From 888e058447122884af22a51a9e9e8fdf3f0b8cd8 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 8 May 2026 15:39:11 +0200
Subject: [PATCH 1/8] Exclude inputs from find search

---
 modules/nf-core/krakenuniq/build/main.nf | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index 7fe9120d1da7..a73f366ea686 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -22,7 +22,17 @@ process KRAKENUNIQ_BUILD {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     custom_db = custom_library_dir ? "mkdir ${prefix} && mv library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
-    run_cleanup = keep_intermediate ? "" : "find -L ${prefix} -type f -not -name \"*.kdb\" -type f -not -name \"*idx\" -not -name \"taxDB\" -not -name \"*.counts\" -delete"
+    run_cleanup = keep_intermediate ? "" : """
+    find -L ${prefix} -type f \\
+        -not -name "*.kdb" \\
+        -not -name "*idx" \\
+        -not -name "taxDB" \\
+        -not -name "*.counts" \\
+        -not -path "${prefix}/library/*" \\
+        -not -path "${prefix}/taxonomy/*" \\
+        -not -name "${custom_seqid2taxid}" \\
+        -delete
+    """
 
     """
     ${custom_db}
@@ -37,7 +47,17 @@ process KRAKENUNIQ_BUILD {
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
-    run_cleanup = keep_intermediate ? "" : "find -L ${prefix} -type f -not -name \"*.kdb\" -type f -not -name \"*idx\" -not -name \"taxDB\" -delete"
+    run_cleanup = keep_intermediate ? "" : """
+    find -L ${prefix} -type f \\
+        -not -name "*.kdb" \\
+        -not -name "*idx" \\
+        -not -name "taxDB" \\
+        -not -name "*.counts" \\
+        -not -path "${prefix}/library/*" \\
+        -not -path "${prefix}/taxonomy/*" \\
+        -not -name "${custom_seqid2taxid}" \\
+        -delete
+    """
     """
     mkdir ${prefix}/
     touch ${prefix}/database-build.log

From 861fea8e189b5c6b0afd6fbe8216fe35413c6eed Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 12 May 2026 09:42:26 +0200
Subject: [PATCH 2/8] Update krakenuniq build test and main

---
 modules/nf-core/krakenuniq/build/main.nf      | 11 +--
 .../krakenuniq/build/tests/main.nf.test       | 84 +++++++++----------
 2 files changed, 45 insertions(+), 50 deletions(-)

diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index a73f366ea686..244fab0eaca7 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -21,17 +21,15 @@ process KRAKENUNIQ_BUILD {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    custom_db = custom_library_dir ? "mkdir ${prefix} && mv library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
+    custom_db = custom_library_dir ? "mkdir ${prefix} && cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
     run_cleanup = keep_intermediate ? "" : """
     find -L ${prefix} -type f \\
         -not -name "*.kdb" \\
         -not -name "*idx" \\
         -not -name "taxDB" \\
         -not -name "*.counts" \\
-        -not -path "${prefix}/library/*" \\
-        -not -path "${prefix}/taxonomy/*" \\
-        -not -name "${custom_seqid2taxid}" \\
-        -delete
+        -delete && \\
+    find -type d -empty -delete
     """
 
     """
@@ -53,9 +51,6 @@ process KRAKENUNIQ_BUILD {
         -not -name "*idx" \\
         -not -name "taxDB" \\
         -not -name "*.counts" \\
-        -not -path "${prefix}/library/*" \\
-        -not -path "${prefix}/taxonomy/*" \\
-        -not -name "${custom_seqid2taxid}" \\
         -delete
     """
     """
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test
index da55baf00ac4..9792e38ccfcc 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test
@@ -12,12 +12,12 @@ nextflow_process {
     tag "krakenuniq/download"
 
     setup {
-        run("KRAKENUNIQ_DOWNLOAD"){
+        run("KRAKENUNIQ_DOWNLOAD") {
             script "../../download/main.nf"
             process {
-            """
-            input[0] = 'taxonomy'
-            """
+                """
+                input[0] = 'taxonomy'
+                """
             }
         }
     }
@@ -31,13 +31,9 @@ nextflow_process {
                 ch_seqid2mapid = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/seqid2taxid.map', checkIfExists: true)
 
                 ch_input = ch_fastas
-                            .combine(KRAKENUNIQ_DOWNLOAD.out.output)
-                            .combine(ch_seqid2mapid)
-                            .map {
-                                fna, tax, map ->
-
-                                [ [id:'test'] , fna, tax, map ]
-                            }
+                    .combine(KRAKENUNIQ_DOWNLOAD.out.output.map{ dir -> [ dir.listFiles().toList() ] })
+                    .combine(ch_seqid2mapid)
+                    .map { fna, tax, map -> [ [id:'test'], fna, tax, map ] }
 
                 input[0] = ch_input
                 input[1] = false
@@ -46,24 +42,28 @@ nextflow_process {
         }
 
         then {
-            def stablefiles = []
-            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
-            def unstablefiles = []
-            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
+            def unstableNames = ["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def stableFiles   = []
+            def unstableFiles = []
+
+            file(process.out.db.get(0).get(1)).eachFileRecurse { f ->
+                if (f.isDirectory()) return
+                if (unstableNames.any { f.name.endsWith(it) }) unstableFiles << f.name
+                else stableFiles << f
+            }
+
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                        stablefiles.sort(),
-                        unstablefiles.sort(),
-                        process.out.findAll { key, val -> key.startsWith('versions') }
-                    ).match()
-                }
+                    stableFiles.sort(),
+                    unstableFiles.sort(),
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
-
     }
 
-test("sarscov2 - fasta - nocleanup") {
+    test("sarscov2 - fasta - nocleanup") {
 
         when {
             process {
@@ -72,13 +72,9 @@ test("sarscov2 - fasta - nocleanup") {
                 ch_seqid2mapid = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/seqid2taxid.map', checkIfExists: true)
 
                 ch_input = ch_fastas
-                            .combine(KRAKENUNIQ_DOWNLOAD.out.output)
-                            .combine(ch_seqid2mapid)
-                            .map {
-                                fna, tax, map ->
-
-                                [ [id:'test'] , fna, tax, map ]
-                            }
+                    .combine(KRAKENUNIQ_DOWNLOAD.out.output.map{ dir -> [ dir.listFiles().toList() ] })
+                    .combine(ch_seqid2mapid)
+                    .map { fna, tax, map -> [ [id:'test'], fna, tax, map ] }
 
                 input[0] = ch_input
                 input[1] = true
@@ -87,21 +83,25 @@ test("sarscov2 - fasta - nocleanup") {
         }
 
         then {
-            def stablefiles = []
-            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
-            def unstablefiles = []
-            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
+            def unstableNames = ["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def stableFiles   = []
+            def unstableFiles = []
+
+            file(process.out.db.get(0).get(1)).eachFileRecurse { f ->
+                if (f.isDirectory()) return
+                if (unstableNames.any { f.name.endsWith(it) }) unstableFiles << f.name
+                else stableFiles << f
+            }
+
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                        stablefiles.sort(),
-                        unstablefiles.sort(),
-                        process.out.findAll { key, val -> key.startsWith('versions') }
-                    ).match()
-                }
+                    stableFiles.sort(),
+                    unstableFiles.sort(),
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
-
     }
 
     test("sarscov2 - fasta - stub") {
@@ -110,7 +110,7 @@ test("sarscov2 - fasta - nocleanup") {
         when {
             process {
                 """
-                input[0] = [[id:'test'], [] , [] , []]
+                input[0] = [[id:'test'], [], [], []]
                 input[1] = false
                 """
             }
@@ -120,7 +120,7 @@ test("sarscov2 - fasta - nocleanup") {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                )
+            )
         }
     }
-}
+}
\ No newline at end of file

From 362f0523c12d99e0769fc1a1c6f47386ca2de1ff Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 12 May 2026 10:32:37 +0200
Subject: [PATCH 3/8] Fix linting and remove redundant code

---
 modules/nf-core/krakenuniq/build/main.nf            | 12 +++---------
 modules/nf-core/krakenuniq/build/tests/main.nf.test |  8 +++++---
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index 244fab0eaca7..29bcdc416917 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -22,7 +22,9 @@ process KRAKENUNIQ_BUILD {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     custom_db = custom_library_dir ? "mkdir ${prefix} && cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
-    run_cleanup = keep_intermediate ? "" : """
+    run_cleanup = ""
+    run_cleanup << custom_library_dir ? "rm -r ${prefix}/{library,taxonomy,${custom_seqid2taxid}}" : ""
+    run_cleanup << keep_intermediate ? "" : """
     find -L ${prefix} -type f \\
         -not -name "*.kdb" \\
         -not -name "*idx" \\
@@ -45,14 +47,6 @@ process KRAKENUNIQ_BUILD {
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
-    run_cleanup = keep_intermediate ? "" : """
-    find -L ${prefix} -type f \\
-        -not -name "*.kdb" \\
-        -not -name "*idx" \\
-        -not -name "taxDB" \\
-        -not -name "*.counts" \\
-        -delete
-    """
     """
     mkdir ${prefix}/
     touch ${prefix}/database-build.log
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test
index 9792e38ccfcc..5cf9d4771260 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test
@@ -42,7 +42,8 @@ nextflow_process {
         }
 
         then {
-            def unstableNames = ["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def inputs = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def unstableNames = ["database-build.log", "database.report.tsv"] + inputs
             def stableFiles   = []
             def unstableFiles = []
 
@@ -83,7 +84,8 @@ nextflow_process {
         }
 
         then {
-            def unstableNames = ["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def inputs = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def unstableNames = ["database-build.log", "database.report.tsv"] + inputs
             def stableFiles   = []
             def unstableFiles = []
 
@@ -123,4 +125,4 @@ nextflow_process {
             )
         }
     }
-}
\ No newline at end of file
+}

From dbc7aa5fcc339c35157a2133e0605535ce28cd14 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 12 May 2026 10:58:24 +0200
Subject: [PATCH 4/8] Simplify

---
 modules/nf-core/krakenuniq/build/main.nf            |  8 +++-----
 modules/nf-core/krakenuniq/build/tests/main.nf.test | 10 ++++++----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index 29bcdc416917..17177cce0b73 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -21,10 +21,7 @@ process KRAKENUNIQ_BUILD {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    custom_db = custom_library_dir ? "mkdir ${prefix} && cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
-    run_cleanup = ""
-    run_cleanup << custom_library_dir ? "rm -r ${prefix}/{library,taxonomy,${custom_seqid2taxid}}" : ""
-    run_cleanup << keep_intermediate ? "" : """
+    run_cleanup = keep_intermediate ? "" : """
     find -L ${prefix} -type f \\
         -not -name "*.kdb" \\
         -not -name "*idx" \\
@@ -35,13 +32,14 @@ process KRAKENUNIQ_BUILD {
     """
 
     """
-    ${custom_db}
+    mkdir ${prefix} && cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}
 
     krakenuniq-build \\
         ${args} \\
         --threads ${task.cpus} \\
         --db ${prefix}
 
+    rm -r ${prefix}/{library,taxonomy,${custom_seqid2taxid}}
     ${run_cleanup}
     """
 
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test
index 5cf9d4771260..d8f67585e0ee 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test
@@ -43,18 +43,19 @@ nextflow_process {
 
         then {
             def inputs = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
-            def unstableNames = ["database-build.log", "database.report.tsv"] + inputs
+            def unstableOutputs = ["database-build.log", "database.report.tsv"]
             def stableFiles   = []
             def unstableFiles = []
 
             file(process.out.db.get(0).get(1)).eachFileRecurse { f ->
                 if (f.isDirectory()) return
-                if (unstableNames.any { f.name.endsWith(it) }) unstableFiles << f.name
+                if (unstableOutputs.any { f.name.endsWith(it) }) unstableFiles << f.name
                 else stableFiles << f
             }
 
             assertAll(
                 { assert process.success },
+                { assert file(process.out.db.get(0).get(1)).eachFileRecurse { f -> f.name !in inputs } },
                 { assert snapshot(
                     stableFiles.sort(),
                     unstableFiles.sort(),
@@ -85,18 +86,19 @@ nextflow_process {
 
         then {
             def inputs = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
-            def unstableNames = ["database-build.log", "database.report.tsv"] + inputs
+            def unstableOutputs = ["database-build.log", "database.report.tsv"]
             def stableFiles   = []
             def unstableFiles = []
 
             file(process.out.db.get(0).get(1)).eachFileRecurse { f ->
                 if (f.isDirectory()) return
-                if (unstableNames.any { f.name.endsWith(it) }) unstableFiles << f.name
+                if (unstableOutputs.any { f.name.endsWith(it) }) unstableFiles << f.name
                 else stableFiles << f
             }
 
             assertAll(
                 { assert process.success },
+                { assert file(process.out.db.get(0).get(1)).eachFileRecurse { f -> f.name !in inputs } },
                 { assert snapshot(
                     stableFiles.sort(),
                     unstableFiles.sort(),

From 2546c554c7d48c2a02bddccac2cfb090307c6477 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 12 May 2026 11:29:04 +0200
Subject: [PATCH 5/8] Update tested files and snapshot

---
 .../krakenuniq/build/tests/main.nf.test       | 36 +++++++++----------
 .../krakenuniq/build/tests/main.nf.test.snap  | 32 ++++-------------
 2 files changed, 25 insertions(+), 43 deletions(-)

diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test
index d8f67585e0ee..23f07a1bfd52 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test
@@ -42,20 +42,20 @@ nextflow_process {
         }
 
         then {
-            def inputs = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def inputs          = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
             def unstableOutputs = ["database-build.log", "database.report.tsv"]
-            def stableFiles   = []
-            def unstableFiles = []
 
-            file(process.out.db.get(0).get(1)).eachFileRecurse { f ->
-                if (f.isDirectory()) return
-                if (unstableOutputs.any { f.name.endsWith(it) }) unstableFiles << f.name
-                else stableFiles << f
-            }
+            def dbDir    = file(process.out.db.get(0).get(1))
+            def allFiles = []
+            dbDir.eachFileRecurse { f -> if (!f.isDirectory()) allFiles << f }
+
+            def stableFiles   = allFiles.findAll { f -> !unstableOutputs.any { f.name.endsWith(it) } }
+            def unstableFiles = allFiles.findAll { f ->  unstableOutputs.any { f.name.endsWith(it) } }
+                                        .collect { it.name }
 
             assertAll(
                 { assert process.success },
-                { assert file(process.out.db.get(0).get(1)).eachFileRecurse { f -> f.name !in inputs } },
+                { assert !allFiles.any { it.name in inputs } },
                 { assert snapshot(
                     stableFiles.sort(),
                     unstableFiles.sort(),
@@ -85,20 +85,20 @@ nextflow_process {
         }
 
         then {
-            def inputs = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
+            def inputs          = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
             def unstableOutputs = ["database-build.log", "database.report.tsv"]
-            def stableFiles   = []
-            def unstableFiles = []
 
-            file(process.out.db.get(0).get(1)).eachFileRecurse { f ->
-                if (f.isDirectory()) return
-                if (unstableOutputs.any { f.name.endsWith(it) }) unstableFiles << f.name
-                else stableFiles << f
-            }
+            def dbDir    = file(process.out.db.get(0).get(1))
+            def allFiles = []
+            dbDir.eachFileRecurse { f -> if (!f.isDirectory()) allFiles << f }
+
+            def stableFiles   = allFiles.findAll { f -> !unstableOutputs.any { f.name.endsWith(it) } }
+            def unstableFiles = allFiles.findAll { f ->  unstableOutputs.any { f.name.endsWith(it) } }
+                                        .collect { it.name }
 
             assertAll(
                 { assert process.success },
-                { assert file(process.out.db.get(0).get(1)).eachFileRecurse { f -> f.name !in inputs } },
+                { assert !allFiles.any { it.name in inputs } },
                 { assert snapshot(
                     stableFiles.sort(),
                     unstableFiles.sort(),
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
index cf902f8a687b..bc2b61223639 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
@@ -66,29 +66,11 @@
                 "database.kraken.tsv:md5,be9bd0cb3a8bea30989e65aa42a73727",
                 "database0.kdb:md5,46542be19979e867075f9e455a314e00",
                 "library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717",
-                "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                "seqid2taxid.map:md5,fe738f2333d57dde0db32239c04a93b8",
-                "taxDB:md5,2a6c6234f8f4edba2b94ec75ea9f1b4c",
-                "citations.dmp:md5,7b2e5d0fbea3da110c4a0e3bb7c3720d",
-                "division.dmp:md5,f93fc4c838fdaa4b8923f003e8c11712",
-                "gc.prt:md5,accfbf13bca0899e7ba9849195af241a",
-                "gencode.dmp:md5,a5f39fc7a6608775d4c62a96cf1d170c",
-                "images.dmp:md5,3855c67cfa06ef8ae713cab73f009e3d",
-                "merged.dmp:md5,5e78eb1c4a235889458ef9f83a64e81e",
-                "readme.txt:md5,051060a90b7b89ad8e0fa33fe280211c"
+                "taxDB:md5,5568e58a8acde137a258ce0b29ffa098"
             ],
             [
                 "database-build.log",
-                "database-build.log",
-                "database.report.tsv",
-                "delnodes.dmp",
-                "names.dmp",
-                "names.dmp",
-                "nodes.dmp",
-                "nodes.dmp",
-                "taxdump.tar.gz",
-                "taxdump.tar.gz",
-                "timestamp"
+                "database.report.tsv"
             ],
             {
                 "versions_krakenuniq": [
@@ -100,10 +82,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-25T13:34:38.850675715",
+        "timestamp": "2026-05-12T11:03:20.471692",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.0"
         }
     },
     "sarscov2 - fasta": {
@@ -113,7 +95,7 @@
                 "database.kdb:md5,46542be19979e867075f9e455a314e00",
                 "database.kdb.counts:md5,a82149480a435210ec1e870f06b6cdb3",
                 "database0.kdb:md5,46542be19979e867075f9e455a314e00",
-                "taxDB:md5,2a6c6234f8f4edba2b94ec75ea9f1b4c"
+                "taxDB:md5,5568e58a8acde137a258ce0b29ffa098"
             ],
             [
                 
@@ -128,10 +110,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-25T13:33:43.689590026",
+        "timestamp": "2026-05-12T11:01:33.50659",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file

From 24ab22f774ad3a9568b61e71572c47fd346298f2 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 12 May 2026 13:58:02 +0200
Subject: [PATCH 6/8] Add def to run_cleanup

---
 modules/nf-core/krakenuniq/build/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index 17177cce0b73..299f560930af 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -21,7 +21,7 @@ process KRAKENUNIQ_BUILD {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    run_cleanup = keep_intermediate ? "" : """
+    def run_cleanup = keep_intermediate ? "" : """
     find -L ${prefix} -type f \\
         -not -name "*.kdb" \\
         -not -name "*idx" \\

From 071215e0db3b0cd2b3cf5ced20964383d84d09c4 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 13 May 2026 11:00:30 +0200
Subject: [PATCH 7/8] Remove deference in copy

---
 modules/nf-core/krakenuniq/build/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index 299f560930af..6f1c8665904a 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -32,7 +32,7 @@ process KRAKENUNIQ_BUILD {
     """
 
     """
-    mkdir ${prefix} && cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}
+    mkdir ${prefix} && cp -r library taxonomy ${custom_seqid2taxid} ${prefix}
 
     krakenuniq-build \\
         ${args} \\

From cbee74513c42404949313d21b7956e4c780e0c2f Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 13 May 2026 15:52:17 +0200
Subject: [PATCH 8/8] Update test and snapshot

---
 .../nf-core/krakenuniq/build/tests/main.nf.test   | 12 ++++++++++--
 .../krakenuniq/build/tests/main.nf.test.snap      | 15 +++++++--------
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test
index 23f07a1bfd52..45451c30d725 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test
@@ -43,7 +43,11 @@ nextflow_process {
 
         then {
             def inputs          = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
-            def unstableOutputs = ["database-build.log", "database.report.tsv"]
+            def unstableOutputs = [
+                "database-build.log",  // Every line has a timestamp
+                "database.report.tsv", // Timestamp and test filepath on first line
+                "taxDB"                // Present species and species labels change: Probably because of KRAKENUNIQ_DOWNLOAD which fetches from NCBI.
+            ]
 
             def dbDir    = file(process.out.db.get(0).get(1))
             def allFiles = []
@@ -86,7 +90,11 @@ nextflow_process {
 
         then {
             def inputs          = ["timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"]
-            def unstableOutputs = ["database-build.log", "database.report.tsv"]
+            def unstableOutputs = [
+                "database-build.log",  // Every line has a timestamp
+                "database.report.tsv", // Timestamp and test filepath on first line
+                "taxDB"                // Present species and species labels change: Probably because of KRAKENUNIQ_DOWNLOAD which fetches from NCBI.
+            ]
 
             def dbDir    = file(process.out.db.get(0).get(1))
             def allFiles = []
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
index bc2b61223639..9310d953cb03 100644
--- a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
@@ -65,12 +65,12 @@
                 "database.kdb.counts:md5,a82149480a435210ec1e870f06b6cdb3",
                 "database.kraken.tsv:md5,be9bd0cb3a8bea30989e65aa42a73727",
                 "database0.kdb:md5,46542be19979e867075f9e455a314e00",
-                "library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717",
-                "taxDB:md5,5568e58a8acde137a258ce0b29ffa098"
+                "library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717"
             ],
             [
                 "database-build.log",
-                "database.report.tsv"
+                "database.report.tsv",
+                "taxDB"
             ],
             {
                 "versions_krakenuniq": [
@@ -82,7 +82,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T11:03:20.471692",
+        "timestamp": "2026-05-13T14:59:07.323282",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -94,11 +94,10 @@
                 "database.idx:md5,f5298aa4215c956d2f737b5988721a24",
                 "database.kdb:md5,46542be19979e867075f9e455a314e00",
                 "database.kdb.counts:md5,a82149480a435210ec1e870f06b6cdb3",
-                "database0.kdb:md5,46542be19979e867075f9e455a314e00",
-                "taxDB:md5,5568e58a8acde137a258ce0b29ffa098"
+                "database0.kdb:md5,46542be19979e867075f9e455a314e00"
             ],
             [
-                
+                "taxDB"
             ],
             {
                 "versions_krakenuniq": [
@@ -110,7 +109,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T11:01:33.50659",
+        "timestamp": "2026-05-13T14:57:23.476447",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"