From 187966e629ef3100960064773b0cc692a5b65830 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 26 Aug 2026 09:03:14 +0100
Subject: [PATCH 1/4] Fix single alingment of genomes

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

diff --git a/main.nf b/main.nf
index baab5f2..107f8f4 100644
--- a/main.nf
+++ b/main.nf
@@ -114,8 +114,8 @@ no_maf          : $params.no_maf"""
         }
 
         DATA()
-        ch_source = DATA.out.ch_source
-        ch_target = DATA.out.ch_target
+        ch_source = DATA.out.ch_source | collect
+        ch_target = DATA.out.ch_target | collect
 
         // Preprocess the data
         preproc_ch = PREPROC( ch_source, ch_target )

From 90a6a0e15fa29567c1c9c3dc5131b4cdfd178673 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 26 Aug 2026 09:03:24 +0100
Subject: [PATCH 2/4] Update documentation

---
 README.md          | 2 +-
 docs/alignments.md | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 1b64478..53d5a7d 100644
--- a/README.md
+++ b/README.md
@@ -91,7 +91,7 @@ The source and target genomes can be specified as local or remote (un)compressed
 ### Download from NCBI
 *nf-LO* can download fasta files from ncbi directly using the [datasets API](https://www.ncbi.nlm.nih.gov/datasets/). Users provide a GCA/GCF code in the `--source`/`--target` field, and add the `--ncbi_source` and `--ncbi_target` flags as follow:
 ```
-nextflow run evotools/nf-LO --source "GCF_001549955.1" --target "GCF_011751205.1" --ncbi_source --ncbi_target  -profile conda 
+nextflow run evotools/nf-LO --source "GCF_001549955.1" --target "GCF_011751205.1" --ncbi_source --ncbi_target -profile conda 
 ```
 ### Download from iGenomes
 *nf-LO* can also download genomes from the [iGenomes](https://emea.support.illumina.com/sequencing/sequencing_software/igenome.html) site. Users provide a GCA/GCF code in the `--source`/`--target` field, and add the `--igenomes_source` and `--igenomes_target` flags as follow:
diff --git a/docs/alignments.md b/docs/alignments.md
index 2ff5f11..3f36eb9 100644
--- a/docs/alignments.md
+++ b/docs/alignments.md
@@ -90,8 +90,10 @@ Analogously, you can define the fragmentation of the source genome using:
 You can apply your own custom parameters to an alignment simply with the `--custom` flag:
 ```
 nextflow run evotools/nf-LO \
-   --igenome_source GRCh37 \
-   --igenome_target GRCh38 \
+   --source GRCh37 \
+   --target GRCh38 \
+   --igenome_source \
+   --igenome_target \
    --custom '-cx asm5 -l 10000' \
    --aligner minimap2  
 ``` 

From edee28d3d88dac1f9a343f63e80d4c33a98910c0 Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 26 Aug 2026 09:04:09 +0100
Subject: [PATCH 3/4] Fix broken ncbi dataset pull of genomes

---
 environment.yml                    |  2 +-
 modules/processes/datasets/main.nf | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/environment.yml b/environment.yml
index 09e7cd6..ba9998e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -11,7 +11,7 @@ dependencies:
   - last=1454
   - lastz=1.04.22
   - minimap2=2.28
-  - ncbi-datasets-cli=13.32.0
+  - ncbi-datasets-cli>13
   - p7zip=16.02
   - conda-forge::r-tidyverse=1.3.1
   - conda-forge::r-markdown=1.1
diff --git a/modules/processes/datasets/main.nf b/modules/processes/datasets/main.nf
index 0e7a0ad..5a2b642 100644
--- a/modules/processes/datasets/main.nf
+++ b/modules/processes/datasets/main.nf
@@ -4,20 +4,20 @@ process dataset_genome {
     label "small"
 
     input:
-    val genome
+    val accession
     
     output:
-    path "${genome}.fasta"
+    path "${accession}.fasta"
 
     script:
     """
-    datasets download genome accession --exclude-rna --exclude-protein --exclude-protein --exclude-gff3 --exclude-genomic-cds ${genome} &&
-        7za x ncbi_dataset.zip && \
-        cat ncbi_dataset/data/${genome}/*.fna > ${genome}.fasta && rm -rf ncbi_dataset*
+    datasets download genome accession ${accession} --include genome && \\
+        7za x ncbi_dataset.zip && \\
+        cat ncbi_dataset/data/${accession}/*.fna > ${accession}.fasta && rm -rf ncbi_dataset*
     """
 
     stub:
     """
-    touch ${genome}.fasta
+    touch ${accession}.fasta
     """
 }

From 5e4a547cd172d09335f571c079914297194d1ade Mon Sep 17 00:00:00 2001
From: Andrea Talenti <23279528+RenzoTale88@users.noreply.github.com>
Date: Wed, 26 Aug 2026 09:04:16 +0100
Subject: [PATCH 4/4] C.log

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e86afc..cb3f403 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,10 @@
 # Changelog
+## [v1.8.8]
+- Fix compatibility issues with NCBI datasets >= 14
+- Update documentation for iGenomes examples
+- Fix bug running a single alignment instance per genome
+    - The bug was linked to moving from `file` to `Channel`
+
 ## [v1.8.7]
 - Fixed a broken reference to `params.annotation` by using the new `params.annotation_format` instead
 - Add options to tweak minimap2 and GSAlign memory (e.g. `--gsalign_memory 6.GB` or `--minimap2_memory 8.GB`).