Merge pull request nf-core#39 from nf-core/milestone_2.0.0

Milestone 2.0.0

CHANGELOG.md

@@ -3,16 +3,66 @@
 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).
 
-## v2.0.0dev - [unreleased]
+## [v2.0.0](https://github.com/nf-core/pairgenomealign/releases/tag/2.0.0) "Naga imo" - [January 31st, 2025]
+
+### `Breaking changes`
+
+- The LAST software was updated and it has new defaults for some of its
+  parameters. The alignments ran with this pipeline will not be identical to
+  the ones from older versions.
+
+### `Added`
+
+- The `alignment/lastdb` directory is not output anymore. It consumed space,
+  is not usually needed for downstream analysis, and can be re-computed
+  identically if needed.
+- The _many-to-one_ alignment file is not output anymore by default, to save
+  space. To keep this file, you can run the pipeline in `many-to-many` mode
+  with the `--m2m` parameter.
+- The `--seed` parameter allows for all the existing values in the `lastdb`
+  program.
+- Errors caused by absence of alignments at training or plotting steps
+  are now ignored.
+- New parameter `--export_aln_to` that creates additional files containing
+  the alignments in a different format such as Axt, Chain, GFF or SAM.
+
+### `Fixed`
+
+- Incorrect detection of regions with 10 or more `N`s was corrected ([#18](https://github.com/nf-core/pairgenomealign/issues/18)).
+- The `--lastal_params` now works as intended instead of being ignored ([#22](https://github.com/nf-core/pairgenomealign/issues/22)).
+- The _workflow summary_ is now properly sorted at the end of the MultiQC report ([#32](https://github.com/nf-core/pairgenomealign/issues/32)).
+
+### `Parameters`
+
+| Old parameter | New parameter     |
+| ------------- | ----------------- |
+|               | `--export_aln_to` |
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `LAST`     | 1542        | 1608        |
+| `MultiQC`  | 1.25.1      | 1.27        |
 
 ## [v1.1.1](https://github.com/nf-core/pairgenomealign/releases/tag/1.1.1) "Kani nabe" - [December 17th, 2024]
 
-This release brings the pipeline to the standards of Nextflow 24.10.1 and
-nf-core 3.1.0. No changes were made to the alignment process.
+### `Fixed`
+
+- This release brings the pipeline to the standards of Nextflow 24.10.1 and
+  nf-core 3.1.0.
 
 ## [v1.1.0](https://github.com/nf-core/pairgenomealign/releases/tag/1.1.0) "Nattou maki" - [September 27th, 2024]
 
-Added a new `softmask` parameter, to optionally keep original softmasking.
+### `Added`
+
+- Added a new `softmask` parameter, to optionally keep original softmasking.
+
+### `Parameters`
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+|               | `--softmask`  |
 
 ## [v1.0.0](https://github.com/nf-core/pairgenomealign/releases/tag/1.0.0) "Sweet potato" - [August 27th, 2024]
 

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/tree/dev" 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/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/2.0.0"
+  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/2.0.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":
     order: -1000

conf/modules.config

@@ -19,11 +19,11 @@ process {
     ]
 
     withName: CUTN_TARGET {
-        ext.args = { "-n 10" }
+        ext.args = { "-n 10 -p 100000" }
     }
 
     withName: CUTN_QUERY {
-        ext.args = { "-n 10" }
+        ext.args = { "-n 10 -p 100000" }
     }
 
     withName: 'ALIGNMENT_LASTDB' {
@@ -33,18 +33,16 @@ process {
         // -c: soft-mask lowercase letters
         // -S2: index both strands
         ext.args = { "${params.softmask=="tantan" ? '-R01' : '-R11'} -c -u${params.seed} -S2" }
+        publishDir = [
+            enabled: false
+        ]
     }
 
     withName: 'ALIGNMENT_SPLIT_O2M' {
         ext.prefix = { "${meta.id}.o2m_aln" }
         ext.args = { "--reverse -m${params.last_split_mismap}" }
     }
 
-    withName: 'ALIGNMENT_DOTPLOT_O2M' {
-        ext.prefix = { "${meta.id}.o2m_plt" }
-        ext.args = { "--rot2=h --sort2=3 --strands2=1 ${params.dotplot_options}" }
-    }
-
     withName: 'ALIGNMENT_SPLIT_M2O' {
         ext.prefix = { "${meta.id}.m2o_aln" }
         ext.args = { "-m${params.last_split_mismap}" }
@@ -56,32 +54,46 @@ process {
     }
 
     withName: 'ALIGNMENT_TRAIN' {
+        // If the training step fails, it is likely that there are no
+        // alignments to be found with the selected seed. Ignore and therefore
+        // skip alignments instead of crashing the pipeline.
+        errorStrategy = { task.exitStatus in (130..145) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
         ext.args = { "--revsym ${params.lastal_args}" }
     }
 
     withName: 'ALIGNMENT_LASTAL_M2O' {
         ext.prefix = { "${meta.id}.m2o_aln" }
         ext.args = { "--split-f=MAF+ ${params.lastal_args} ${params.lastal_extr_args}" }
+        publishDir = [
+            enabled: false
+        ]
     }
 
     withName: 'ALIGNMENT_LASTAL_M2M' {
         ext.prefix = { "${meta.id}.m2m_aln" }
         ext.args = { "${params.lastal_args} ${params.lastal_extr_args}" }
     }
 
+    withName: 'LAST_DOTPLOT' {
+        // The number one cause of failure is absence of alignments.
+        errorStrategy = { task.exitStatus in (130..145) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
+        ext.args = { "--rot2=h --sort2=3 --strands2=1 ${params.dotplot_options}" }
+    }
+
     withName: 'ALIGNMENT_DOTPLOT_O2O' {
         ext.prefix = { "${meta.id}.o2o_plt" }
-        ext.args = { "--rot2=h --sort2=3 --strands2=1 ${params.dotplot_options}" }
     }
 
     withName: 'ALIGNMENT_DOTPLOT_M2O' {
         ext.prefix = { "${meta.id}.m2o_plt" }
-        ext.args = { "--rot2=h --sort2=3 --strands2=1 ${params.dotplot_options}" }
+    }
+
+    withName: 'ALIGNMENT_DOTPLOT_O2M' {
+        ext.prefix = { "${meta.id}.o2m_plt" }
     }
 
     withName: 'ALIGNMENT_DOTPLOT_M2M' {
         ext.prefix = { "${meta.id}.m2m_plt" }
-        ext.args = { "--rot2=h --sort2=3 --strands2=1 ${params.dotplot_options}" }
     }
 
     withName: 'MULTIQC' {