Release v3.0.2 "Tokoroten shiki"

.nf-core.yml

@@ -11,4 +11,4 @@ template:
   name: pairgenomealign
   org: nf-core
   outdir: .
-  version: 3.0.1
+  version: 3.0.2

CHANGELOG.md

@@ -3,6 +3,24 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v3.0.2](https://github.com/nf-core/pairgenomealign/releases/tag/3.0.2) "Tokoroten shiki" - [July 16th 2026]
+
+### `Fixed`
+
+- Restore maximum tandem repeat unit length to 400 for genome masking, to prevent running out of memory on centromeric repeats. LASTs default changed to 100 in version 1638, causing a regression in this pipeline's v3.0.0 release ([#139](https://github.com/nf-core/pairgenomealign/issues/139))
+- Restore missing `fasta` in the _target_ genome name indexed for CRAM files ([#140](https://github.com/nf-core/pairgenomealign/pull/140)).
+- Avoid collisions by adding `.cuts` to the name of the file defining the regions of more than 10 `N`s in the _target_ genome. ([#138](https://github.com/nf-core/pairgenomealign/pull/138)).
+- Fix blasttab+ export option by correcting Nextflow schema. Thanks, `@sapunyangkut` ([#141](https://github.com/nf-core/pairgenomealign/pull/141)).
+- Fix blasttab+ format by upgrading LAST to version 1652 (no other changes). For consistency, Samtools and Bcftools were also upgraded (no visible changes expected).
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `LAST`     | 1651        | 1652        |
+| `BCFTOOLS` | 1.23.1      | 1.24        |
+| `SAMTOOLS` | 1.23.1      | 1.24        |
+
 ## [v3.0.1](https://github.com/nf-core/pairgenomealign/releases/tag/3.0.1) "Tokoroten" - [June 29th 2026]
 
 ### `Fixed`

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/3.0.1" target="_blank">nf-core/pairgenomealign</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/3.0.1/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/3.0.2" target="_blank">nf-core/pairgenomealign</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/3.0.2/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":
     order: -1000

conf/modules.config

@@ -34,8 +34,9 @@ process {
         // -R01: uppercase all sequences and then lowercase simple repeats with tantan
         // -R10: keep original lowercase masking
         // -c: soft-mask lowercase letters
+        // -U: Maximum length of the repeating unit, for tandem repeats found by tantan.
         // -S2: index both strands, -S1: index the forward strand only.
-        ext.args = { "${params.softmask=="tantan" ? '-R01' : '-R11'} -c -u${params.seed} ${params.strand=="both" ? '-S2' : '-S1'}" }
+        ext.args = { "${params.softmask=="tantan" ? '-R01' : '-R11'} -c -U400 -u${params.seed} ${params.strand=="both" ? '-S2' : '-S1'}" }
         publishDir = [
             enabled: false
         ]

docs/usage.md

@@ -57,6 +57,7 @@ The parameters are described in details in the [online documentation](https://nf
 [LAST cookbook]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-cookbook.rst
 [LAST tuning]: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-tuning.rst
 
+- Tandem repeat masking before _target_ genome indexing searches for repeat units as long as 400 nt (`lastdb -U400`), for efficient memory usage when aligning centromeric repeats.
 - The pipeline uses `lastal --split` by default unless `--m2m` is enabled. With `--split`, LAST directly computes a _many‑to‑one_ (m2o) alignment during alignment, rather than generating a full _many‑to‑many_ (m2m) alignment first, which significantly reduces disk usage and post‑processing overhead. In LAST, the progression m2m → m2o → o2o corresponds to the classical notion of chaining, but is formulated as a single global optimisation problem rather than a post‑hoc chaining step. See the [`last-split` documentation](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-split.rst)
 - The `last-train` commands runs with `--revsym --gapsym --matsym` as the DNA strands play equivalent roles in the studied genomes.
 

modules.json

@@ -12,43 +12,43 @@
                     },
                     "htslib/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "22edd7ce9462025093b25e3b55006f7720ff0d8e",
+                        "git_sha": "37f69c8ca3eb3d038a5d44f33a329e49f44bd4f2",
                         "installed_by": ["fasta_bgzip_index_dict_samtools"],
                         "patch": "modules/nf-core/htslib/bgziptabix/htslib-bgziptabix.diff"
                     },
                     "last/dotplot": {
                         "branch": "master",
-                        "git_sha": "e972519eb46cf42c31587bdfb663026e915d76b2",
+                        "git_sha": "a37e7925c5dbd382ddd23a1b3b7d6326449b1aa2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/last/dotplot/last-dotplot.diff"
                     },
                     "last/lastal": {
                         "branch": "master",
-                        "git_sha": "204a4fbb6b1087a3fd3dc9367740e8e19a869b55",
+                        "git_sha": "a37e7925c5dbd382ddd23a1b3b7d6326449b1aa2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/last/lastal/last-lastal.diff"
                     },
                     "last/lastdb": {
                         "branch": "master",
-                        "git_sha": "e972519eb46cf42c31587bdfb663026e915d76b2",
+                        "git_sha": "a37e7925c5dbd382ddd23a1b3b7d6326449b1aa2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/last/lastdb/last-lastdb.diff"
                     },
                     "last/mafconvert": {
                         "branch": "master",
-                        "git_sha": "9d3f43456cee409e1f70ccef8661b245fdda5069",
+                        "git_sha": "a37e7925c5dbd382ddd23a1b3b7d6326449b1aa2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/last/mafconvert/last-mafconvert.diff"
                     },
                     "last/split": {
                         "branch": "master",
-                        "git_sha": "204a4fbb6b1087a3fd3dc9367740e8e19a869b55",
+                        "git_sha": "a37e7925c5dbd382ddd23a1b3b7d6326449b1aa2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/last/split/last-split.diff"
                     },
                     "last/train": {
                         "branch": "master",
-                        "git_sha": "e972519eb46cf42c31587bdfb663026e915d76b2",
+                        "git_sha": "a37e7925c5dbd382ddd23a1b3b7d6326449b1aa2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/last/train/last-train.diff"
                     },
@@ -59,19 +59,19 @@
                     },
                     "samtools/dict": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["fasta_bgzip_index_dict_samtools", "modules"],
                         "patch": "modules/nf-core/samtools/dict/samtools-dict.diff"
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["fasta_bgzip_index_dict_samtools", "modules"],
                         "patch": "modules/nf-core/samtools/faidx/samtools-faidx.diff"
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/merge/samtools-merge.diff"
                     },