Release v2.0.0

.editorconfig

@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/pairgenomealign pipeline documentation](https://nf-co.re/pairgenomealign/usage)
-
   - type: textarea
     id: description
     attributes:

.github/workflows/ci.yml

@@ -46,6 +46,8 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

.github/workflows/download_pipeline.yml

@@ -28,8 +28,23 @@ env:
   NXF_ANSI_LOG: false
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
   download:
     runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -52,12 +67,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
@@ -66,55 +75,59 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
           --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:

.nf-core.yml

@@ -3,7 +3,7 @@ lint:
     - assets/nf-core-pairgenomealign_logo_light.png
     - docs/images/nf-core-pairgenomealign_logo_light.png
     - docs/images/nf-core-pairgenomealign_logo_dark.png
-nf_core_version: 3.1.0
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: charles-plessy

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json

CHANGELOG.md

@@ -3,14 +3,67 @@
 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).
 
+## [v2.0.0](https://github.com/nf-core/pairgenomealign/releases/tag/2.0.0) "Naga imo" - [February 5th, 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)).
+- Conforms to nf-core template version 3.2.0 ([#40](https://github.com/nf-core/pairgenomealign/pull/40)).
+
+### `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]
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) charles-plessy
+Copyright (c) The nf-core/pairgenomealign team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -23,6 +23,13 @@
 
 ![Tubemap workflow summary](docs/images/pairgenomealign-tubemap.png "Tubemap workflow summary")
 
+The main steps of the pipeline are:
+
+1. Genome QC ([`assembly-scan`](https://github.com/rpetit3/assembly-scan)).
+2. Genome indexing ([`lastdb`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst)).
+3. Genome pairwise alignments ([`lastal`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastal.rst)).
+4. Alignment plotting ([`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst)).
+
 The pipeline can generate four kinds of outputs, called _many-to-many_, _many-to-one_, _one-to-many_ and _one-to-one_, depending on whether sequences of one genome are allowed match the other genome multiple times or not.
 
 These alignments are output in [MAF](https://genome.ucsc.edu/FAQ/FAQformat.html#format5) format, and optional line plot representations are output in PNG format.

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/1.1.1"
+  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/1.1.1/docs/output"
+  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":

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' {