From fa46b889b57fdee77ce584baa18d4477d1f755fb Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 10:49:29 +0200
Subject: [PATCH 01/18] snapzipsort: use ubam for alignment

---
 conf/modules.config                     |  4 ++--
 modules/local/fgumi/snapzipsort/main.nf | 14 +++++---------
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 9da06635..28a21a4d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -252,7 +252,7 @@ process {
     //// FGUMI fastq | SNAP | zipper (step 3a)
     withName: RAW_FGUMI_SNAPZIPSORT {
         ext.prefix = { "${meta.id}.fgumi" }
-        ext.args2  = {
+        ext.args  = {
             [
                 "-b-",
                 "-sm 20",
@@ -264,7 +264,7 @@ process {
                 meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "",
             ].join(" ").trim()
         }
-        ext.args4  = {
+        ext.args3  = {
             [
                 "--order template-coordinate",
                 "--max-memory ${task.memory.toGiga()}G",
diff --git a/modules/local/fgumi/snapzipsort/main.nf b/modules/local/fgumi/snapzipsort/main.nf
index 88c34893..d6277e55 100644
--- a/modules/local/fgumi/snapzipsort/main.nf
+++ b/modules/local/fgumi/snapzipsort/main.nf
@@ -23,7 +23,6 @@ process FGUMI_SNAPZIPSORT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
-    def args4 = task.ext.args4 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}.fgumi"
 
     """
@@ -32,25 +31,22 @@ process FGUMI_SNAPZIPSORT {
     [ -z "\$INDEX_FILE" ] && echo "Snap index files not found" 1>&2 && exit 1
     INDEX=\$(dirname "\$INDEX_FILE")
 
-    fgumi fastq \\
-        --input ${unmapped_bam} \\
-        ${args} \\
-    | snap-aligner paired \\
+    snap-aligner paired \\
         \$INDEX \\
-        -pairedInterleavedFastq - \\
+        -bam - \\
         -t ${task.cpus} \\
         -o -bam - \\
-        ${args2} \\
+        ${args} \\
     | fgumi zipper \\
         --unmapped ${unmapped_bam} \\
         --reference ${fasta} \\
         --threads ${task.cpus} \\
-        ${args3} \\
+        ${args2} \\
     | fgumi sort \\
         --input - \\
         --output ${prefix}.bam \\
         --threads ${task.cpus} \\
-        ${args4}
+        ${args3}
     """
 
     stub:

From 25a1340606b2b4e07b9491439b1fdfec73b505b0 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 10:56:15 +0200
Subject: [PATCH 02/18] Update modules/local/fgumi/snapzipsort/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
---
 modules/local/fgumi/snapzipsort/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/fgumi/snapzipsort/main.nf b/modules/local/fgumi/snapzipsort/main.nf
index d6277e55..eb3f36e6 100644
--- a/modules/local/fgumi/snapzipsort/main.nf
+++ b/modules/local/fgumi/snapzipsort/main.nf
@@ -33,7 +33,7 @@ process FGUMI_SNAPZIPSORT {
 
     snap-aligner paired \\
         \$INDEX \\
-        -bam - \\
+        -bam ${unmapped_bam} \\
         -t ${task.cpus} \\
         -o -bam - \\
         ${args} \\

From 74f35f76df58f82df1b13279f267f6679e3ec3e8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 12:28:39 +0200
Subject: [PATCH 03/18] fix sorting

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index 28a21a4d..5ab72c9b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -268,6 +268,7 @@ process {
             [
                 "--order template-coordinate",
                 "--max-memory ${task.memory.toGiga()}G",
+                "--key-types mi"
             ].join(" ").trim()
         }
     }

From 1bc575a1329f480db0fdb367da83b8f55acb6c5b Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 12:43:46 +0200
Subject: [PATCH 04/18] fix test

---
 tests/modules/local/fgumi/snapzipsort/main.nf.test    | 1 +
 tests/modules/local/fgumi/snapzipsort/nextflow.config | 5 +++++
 2 files changed, 6 insertions(+)
 create mode 100644 tests/modules/local/fgumi/snapzipsort/nextflow.config

diff --git a/tests/modules/local/fgumi/snapzipsort/main.nf.test b/tests/modules/local/fgumi/snapzipsort/main.nf.test
index 5c2c404b..f9aa8784 100644
--- a/tests/modules/local/fgumi/snapzipsort/main.nf.test
+++ b/tests/modules/local/fgumi/snapzipsort/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process FGUMI_SNAPZIPSORT"
     script "modules/local/fgumi/snapzipsort/main.nf"
     process "FGUMI_SNAPZIPSORT"
+    config "./nextflow.config"
 
     tag "modules"
     tag "modules/local"
diff --git a/tests/modules/local/fgumi/snapzipsort/nextflow.config b/tests/modules/local/fgumi/snapzipsort/nextflow.config
new file mode 100644
index 00000000..ec000128
--- /dev/null
+++ b/tests/modules/local/fgumi/snapzipsort/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'FGUMI_SNAPZIPSORT' {
+        ext.args = "--order template-coordinate --max-memory ${task.memory.toGiga()}G --key-types mi"
+    }
+}

From 436d2651a962fb04926554b9789161145ba8170f Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 12:53:50 +0200
Subject: [PATCH 05/18] fix test

---
 tests/modules/local/fgumi/snapzipsort/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/local/fgumi/snapzipsort/nextflow.config b/tests/modules/local/fgumi/snapzipsort/nextflow.config
index ec000128..7d4872e5 100644
--- a/tests/modules/local/fgumi/snapzipsort/nextflow.config
+++ b/tests/modules/local/fgumi/snapzipsort/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: 'FGUMI_SNAPZIPSORT' {
-        ext.args = "--order template-coordinate --max-memory ${task.memory.toGiga()}G --key-types mi"
+        ext.args = "--order template-coordinate --key-types mi"
     }
 }

From c6d9e372ded6877897477e1f58576db7019cb9a0 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 12:55:10 +0200
Subject: [PATCH 06/18] fix subwf test

---
 .../subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test | 1 +
 .../local/fastq_umiconsensus_fgumi/nextflow.config           | 5 +++++
 2 files changed, 6 insertions(+)
 create mode 100644 tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config

diff --git a/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test b/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test
index b1b4d573..63dbe8b3 100644
--- a/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test
+++ b/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test
@@ -3,6 +3,7 @@ nextflow_workflow {
     name "Test Workflow FASTQ_UMICONSENSUS_FGUMI"
     script "subworkflows/local/fastq_umiconsensus_fgumi/main.nf"
     workflow "FASTQ_UMICONSENSUS_FGUMI"
+    config "./nextflow.config"
 
     tag "subworkflows"
     tag "subworkflows/local"
diff --git a/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config b/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config
new file mode 100644
index 00000000..7d4872e5
--- /dev/null
+++ b/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'FGUMI_SNAPZIPSORT' {
+        ext.args = "--order template-coordinate --key-types mi"
+    }
+}

From 5b731ad20ad66a46c81134259d7afd8956f03e69 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 9 Jul 2026 13:13:06 +0200
Subject: [PATCH 07/18] actually set the test args

---
 tests/modules/local/fgumi/snapzipsort/nextflow.config           | 2 +-
 .../subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/local/fgumi/snapzipsort/nextflow.config b/tests/modules/local/fgumi/snapzipsort/nextflow.config
index 7d4872e5..74ecf260 100644
--- a/tests/modules/local/fgumi/snapzipsort/nextflow.config
+++ b/tests/modules/local/fgumi/snapzipsort/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: 'FGUMI_SNAPZIPSORT' {
-        ext.args = "--order template-coordinate --key-types mi"
+        ext.args3 = "--order template-coordinate --key-types mi"
     }
 }
diff --git a/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config b/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config
index 7d4872e5..74ecf260 100644
--- a/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config
+++ b/tests/subworkflows/local/fastq_umiconsensus_fgumi/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: 'FGUMI_SNAPZIPSORT' {
-        ext.args = "--order template-coordinate --key-types mi"
+        ext.args3 = "--order template-coordinate --key-types mi"
     }
 }

From 22c5d97852663f185e88d365d353523958a8569a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 10:42:42 +0200
Subject: [PATCH 08/18] fix snap

---
 tests/modules/local/fgumi/snapzipsort/main.nf.test.snap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap b/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap
index bea6ad48..7951f68d 100644
--- a/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap
+++ b/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap
@@ -11,7 +11,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fgumi.bam:md5,6bab0c75514fda4b4e7efbbae5e33cc8"
+                        "test.fgumi.bam:md5,12bd726ae1623b7133398e231f866cd8"
                     ]
                 ]
             },
@@ -30,7 +30,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-06T13:16:43.167620236",
+        "timestamp": "2026-07-15T10:27:42.862700628",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"

From 95e68f06fc7cb8d92072e99c214979adff7ed85d Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 12:46:26 +0200
Subject: [PATCH 09/18] fix args

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5ab72c9b..688a6e70 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -293,7 +293,7 @@ process {
     //// FGUMI consensus alignment (step 8)
     withName: UMI_FGUMI_SNAPZIPSORT {
         ext.prefix = { "${meta.id}.fgumi" }
-        ext.args2  = {
+        ext.args  = {
             [
                 "-b-",
                 "-sm 20",
@@ -305,7 +305,7 @@ process {
                 meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "",
             ].join(" ").trim()
         }
-        ext.args4  = {
+        ext.args3  = {
             [
                 "--order coordinate",
                 "--max-memory ${task.memory.toGiga()}G",

From 0c09cd0ec07ed90ca424b9d1f18b7efb77437f1f Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 12:51:14 +0200
Subject: [PATCH 10/18] fix memory issues

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 688a6e70..d2f0de1b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -267,7 +267,7 @@ process {
         ext.args3  = {
             [
                 "--order template-coordinate",
-                "--max-memory ${task.memory.toGiga()}G",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
                 "--key-types mi"
             ].join(" ").trim()
         }
@@ -308,7 +308,7 @@ process {
         ext.args3  = {
             [
                 "--order coordinate",
-                "--max-memory ${task.memory.toGiga()}G",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
                 "--write-index",
             ].join(" ").trim()
         }

From eb1afcf2e6282117fcad6f922bd3541823679638 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 13:20:55 +0200
Subject: [PATCH 11/18] use -samNoSQ for snap input

---
 modules/local/fgumi/snapzipsort/main.nf            |  2 +-
 .../local/fgumi/snapzipsort/main.nf.test.snap      |  4 ++--
 .../fastq_umiconsensus_fgumi/main.nf.test.snap     | 14 +++++++-------
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/local/fgumi/snapzipsort/main.nf b/modules/local/fgumi/snapzipsort/main.nf
index eb3f36e6..4ffd9d2d 100644
--- a/modules/local/fgumi/snapzipsort/main.nf
+++ b/modules/local/fgumi/snapzipsort/main.nf
@@ -33,7 +33,7 @@ process FGUMI_SNAPZIPSORT {
 
     snap-aligner paired \\
         \$INDEX \\
-        -bam ${unmapped_bam} \\
+        -samNoSQ ${unmapped_bam} \\
         -t ${task.cpus} \\
         -o -bam - \\
         ${args} \\
diff --git a/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap b/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap
index 7951f68d..f3187dd5 100644
--- a/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap
+++ b/tests/modules/local/fgumi/snapzipsort/main.nf.test.snap
@@ -11,7 +11,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fgumi.bam:md5,12bd726ae1623b7133398e231f866cd8"
+                        "test.fgumi.bam:md5,9bfbd21ebea8ca63427cec8dd13e6063"
                     ]
                 ]
             },
@@ -30,7 +30,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-15T10:27:42.862700628",
+        "timestamp": "2026-07-15T13:19:00.257043127",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"
diff --git a/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap b/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap
index 68e5d648..f6360e82 100644
--- a/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap
+++ b/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap
@@ -22,8 +22,8 @@
                                 }
                             }
                         },
-                        "test.fgumi.bam:md5,d8847959ea89503e93669d3d5526813c",
-                        "test.fgumi.bam.bai:md5,6b054c31ca1e0c5cdf99d6fdc6229654"
+                        "test.fgumi.bam:md5,271e203740c8d65a49458ed13cb8be7d",
+                        "test.fgumi.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
                     ]
                 ],
                 "consensus_metrics": [
@@ -46,7 +46,7 @@
                                 }
                             }
                         },
-                        "test.fgumi.simplex.stats.txt:md5,c259ad6db7c02de9e0f1b9f95a3d6ab0"
+                        "test.fgumi.simplex.stats.txt:md5,8729c0587ff37d0e71b466c694bc62e4"
                     ]
                 ],
                 "family_size_histogram": [
@@ -69,7 +69,7 @@
                                 }
                             }
                         },
-                        "test.fgumi.group.family_size_histogram.txt:md5,57742826c7e781f773840f1c977f5f0b"
+                        "test.fgumi.group.family_size_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "filtering_metrics": [
@@ -92,7 +92,7 @@
                                 }
                             }
                         },
-                        "test.fgumi.filter.stats.txt:md5,01b1b32c9151552a623eef933b8d1f96"
+                        "test.fgumi.filter.stats.txt:md5,88b8f839f5e05e7944504f526949763c"
                     ]
                 ],
                 "grouping_metrics": [
@@ -115,12 +115,12 @@
                                 }
                             }
                         },
-                        "test.fgumi.group.grouping_metrics.txt:md5,deb6be58b11022b67145fe4e2c7ca299"
+                        "test.fgumi.group.grouping_metrics.txt:md5,b177c7de45cf25495c61f7bced9d8416"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-07-06T13:29:57.554096841",
+        "timestamp": "2026-07-15T13:16:45.581965003",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"

From 72a8b83cc14a713c0c6d4fd7643d21a7b817ce93 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 14:08:09 +0200
Subject: [PATCH 12/18] enable deadlock recovery

---
 conf/modules.config | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index d2f0de1b..b32bee46 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -276,7 +276,12 @@ process {
     //// FGUMI group (step 4)
     withName: '.*FGUMI_GROUP' {
         ext.prefix = { "${meta.id}.fgumi.group" }
-        ext.args   = { "--edits ${meta.fgumi_group_edits != null ? meta.fgumi_group_edits : 1}" }
+        ext.args   = { 
+            [
+                "--edits ${meta.fgumi_group_edits != null ? meta.fgumi_group_edits : 1}" ,
+                "--deadlock-recover" // Prevents deadlocks from occurring by temporarily bumping memory limits
+            ].join(" ").trim()
+        }
     }
 
     //// FGUMI simplex (step 5)

From 29542d4240c1c1747d87905d5a451cdfb3572ea0 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 14:39:33 +0200
Subject: [PATCH 13/18] remove deadlock recovery + fix memory assignment in
 fgumi

---
 conf/modules.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index b32bee46..f06ee0a5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -279,7 +279,7 @@ process {
         ext.args   = { 
             [
                 "--edits ${meta.fgumi_group_edits != null ? meta.fgumi_group_edits : 1}" ,
-                "--deadlock-recover" // Prevents deadlocks from occurring by temporarily bumping memory limits
+                "--max-memory ${task.memory.toGiga() / task.cpus}G"
             ].join(" ").trim()
         }
     }
@@ -287,12 +287,13 @@ process {
     //// FGUMI simplex (step 5)
     withName: '.*FGUMI_SIMPLEX' {
         ext.prefix = { "${meta.id}.fgumi.simplex" }
-        ext.args   = { "--max-memory ${task.memory.toGiga()}G" }
+        ext.args   = { "--max-memory ${task.memory.toGiga() / task.cpus}G" }
     }
 
     //// FGUMI filter + coordinate sort/index (step 7)
     withName: '.*FGUMI_FILTER' {
         ext.prefix = { "${meta.id}.fgumi.filter" }
+        ext.args   = { "--max-memory ${task.memory.toGiga() / task.cpus}G" }
     }
 
     //// FGUMI consensus alignment (step 8)

From ef63dbaaba0e5ad644e931beb81db1e932a1db8a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 16:00:51 +0200
Subject: [PATCH 14/18] fix joining

---
 subworkflows/local/fastq_umiconsensus_fgumi/main.nf          | 5 ++---
 .../local/fastq_umiconsensus_fgumi/main.nf.test.snap         | 4 ++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/main.nf b/subworkflows/local/fastq_umiconsensus_fgumi/main.nf
index e2416f9b..3b77450d 100644
--- a/subworkflows/local/fastq_umiconsensus_fgumi/main.nf
+++ b/subworkflows/local/fastq_umiconsensus_fgumi/main.nf
@@ -84,7 +84,7 @@ workflow FASTQ_UMICONSENSUS_FGUMI {
 
     // Step 7: filter consensus reads, then coordinate-sort/index for downstream CRAM conversion.
     FGUMI_FILTER(
-        FGUMI_SIMPLEX.out.bam.join(ch_meta_fastqs).map { meta, simplex_bams, _fastqs ->
+        FGUMI_SIMPLEX.out.bam.map { meta, simplex_bams ->
             [meta, simplex_bams, getGenomeAttribute(meta.genome_data, 'fasta')]
         },
         '1,1,1',
@@ -93,8 +93,7 @@ workflow FASTQ_UMICONSENSUS_FGUMI {
 
     UMI_FGUMI_SNAPZIPSORT(
         FGUMI_FILTER.out.bam
-            .join(ch_meta_fastqs)
-            .map { meta, filtered_bams, _fastqs ->
+            .map { meta, filtered_bams ->
                 [
                     meta,
                     filtered_bams,
diff --git a/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap b/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap
index f6360e82..27975a12 100644
--- a/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap
+++ b/tests/subworkflows/local/fastq_umiconsensus_fgumi/main.nf.test.snap
@@ -22,7 +22,7 @@
                                 }
                             }
                         },
-                        "test.fgumi.bam:md5,271e203740c8d65a49458ed13cb8be7d",
+                        "test.fgumi.bam:md5,c4a33382a1fb8a6361d23928359d672f",
                         "test.fgumi.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
                     ]
                 ],
@@ -120,7 +120,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-15T13:16:45.581965003",
+        "timestamp": "2026-07-15T15:59:40.968881197",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"

From f08b369c62530b4ee72d258ef4672d523f66dd83 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 15 Jul 2026 16:18:14 +0200
Subject: [PATCH 15/18] fix snap + run prek

---
 conf/modules.config                           |  2 +-
 .../fastq_to_aligned_cram/main.nf.test.snap   | 54 +++++++++----------
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f06ee0a5..1dc32dd5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -276,7 +276,7 @@ process {
     //// FGUMI group (step 4)
     withName: '.*FGUMI_GROUP' {
         ext.prefix = { "${meta.id}.fgumi.group" }
-        ext.args   = { 
+        ext.args   = {
             [
                 "--edits ${meta.fgumi_group_edits != null ? meta.fgumi_group_edits : 1}" ,
                 "--max-memory ${task.memory.toGiga() / task.cpus}G"
diff --git a/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap b/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap
index fa0f4ff7..844972d2 100644
--- a/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap
+++ b/tests/subworkflows/local/fastq_to_aligned_cram/main.nf.test.snap
@@ -3,7 +3,7 @@
         "content": [
             {
                 "align_reports": [
-
+                    
                 ],
                 "cram_crai": [
                     [
@@ -26,16 +26,16 @@
                     ]
                 ],
                 "family_size_histogram": [
-
+                    
                 ],
                 "rna_junctions": [
-
+                    
                 ],
                 "rna_splice_junctions": [
-
+                    
                 ],
                 "sormadup_metrics": [
-
+                    
                 ]
             }
         ],
@@ -49,7 +49,7 @@
         "content": [
             {
                 "align_reports": [
-
+                    
                 ],
                 "cram_crai": [
                     [
@@ -72,13 +72,13 @@
                     ]
                 ],
                 "family_size_histogram": [
-
+                    
                 ],
                 "rna_junctions": [
-
+                    
                 ],
                 "rna_splice_junctions": [
-
+                    
                 ],
                 "sormadup_metrics": [
                     [
@@ -111,7 +111,7 @@
         "content": [
             {
                 "align_reports": [
-
+                    
                 ],
                 "cram_crai": [
                     [
@@ -134,13 +134,13 @@
                     ]
                 ],
                 "family_size_histogram": [
-
+                    
                 ],
                 "rna_junctions": [
-
+                    
                 ],
                 "rna_splice_junctions": [
-
+                    
                 ],
                 "sormadup_metrics": [
                     [
@@ -173,7 +173,7 @@
         "content": [
             {
                 "align_reports": [
-
+                    
                 ],
                 "cram_crai": [
                     [
@@ -197,7 +197,7 @@
                     ]
                 ],
                 "family_size_histogram": [
-
+                    
                 ],
                 "rna_junctions": [
                     [
@@ -271,7 +271,7 @@
         "content": [
             {
                 "align_reports": [
-
+                    
                 ],
                 "cram_crai": [
                     [
@@ -294,16 +294,16 @@
                     ]
                 ],
                 "family_size_histogram": [
-
+                    
                 ],
                 "rna_junctions": [
-
+                    
                 ],
                 "rna_splice_junctions": [
-
+                    
                 ],
                 "sormadup_metrics": [
-
+                    
                 ]
             }
         ],
@@ -317,7 +317,7 @@
         "content": [
             {
                 "align_reports": [
-
+                    
                 ],
                 "cram_crai": [
                     [
@@ -365,24 +365,24 @@
                                 }
                             }
                         },
-                        "test.fgumi.group.family_size_histogram.txt:md5,57742826c7e781f773840f1c977f5f0b"
+                        "test.fgumi.group.family_size_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "rna_junctions": [
-
+                    
                 ],
                 "rna_splice_junctions": [
-
+                    
                 ],
                 "sormadup_metrics": [
-
+                    
                 ]
             }
         ],
-        "timestamp": "2026-07-06T13:26:52.23745498",
+        "timestamp": "2026-07-15T16:14:27.2930013",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"
         }
     }
-}
+}
\ No newline at end of file

From 33b15021c643fe7e39b4a4989ec983fd267ba380 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 16 Jul 2026 11:27:22 +0200
Subject: [PATCH 16/18] remove samNoSQ and let snap decide for itself

---
 modules/local/fgumi/snapzipsort/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/fgumi/snapzipsort/main.nf b/modules/local/fgumi/snapzipsort/main.nf
index 4ffd9d2d..d9a6ea7d 100644
--- a/modules/local/fgumi/snapzipsort/main.nf
+++ b/modules/local/fgumi/snapzipsort/main.nf
@@ -33,7 +33,7 @@ process FGUMI_SNAPZIPSORT {
 
     snap-aligner paired \\
         \$INDEX \\
-        -samNoSQ ${unmapped_bam} \\
+        ${unmapped_bam} \\
         -t ${task.cpus} \\
         -o -bam - \\
         ${args} \\

From 84cca63302499e378c48176abfe5e0220bbd53a6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 16 Jul 2026 11:49:37 +0200
Subject: [PATCH 17/18] add queryname sort before mapping

---
 conf/modules.config                           | 12 +++
 modules.json                                  |  5 ++
 modules/nf-core/fgumi/sort/environment.yml    |  7 ++
 modules/nf-core/fgumi/sort/main.nf            | 45 ++++++++++
 modules/nf-core/fgumi/sort/meta.yml           | 82 +++++++++++++++++
 modules/nf-core/fgumi/sort/tests/main.nf.test | 89 +++++++++++++++++++
 .../fgumi/sort/tests/main.nf.test.snap        | 87 ++++++++++++++++++
 .../nf-core/fgumi/sort/tests/nextflow.config  |  5 ++
 .../local/fastq_umiconsensus_fgumi/main.nf    |  7 +-
 9 files changed, 338 insertions(+), 1 deletion(-)
 create mode 100644 modules/nf-core/fgumi/sort/environment.yml
 create mode 100644 modules/nf-core/fgumi/sort/main.nf
 create mode 100644 modules/nf-core/fgumi/sort/meta.yml
 create mode 100644 modules/nf-core/fgumi/sort/tests/main.nf.test
 create mode 100644 modules/nf-core/fgumi/sort/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/fgumi/sort/tests/nextflow.config

diff --git a/conf/modules.config b/conf/modules.config
index 1dc32dd5..2286ab89 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -249,6 +249,18 @@ process {
         }
     }
 
+    withName: '.*FGUMI_SORT' {
+        ext.prefix = { "${meta.id}.fgumi.unmapped.sorted" }
+        ext.args   = {
+            [
+                "--order queryname",
+                "--compression-level 0",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--tmp-dir .",
+            ].join(" ").trim()
+        }
+    }
+
     //// FGUMI fastq | SNAP | zipper (step 3a)
     withName: RAW_FGUMI_SNAPZIPSORT {
         ext.prefix = { "${meta.id}.fgumi" }
diff --git a/modules.json b/modules.json
index ccf88121..5bbcd04d 100644
--- a/modules.json
+++ b/modules.json
@@ -77,6 +77,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fgumi/simplex/fgumi-simplex.diff"
                     },
+                    "fgumi/sort": {
+                        "branch": "master",
+                        "git_sha": "c3e04783b2ac99ffc011745ec092614a7bef86ca",
+                        "installed_by": ["modules"]
+                    },
                     "gnu/sort": {
                         "branch": "master",
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
diff --git a/modules/nf-core/fgumi/sort/environment.yml b/modules/nf-core/fgumi/sort/environment.yml
new file mode 100644
index 00000000..68aafa2b
--- /dev/null
+++ b/modules/nf-core/fgumi/sort/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fgumi=0.4.0"
diff --git a/modules/nf-core/fgumi/sort/main.nf b/modules/nf-core/fgumi/sort/main.nf
new file mode 100644
index 00000000..a3262e5d
--- /dev/null
+++ b/modules/nf-core/fgumi/sort/main.nf
@@ -0,0 +1,45 @@
+process FGUMI_SORT {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4a62b457c53300603da026225f95b4db04d1c9f8ba7f734787818fc105d51323/data'
+        : 'community.wave.seqera.io/library/fgumi:0.4.0--1fb5dc6de05ce63b'}"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.{csi,bai}"), emit: index, optional: true
+    tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_sorted"
+
+    if ("${bam}" == "${prefix}.bam") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
+
+    """
+    fgumi sort \\
+        --input ${bam} \\
+        --output ${prefix}.bam \\
+        --threads ${task.cpus} \\
+        ${args}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}_sorted"
+    if ("${bam}" == "${prefix}.bam") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
+    """
+    touch ${prefix}.bam
+    """
+}
diff --git a/modules/nf-core/fgumi/sort/meta.yml b/modules/nf-core/fgumi/sort/meta.yml
new file mode 100644
index 00000000..1dc25228
--- /dev/null
+++ b/modules/nf-core/fgumi/sort/meta.yml
@@ -0,0 +1,82 @@
+name: "fgumi_sort"
+description: |
+  Sorts a SAM or BAM file. Several sort orders are available, including coordinate,
+  queryname, and template-coordinate. This is a high-performance replacement for fgbio SortBam.
+keywords:
+  - sort
+  - bam
+  - sam
+tools:
+  - "fgumi":
+      description: "High-performance tools for working with UMI-tagged sequencing data."
+      homepage: "https://github.com/fulcrumgenomics/fgumi"
+      documentation: "https://docs.rs/fgumi"
+      tool_dev_url: "https://github.com/fulcrumgenomics/fgumi"
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: |
+          The input SAM or BAM file to be sorted.
+        pattern: "*.{bam,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572"
+output:
+  bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: |
+            Sorted output BAM file.
+          pattern: "*.bam"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572"
+  index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{csi,bai}":
+          type: file
+          description: |
+            Index file if the bam file is coordinate sorted.
+          pattern: "*.{csi,bai}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3327"
+  versions_fgumi:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fgumi:
+          type: string
+          description: The tool name
+      - 'fgumi --version | sed "s/^fgumi //"':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fgumi:
+          type: string
+          description: The tool name
+      - 'fgumi --version | sed "s/^fgumi //"':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@sppearce"
+maintainers:
+  - "@sppearce"
diff --git a/modules/nf-core/fgumi/sort/tests/main.nf.test b/modules/nf-core/fgumi/sort/tests/main.nf.test
new file mode 100644
index 00000000..fc549bf5
--- /dev/null
+++ b/modules/nf-core/fgumi/sort/tests/main.nf.test
@@ -0,0 +1,89 @@
+nextflow_process {
+
+    name "Test Process FGUMI_SORT"
+    script "../main.nf"
+    process "FGUMI_SORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fgumi"
+    tag "fgumi/sort"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    bam(process.out.bam.get(0).get(1)).getReadsMD5(),
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - template-coordinate") {
+
+        when {
+            params {
+                module_args = '--order template-coordinate'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    bam(process.out.bam.get(0).get(1)).getReadsMD5(),
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fgumi/sort/tests/main.nf.test.snap b/modules/nf-core/fgumi/sort/tests/main.nf.test.snap
new file mode 100644
index 00000000..ad6dfc3b
--- /dev/null
+++ b/modules/nf-core/fgumi/sort/tests/main.nf.test.snap
@@ -0,0 +1,87 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        "FGUMI_SORT",
+                        "fgumi",
+                        "0.4.0"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "index": [
+                    
+                ],
+                "versions_fgumi": [
+                    [
+                        "FGUMI_SORT",
+                        "fgumi",
+                        "0.4.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-26T13:03:56.414869",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - bam": {
+        "content": [
+            "461d8083b03a321eb1902ad544fd7d2f",
+            {
+                "versions_fgumi": [
+                    [
+                        "FGUMI_SORT",
+                        "fgumi",
+                        "0.4.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-26T13:03:43.67993",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - bam - template-coordinate": {
+        "content": [
+            "461d8083b03a321eb1902ad544fd7d2f",
+            {
+                "versions_fgumi": [
+                    [
+                        "FGUMI_SORT",
+                        "fgumi",
+                        "0.4.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-26T13:03:47.645547",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fgumi/sort/tests/nextflow.config b/modules/nf-core/fgumi/sort/tests/nextflow.config
new file mode 100644
index 00000000..4ad67e9b
--- /dev/null
+++ b/modules/nf-core/fgumi/sort/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: FGUMI_SORT {
+        ext.args   = { params.module_args }
+    }
+}
diff --git a/subworkflows/local/fastq_umiconsensus_fgumi/main.nf b/subworkflows/local/fastq_umiconsensus_fgumi/main.nf
index 3b77450d..2353e259 100644
--- a/subworkflows/local/fastq_umiconsensus_fgumi/main.nf
+++ b/subworkflows/local/fastq_umiconsensus_fgumi/main.nf
@@ -2,6 +2,7 @@
 
 // MODULES
 include { FGUMI_EXTRACT                              } from "../../../modules/nf-core/fgumi/extract/main.nf"
+include { FGUMI_SORT                                 } from "../../../modules/nf-core/fgumi/sort/main.nf"
 include { FGUMI_FILTER                               } from "../../../modules/nf-core/fgumi/filter/main.nf"
 include { FGUMI_GROUP                                } from "../../../modules/nf-core/fgumi/group/main.nf"
 include { FGUMI_MERGE                                } from "../../../modules/nf-core/fgumi/merge/main.nf"
@@ -25,9 +26,13 @@ workflow FASTQ_UMICONSENSUS_FGUMI {
             .map { meta, fastqs -> [meta, fastqs, (meta.readgroup?.LB ?: meta.library ?: meta.id)] }
     )
 
+    FGUMI_SORT(
+        FGUMI_EXTRACT.out.bam
+    )
+
     // Step 3: align with SNAP, zipper tags back, then template-coordinate sort.
     RAW_FGUMI_SNAPZIPSORT(
-        FGUMI_EXTRACT.out.bam
+        FGUMI_SORT.out.bam
             .join(ch_meta_fastqs)
             .map { meta, ubams, _fastqs ->
                 [

From f2f3a183d23e1a3b860777248e7ae72f2879eae9 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 16 Jul 2026 13:47:44 +0200
Subject: [PATCH 18/18] add sorting directly to mapping output

---
 conf/modules.config                     | 26 ++++++++++++++++++++++---
 modules/local/fgumi/snapzipsort/main.nf | 14 ++++++++++---
 2 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 2286ab89..5cbc5b31 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -257,6 +257,7 @@ process {
                 "--compression-level 0",
                 "--max-memory ${task.memory.toGiga() / task.cpus}G",
                 "--tmp-dir .",
+                "--key-types mi"
             ].join(" ").trim()
         }
     }
@@ -276,13 +277,23 @@ process {
                 meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "",
             ].join(" ").trim()
         }
-        ext.args3  = {
+        ext.args2  = {
             [
-                "--order template-coordinate",
+                "--order queryname",
+                "--compression-level 0",
                 "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--tmp-dir .",
                 "--key-types mi"
             ].join(" ").trim()
         }
+        ext.args4  = {
+            [
+                "--order template-coordinate",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--key-types mi",
+                "--tmp-dir .",
+            ].join(" ").trim()
+        }
     }
 
     //// FGUMI group (step 4)
@@ -323,7 +334,16 @@ process {
                 meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "",
             ].join(" ").trim()
         }
-        ext.args3  = {
+        ext.args2  = {
+            [
+                "--order queryname",
+                "--compression-level 0",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--tmp-dir .",
+                "--key-types mi"
+            ].join(" ").trim()
+        }
+        ext.args4  = {
             [
                 "--order coordinate",
                 "--max-memory ${task.memory.toGiga() / task.cpus}G",
diff --git a/modules/local/fgumi/snapzipsort/main.nf b/modules/local/fgumi/snapzipsort/main.nf
index d9a6ea7d..9139df7a 100644
--- a/modules/local/fgumi/snapzipsort/main.nf
+++ b/modules/local/fgumi/snapzipsort/main.nf
@@ -23,6 +23,7 @@ process FGUMI_SNAPZIPSORT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
+    def args4 = task.ext.args4 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}.fgumi"
 
     """
@@ -37,16 +38,23 @@ process FGUMI_SNAPZIPSORT {
         -t ${task.cpus} \\
         -o -bam - \\
         ${args} \\
-    | fgumi zipper \\
+    | fgumi sort \\
+        --input - \\
+        --output ${prefix}.intermediate.bam \\
+        --threads ${task.cpus} \\
+        ${args2}
+
+    fgumi zipper \\
+        --input ${prefix}.intermediate.bam \\
         --unmapped ${unmapped_bam} \\
         --reference ${fasta} \\
         --threads ${task.cpus} \\
-        ${args2} \\
+        ${args3} \\
     | fgumi sort \\
         --input - \\
         --output ${prefix}.bam \\
         --threads ${task.cpus} \\
-        ${args3}
+        ${args4}
     """
 
     stub: