From beed6d0260b764cd7bd02df0ae3ec49d229bee2e Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 30 Jun 2026 11:47:30 +0200
Subject: [PATCH 1/9] Use `--skip_preseq` by default

---
 CHANGELOG.md         | 2 +-
 README.md            | 4 +++-
 nextflow.config      | 2 +-
 nextflow_schema.json | 3 ++-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 482859ca..24042182 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,7 +18,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#484](https://github.com/nf-core/chipseq/issues/484)] - Bulk, updated of modules and subworkflows.
 - [[#489](https://github.com/nf-core/chipseq/issues/489)] - Replace deprecated `CUSTOM_GETCHROMSIZES` with `SAMTOOLS_FAIDX`.
 - [[PR #493](https://github.com/nf-core/chipseq/pull/493)] - Follow up to #487.
-- [[PR #493](https://github.com/nf-core/chipseq/pull/493)] - Follow up to #487.
 - [[#492](https://github.com/nf-core/chipseq/issues/492), [#417](https://github.com/nf-core/chipseq/issues/417)] - Refactor local modules to nf-core standard.
 - [[#416](https://github.com/nf-core/chipseq/issues/416)] - Moved the `KHMER_UNIQUEKMERS` logic to prepare_genome
 - [[#440](https://github.com/nf-core/chipseq/issues/440), [#510](https://github.com/nf-core/chipseq/issues/510)] - Fix
@@ -30,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #514](https://github.com/nf-core/chipseq/pull/514)] - Updated pipeline template to [nf-core/tools
   4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2).
 - [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.`.
+- [[#456] (https://github.com/nf-core/chipseq/issues/456)] - - Use `--skip_preseq` by default.
 
 ### Parameters
 
diff --git a/README.md b/README.md
index 2dbd4f4b..f6ced720 100644
--- a/README.md
+++ b/README.md
@@ -58,7 +58,9 @@ You can find numerous talks on the [nf-core events page](https://nf-co.re/events
       - reads that map to different chromosomes ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
       - reads that arent in FR orientation ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
       - reads where only one read of the pair fails the above criteria ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
-   3. Alignment-level QC and estimation of library complexity ([`picard`](https://broadinstitute.github.io/picard/), [`Preseq`](http://smithlabresearch.org/software/preseq/))
+   3. Alignment-level QC and estimation of library complexity:
+      -  [`picard`](https://broadinstitute.github.io/picard/) 
+      - [`Preseq`](http://smithlabresearch.org/software/preseq/) (skipped by default)
    4. Create normalised bigWig files scaled to 1 million mapped reads ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
    5. Generate gene-body meta-profile from bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))
    6. Calculate genome-wide IP enrichment relative to control ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))
diff --git a/nextflow.config b/nextflow.config
index 3a8c7c57..4827658a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -57,7 +57,7 @@ params {
     skip_qc                    = false
     skip_fastqc                = false
     skip_picard_metrics        = false
-    skip_preseq                = false
+    skip_preseq                = true
     skip_plot_profile          = false
     skip_plot_fingerprint      = false
     skip_spp                   = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index fc6f5201..bdf0c769 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -359,7 +359,8 @@
                 "skip_preseq": {
                     "type": "boolean",
                     "description": "Skip Preseq.",
-                    "fa_icon": "fas fa-fast-forward"
+                    "fa_icon": "fas fa-fast-forward",
+                    "default": false
                 },
                 "deseq2_vst": {
                     "type": "boolean",

From 310e319e222b4cb3a05fec5011f77705b1778aaa Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 30 Jun 2026 14:40:45 +0200
Subject: [PATCH 2/9] Fix tyop

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 24042182..0a8c20d9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #514](https://github.com/nf-core/chipseq/pull/514)] - Updated pipeline template to [nf-core/tools
   4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2).
 - [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.`.
-- [[#456] (https://github.com/nf-core/chipseq/issues/456)] - - Use `--skip_preseq` by default.
+- [[#456] (https://github.com/nf-core/chipseq/issues/456)] - Use `--skip_preseq` by default.
 
 ### Parameters
 

From a39bf983744232ed9f81b0eecebd14bb2152b530 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 30 Jun 2026 14:50:05 +0200
Subject: [PATCH 3/9] Make lint happy

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

diff --git a/README.md b/README.md
index f6ced720..4397505f 100644
--- a/README.md
+++ b/README.md
@@ -59,7 +59,7 @@ You can find numerous talks on the [nf-core events page](https://nf-co.re/events
       - reads that arent in FR orientation ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
       - reads where only one read of the pair fails the above criteria ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
    3. Alignment-level QC and estimation of library complexity:
-      -  [`picard`](https://broadinstitute.github.io/picard/) 
+      - [`picard`](https://broadinstitute.github.io/picard/)
       - [`Preseq`](http://smithlabresearch.org/software/preseq/) (skipped by default)
    4. Create normalised bigWig files scaled to 1 million mapped reads ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
    5. Generate gene-body meta-profile from bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))

From 6470f12a1cdfc2f847ce939bac44ab352f120216 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 30 Jun 2026 15:06:05 +0200
Subject: [PATCH 4/9] Set skip_preseq to true in schema

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index bdf0c769..6a2e40c4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -360,7 +360,7 @@
                     "type": "boolean",
                     "description": "Skip Preseq.",
                     "fa_icon": "fas fa-fast-forward",
-                    "default": false
+                    "default": true
                 },
                 "deseq2_vst": {
                     "type": "boolean",

From 7980ff61f21216d84a0af932008ddea212de635a Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Thu, 23 Jul 2026 11:33:41 +0200
Subject: [PATCH 5/9] Update khmer/uniquekmers

---
 conf/containers_conda_lock_files_amd64.config |  2 +-
 conf/containers_conda_lock_files_arm64.config |  2 +-
 modules.json                                  |  2 +-
 modules/nf-core/khmer/uniquekmers/main.nf     | 16 +---
 modules/nf-core/khmer/uniquekmers/meta.yml    | 26 +++++--
 .../khmer/uniquekmers/tests/main.nf.test      |  7 +-
 .../khmer/uniquekmers/tests/main.nf.test.snap | 75 +++++--------------
 7 files changed, 48 insertions(+), 82 deletions(-)

diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index 4e138a66..50ac10e8 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1 +1 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
+process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index ab0f3cff..594c0f93 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1 +1 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
+process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
diff --git a/modules.json b/modules.json
index 05be3347..68ef004c 100644
--- a/modules.json
+++ b/modules.json
@@ -83,7 +83,7 @@
                     },
                     "khmer/uniquekmers": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "995d1b7d65d5a841220304d088161d8bff07378a",
                         "installed_by": ["modules"]
                     },
                     "macs3/callpeak": {
diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf
index 86d55b63..fda91d40 100644
--- a/modules/nf-core/khmer/uniquekmers/main.nf
+++ b/modules/nf-core/khmer/uniquekmers/main.nf
@@ -3,9 +3,9 @@ process KHMER_UNIQUEKMERS {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' :
-        'biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
+        'quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -14,7 +14,7 @@ process KHMER_UNIQUEKMERS {
     output:
     tuple val(meta), path("*.report.txt")  , emit: report
     tuple val(meta), path("*.kmers.txt")   , emit: kmers
-    path "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('khmer'), eval('unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"'), emit: versions_khmer, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,11 +30,6 @@ process KHMER_UNIQUEKMERS {
         $fasta
 
     grep ^number ${prefix}.report.txt | sed 's/^.*:.[[:blank:]]//g' > ${prefix}.kmers.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' )
-    END_VERSIONS
     """
 
     stub:
@@ -42,10 +37,5 @@ process KHMER_UNIQUEKMERS {
     """
     touch ${prefix}.report.txt
     touch ${prefix}.kmers.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/khmer/uniquekmers/meta.yml b/modules/nf-core/khmer/uniquekmers/meta.yml
index 778d1c5c..21b4a537 100644
--- a/modules/nf-core/khmer/uniquekmers/meta.yml
+++ b/modules/nf-core/khmer/uniquekmers/meta.yml
@@ -52,13 +52,27 @@ output:
           description: Text file containing number of kmers
           pattern: "*.kmers.txt"
           ontologies: []
+  versions_khmer:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - khmer:
+          type: string
+          description: The name of the tool
+      - unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - khmer:
+          type: string
+          description: The name of the tool
+      - unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@JoseEspinosa"
 maintainers:
diff --git a/modules/nf-core/khmer/uniquekmers/tests/main.nf.test b/modules/nf-core/khmer/uniquekmers/tests/main.nf.test
index bea179b2..7c577bdf 100644
--- a/modules/nf-core/khmer/uniquekmers/tests/main.nf.test
+++ b/modules/nf-core/khmer/uniquekmers/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -47,10 +47,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/khmer/uniquekmers/tests/main.nf.test.snap b/modules/nf-core/khmer/uniquekmers/tests/main.nf.test.snap
index 96898952..957c0a6c 100644
--- a/modules/nf-core/khmer/uniquekmers/tests/main.nf.test.snap
+++ b/modules/nf-core/khmer/uniquekmers/tests/main.nf.test.snap
@@ -2,25 +2,6 @@
     "sarscov2 - fasta -- stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.kmers.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,5c1c80d104ef7daa0d017bf58024722d"
-                ],
                 "kmers": [
                     [
                         {
@@ -37,44 +18,24 @@
                         "test.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,5c1c80d104ef7daa0d017bf58024722d"
+                "versions_khmer": [
+                    [
+                        "KHMER_UNIQUEKMERS",
+                        "khmer",
+                        "3.0.0a3"
+                    ]
                 ]
-            },
-            {
-                "KHMER_UNIQUEKMERS": {
-                    "khmer": "3.0.0a3"
-                }
             }
         ],
+        "timestamp": "2026-06-04T11:57:31.740881709",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-04-24T19:41:02.690916494"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "sarscov2 - fasta": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.report.txt:md5,ee489abd3b244dea3640649e1790d55e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.kmers.txt:md5,496ebf23653a01c7a42d743e47c19f65"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,5c1c80d104ef7daa0d017bf58024722d"
-                ],
                 "kmers": [
                     [
                         {
@@ -91,15 +52,19 @@
                         "test.report.txt:md5,ee489abd3b244dea3640649e1790d55e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,5c1c80d104ef7daa0d017bf58024722d"
+                "versions_khmer": [
+                    [
+                        "KHMER_UNIQUEKMERS",
+                        "khmer",
+                        "3.0.0a3"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-06-04T11:57:25.950222943",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-04-24T19:40:56.950583876"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file

From f419ab88bd8144f48703896604254f6fbb06ad92 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Thu, 23 Jul 2026 11:45:02 +0200
Subject: [PATCH 6/9] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7c2674c3..071a59f7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#526] (https://github.com/nf-core/chipseq/issues/526)] - Bump Samtools version to 1.24.
 - [[#530] (https://github.com/nf-core/chipseq/issues/530)] - Update `hommer/annotatepeaks` to topic channels.
 - [[#531] (https://github.com/nf-core/chipseq/issues/531)] - Changed chromap decompression - untarfiles (deprecated) to untar modules.
+- [[PR #533](https://github.com/nf-core/chipseq/pull/533)] - Update `khmers/uniquekmers` to topic channels.
 
 ### Parameters
 

From 44aba47ef9dcb0e76fa90f324d9ac73e57e78e3a Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Thu, 23 Jul 2026 11:46:33 +0200
Subject: [PATCH 7/9] Clean changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 071a59f7..9b17c731 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,7 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.`.
 - [[#456] (https://github.com/nf-core/chipseq/issues/456)] - Use `--skip_preseq` by default.
 - [[#526] (https://github.com/nf-core/chipseq/issues/526)] - Bump Samtools version to 1.24.
-- [[#530] (https://github.com/nf-core/chipseq/issues/530)] - Update `hommer/annotatepeaks` to topic channels.
+- [[PR #530](https://github.com/nf-core/chipseq/pull/530)] - Update `hommer/annotatepeaks` to topic channels.
 - [[#531] (https://github.com/nf-core/chipseq/issues/531)] - Changed chromap decompression - untarfiles (deprecated) to untar modules.
 - [[PR #533](https://github.com/nf-core/chipseq/pull/533)] - Update `khmers/uniquekmers` to topic channels.
 

From c342671e5f76aba94e53d51f51832feba341fd23 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Thu, 23 Jul 2026 11:50:13 +0200
Subject: [PATCH 8/9] Make lint happy

---
 conf/containers_conda_lock_files_amd64.config | 2 +-
 conf/containers_conda_lock_files_arm64.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index 50ac10e8..4e138a66 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1 +1 @@
-process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
+process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index 594c0f93..ab0f3cff 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1 +1 @@
-process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
+process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }

From 61785193ff1cb5127ca7e25f8ef168f16990cac2 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Thu, 23 Jul 2026 15:28:05 +0200
Subject: [PATCH 9/9] Update snapshots

---
 tests/bowtie2.nf.test.snap              | 10 ++++++----
 tests/chromap.nf.test.snap              | 10 ++++++----
 tests/default.nf.test.snap              |  6 ++++--
 tests/skip_consensus_peaks.nf.test.snap | 10 ++++++----
 tests/skip_trimming.nf.test.snap        | 10 ++++++----
 tests/star.nf.test.snap                 |  7 ++++---
 6 files changed, 32 insertions(+), 21 deletions(-)

diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap
index a17f7a90..a1a164ba 100644
--- a/tests/bowtie2.nf.test.snap
+++ b/tests/bowtie2.nf.test.snap
@@ -59,6 +59,9 @@
                 "IGV": {
                     "python": "3.12.12"
                 },
+                "KHMER_UNIQUEKMERS": {
+                    "khmer": "3.0.0a3"
+                },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
                 },
@@ -949,21 +952,20 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-07-21T12:38:39.799024",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "26.04.1"
         },
-        "timestamp": "2026-07-15T22:14:42.929516361"
+        "timestamp": "2026-07-23T13:13:17.36470343"
     },
     "bowtie2 with stub": {
         "content": [
             20
         ],
-        "timestamp": "2026-07-21T12:39:15.303231",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
-        }
+        },
+        "timestamp": "2026-07-21T12:39:15.303231"
     }
 }
\ No newline at end of file
diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap
index 58148670..10ca5111 100644
--- a/tests/chromap.nf.test.snap
+++ b/tests/chromap.nf.test.snap
@@ -58,6 +58,9 @@
                 "IGV": {
                     "python": "3.12.12"
                 },
+                "KHMER_UNIQUEKMERS": {
+                    "khmer": "3.0.0a3"
+                },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
                 },
@@ -955,21 +958,20 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-07-21T12:49:50.568622",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "26.04.1"
         },
-        "timestamp": "2026-07-15T22:31:46.117520522"
+        "timestamp": "2026-07-23T13:29:13.96008322"
     },
     "chromap with stub": {
         "content": [
             20
         ],
-        "timestamp": "2026-07-21T12:50:29.057511",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
-        }
+        },
+        "timestamp": "2026-07-21T12:50:29.057511"
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index a7b16c89..d44a6d0c 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -58,6 +58,9 @@
                 "IGV": {
                     "python": "3.12.12"
                 },
+                "KHMER_UNIQUEKMERS": {
+                    "khmer": "3.0.0a3"
+                },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
                 },
@@ -948,11 +951,10 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-07-21T13:00:00.044632",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "26.04.1"
         },
-        "timestamp": "2026-07-15T22:47:34.878161789"
+        "timestamp": "2026-07-23T13:48:35.7050288"
     }
 }
\ No newline at end of file
diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap
index fd9a6ea2..eb404349 100644
--- a/tests/skip_consensus_peaks.nf.test.snap
+++ b/tests/skip_consensus_peaks.nf.test.snap
@@ -3,11 +3,11 @@
         "content": [
             20
         ],
-        "timestamp": "2026-07-21T13:10:05.459362",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
-        }
+        },
+        "timestamp": "2026-07-21T13:10:05.459362"
     },
     "skip_consensus_peaks": {
         "content": [
@@ -61,6 +61,9 @@
                 "IGV": {
                     "python": "3.12.12"
                 },
+                "KHMER_UNIQUEKMERS": {
+                    "khmer": "3.0.0a3"
+                },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
                 },
@@ -889,11 +892,10 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-07-21T13:09:28.447257",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "26.04.1"
         },
-        "timestamp": "2026-07-15T23:01:54.394780524"
+        "timestamp": "2026-07-23T14:02:02.337853806"
     }
 }
\ No newline at end of file
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index 30390f2f..d0119228 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -58,6 +58,9 @@
                 "IGV": {
                     "python": "3.12.12"
                 },
+                "KHMER_UNIQUEKMERS": {
+                    "khmer": "3.0.0a3"
+                },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
                 },
@@ -826,21 +829,20 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-07-21T13:19:06.842802",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "26.04.1"
         },
-        "timestamp": "2026-07-15T23:17:15.190122205"
+        "timestamp": "2026-07-23T14:18:19.305798532"
     },
     "skip_trimming with stub": {
         "content": [
             190
         ],
-        "timestamp": "2026-07-21T13:23:05.44245",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
-        }
+        },
+        "timestamp": "2026-07-21T13:23:05.44245"
     }
 }
\ No newline at end of file
diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap
index 73d5d019..360d870f 100644
--- a/tests/star.nf.test.snap
+++ b/tests/star.nf.test.snap
@@ -51,6 +51,9 @@
                 "IGV": {
                     "python": "3.12.12"
                 },
+                "KHMER_UNIQUEKMERS": {
+                    "khmer": "3.0.0a3"
+                },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
                 },
@@ -980,18 +983,16 @@
                 "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd"
             ]
         ],
-        "timestamp": "2026-07-21T13:32:52.982946",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "26.04.1"
         },
-        "timestamp": "2026-07-16T10:41:11.175438003"
+        "timestamp": "2026-07-23T14:46:30.377133073"
     },
     "star with stub": {
         "content": [
             20
         ],
-        "timestamp": "2026-07-21T13:33:34.284729",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"