 
 singularity {
-  envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
-  runOptions = '-p -B "$TMPDIR"'
-  enabled = true
-  autoMounts = true
-}
\ No newline at end of file
+    envWhitelist             = "APPTAINER_TMPDIR,SINGULARITY_TMPDIR,TMPDIR,CUDA_VISIBLE_DEVICES"
+    runOptions               = '-p -B "$TMPDIR"'
+    enabled                  = true
+    autoMounts               = true
+    // Define the singularity cache directory depending on the presence of the NFX_SGE_PROJECT variable
+    // User without compute project can't access to the shared cache directory.
+    // So, they need to store singularity images into the work directory.
+    cacheDir                 = params.singularity_cache_dir
+}
diff --git a/conf/eddie_conda.config b/conf/eddie_conda.config
index 51b2691..60f92bb 100644
--- a/conf/eddie_conda.config
+++ b/conf/eddie_conda.config
@@ -1,51 +1,58 @@
 /*
  * ------------------------------------------------------
- *  Based on the nf-core/rnaseq Nextflow base config file
+ *  Custom eddie (anaconda) config file
  * ------------------------------------------------------
  */
- //Profile config names for nf-core/configs
+
+// New parameters specific to customize eddie behaviour
 params {
-  // iGenomes reference base
-  saveReference = true
-  igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
   config_profile_description = 'University of Edinburgh (eddie) cluster profile using anaconda tweaked by nf-core/configs.'
-  config_profile_contact = 'Andrea Talenti (@RenzoTale88)'
-  config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'// Add parameter to specify extra flags for eddie
-  extra_cluster_options = ""
-  enable_conda = false
-  cache_dir = null
-  max_memory = 2048.GB
-  max_cpus = 64
-  max_time = 240.h
-  scratch = false
-  queue_size = 100
-  project = "uoe_baseline"
+  config_profile_contact     = 'Andrea Talenti (@RenzoTale88)'
+  config_profile_url         = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'// Add parameter to specify extra flags for eddie
+  extra_cluster_options      = ""
+  enable_conda               = false
+  singularity_cache_dir      = null
+  max_memory                 = 2048.GB
+  max_cpus                   = 64
+  max_time                   = 240.h
+  scratch                    = false
+  queue_size                 = 100
+  project                    = "uoe_baseline"
 }
- 
+
 executor {
-  name = "sge"
-  queueSize = "${params.queue_size}"
+  name                       = "sge"
+  queueSize                  = params.queue_size
 }
  
 process {
-  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus} -R y -P ${params.project} ${params.extra_cluster_options}" : "-R y -P ${params.project ?: ''} ${params.extra_cluster_options}" }
-  scratch = params.scratch
-  penv = { task.cpus > 1 ? "sharedmem" : null }
+  stageInMode                = 'symlink'
+  scratch                    = 'false'
+  penv                       = { task.cpus > 1 ? "sharedmem" : null }
 
+  // This will override all jobs clusterOptions
+  // This is necessary to allow jobs to run on Eddie for many users
+  // For each job, we add an extra 8 Gb of memory.
+  // For example, the process asked 16 Gb of RAM (task.memory). The job will reserve 24 Gb of RAM.
+  // The process will still use 16 Gb (task.memory) leaving 8 Gb for other system processes.
+  // This is very useful any JAVA programs which allocate task.memory RAM for its Virtual Machine
+  // Also it leaves enough memory for singularity to unpack images.
   // common SGE error statuses
-  errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
-  maxErrors = '-1'
-  maxRetries = 3
- 
-  beforeScript =
-  """
-  . /etc/profile.d/modules.sh
-  module load anaconda/2024.02
-  """
+  errorStrategy              = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
+  maxErrors                  = '-1'
+  maxRetries                 = 3
 
-  withName: mafstats {
-    conda = "$projectDir/assets/maf-environment.yml" 
+  clusterOptions           = { 
+    def tot_memory = task.memory.toMega() + 8192
+    def memory_per_core = tot_memory / task.cpus
+    "-l h_vmem=${memory_per_core}M -R y -P ${params.project} ${params.extra_cluster_options}"
   }
+  beforeScript             =
+    """
+    . /etc/profile.d/modules.sh
+    module load anaconda
+    export CUDA_VISIBLE_DEVICES=-1
+    """
 }
 
 env {
diff --git a/nextflow.config b/nextflow.config
index f8c0ab4..b4059af 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -78,12 +78,12 @@ profiles {
     executor.queueSize = Runtime.runtime.availableProcessors() == 1 ? 1 : Runtime.runtime.availableProcessors() - 1
     executor.submitRateLimit = '4sec'
   }
-  eddie {
+  roslin_eddie {
     includeConfig 'conf/eddie.config'
     singularity.enabled = true
     singularity.autoMounts = true 
   }   
-  eddie_conda {
+  roslin_eddie_conda {
     conda.enabled          = true
     includeConfig 'conf/eddie_conda.config'
     process.conda = "$projectDir/environment.yml" 
@@ -181,6 +181,16 @@ dag {
     file    = "${params.outdir}/reports/pipeline_dag.html"
 }
 
+// Define shell behaviour
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
+
 manifest {
   name            = 'evotools/nf-LO'
   author          = 'Andrea Talenti'

From dee9e1158b6ba2c3cc0adb1f81bb79b299eb311c Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Tue, 17 Jun 2025 13:12:00 +0100
Subject: [PATCH 11/12] Improve minimap2 workflow

---
 modules/processes/minimap2/main.nf | 7 ++++---
 modules/subworkflows/preprocess.nf | 6 +++++-
 nextflow.config                    | 1 +
 nextflow_schema.json               | 4 ++++
 4 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/modules/processes/minimap2/main.nf b/modules/processes/minimap2/main.nf
index 763bbb6..11f5a5e 100644
--- a/modules/processes/minimap2/main.nf
+++ b/modules/processes/minimap2/main.nf
@@ -10,10 +10,11 @@ process minimap2 {
 
     output: 
         tuple val(srcname), val(tgtname), file("${srcname}.${tgtname}.psl"), emit: al_files_ch
+        tuple val(srcname), val(tgtname), file("${srcname}.${tgtname}.paf.gz"), emit: paf_files_ch
 
     script:
     def mm2_args = "-cx asm10"
-    if (params.custom) {
+    if (params.custom && params.distance == "custom") {
         mm2_args = params.custom
     } else if (params.distance == 'near'){
         mm2_args = "-cx asm5"
@@ -25,8 +26,8 @@ process minimap2 {
         mm2_args = "-cx asm10"
     }
     """
-    minimap2 -t ${task.cpus} ${mm2_args} --cap-kalloc 100m --cap-sw-mem 50m --cs=long ${srcfile} ${tgtfile} | 
-        paftools.js view -f maf - |
+    minimap2 -t ${task.cpus} ${mm2_args} --cs=long ${srcfile} ${tgtfile} | gzip -c > ${srcname}.${tgtname}.paf.gz
+    paftools.js view -f maf ${srcname}.${tgtname}.paf.gz |
         maf-convert psl - |
         liftUp -type=.psl stdout ${srclift} warn stdin |
         liftUp -type=.psl -pslQ ${srcname}.${tgtname}.psl ${tgtlift} warn stdin 
diff --git a/modules/subworkflows/preprocess.nf b/modules/subworkflows/preprocess.nf
index acfff67..2dc8136 100644
--- a/modules/subworkflows/preprocess.nf
+++ b/modules/subworkflows/preprocess.nf
@@ -49,7 +49,11 @@ workflow PREPROC {
 
         // If minimap2 requested, convert reference to mmi to save memory
         if (params.aligner.toLowerCase() == 'minimap2'){
-            ch_fragm_src_fa = ch_fragm_src_fa | make_mmi | map{it -> [it.baseName, it]}
+            if (!params.skip_mmi){
+                ch_fragm_src_fa = ch_fragm_src_fa | make_mmi | map{it -> [it.baseName, it]}
+            } else {
+                ch_fragm_src_fa = ch_fragm_src_fa | map{it -> [it.baseName, it]}
+            }
         } else {
             ch_fragm_src_fa = ch_fragm_src_fa.map{it -> [it.baseName, it]}
         }
diff --git a/nextflow.config b/nextflow.config
index b4059af..679f3bc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -42,6 +42,7 @@ params {
     minimap2_lowmem = false
     minimap2_memory = "8.GB"
     minimap2_threads = 2
+    skip_mmi = false
     gsalign_threads = 2
     gsalign_memory = "6.GB"
     max_memory = (Runtime.runtime.maxMemory() as nextflow.util.MemoryUnit).toGiga().GB
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 40d6609..824e9ad 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -121,6 +121,10 @@
                     "default": 2,
                     "description": "Threads for the GSAlign alignment"
                 },
+                "skip_mmi": {
+                    "type": "boolean",
+                    "description": "Skip MMI index generation"
+                },
                 "minimap2_threads": {
                     "type": "integer",
                     "default": 2,

From 80096646990280c3fe88c6e2a28012e47b82474a Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 19 Nov 2025 09:39:34 +0000
Subject: [PATCH 12/12] More logging

---
 modules/subworkflows/preprocess.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/subworkflows/preprocess.nf b/modules/subworkflows/preprocess.nf
index 2dc8136..b31f3b2 100644
--- a/modules/subworkflows/preprocess.nf
+++ b/modules/subworkflows/preprocess.nf
@@ -59,6 +59,8 @@ workflow PREPROC {
         }
 
         // Prepare pairs of sequences
+        ch_fragm_src_fa.count().subscribe{ nqry -> log.info "Found ${nqry} source fragments" }
+        ch_fragm_tgt_fa.count().subscribe{ ntgt -> log.info "Found ${ntgt} target fragments" }
         ch_fragm_src_fa
             .combine(ch_fragm_tgt_fa)
             .transpose()