Merge template 2.13

.github/workflows/awsfulltest.yml

@@ -14,10 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
+<<<<<<< HEAD
         uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
+=======
+        uses: seqeralabs/action-tower-launch@v2
+>>>>>>> dev
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/ci.yml

@@ -22,10 +22,24 @@ jobs:
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}"
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        tags:
+          - "test"
+          - "test_nopreprocessing"
+          - "test_noprofiling"
+          - "test_krakenuniq"
+          - "test_malt"
+          - "test_motus"
+          - "test_falco"
+          - "test_fastp"
+          - "test_adapterremoval"
+          - "test_bbduk"
+          - "test_prinseqplusplus"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
@@ -35,12 +49,27 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+<<<<<<< HEAD
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+=======
+      - name: Show current locale
+        run: locale
+
+      - name: Set UTF-8 enabled locale
+        run: |
+          sudo locale-gen en_US.UTF-8
+          sudo update-locale LANG=en_US.UTF-8
+>>>>>>> dev
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          if [[ "${{ matrix.tags }}" == "test_motus" ]]; then
+            wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
+            python downloadDB.py > download_db_log.txt
+            echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
+            echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
+            nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --databases ./database_motus.csv --outdir ./results_${{ matrix.tags }};
+          else
+            nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --outdir ./results_${{ matrix.tags }};
+          fi

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+tests/

CHANGELOG.md

@@ -3,10 +3,195 @@
 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).
 
+<<<<<<< HEAD
 ## v1.1.6dev - [date]
+=======
+## v1.1.6dev - [unreleased]
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
+## v1.1.5 - Augmented Akita Patch [2024-02-08]
+
+### `Added`
+
+- [#439](https://github.com/nf-core/taxprofiler/pull/439) Read deduplication with fastp (added by @maxibor)
+- [#440](https://github.com/nf-core/taxprofiler/pull/440) Include mention of pre-built kaiju databases in tutorial.md (added by @Joon-Klaps)
+- [#442](https://github.com/nf-core/taxprofiler/pull/442) Updated to nf-core pipeline template v2.12 (added by @sofstam)
+
+### `Fixed`
+
+- [#444](https://github.com/nf-core/taxprofiler/pull/444) Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133)
+
+### `Dependencies`
+
+| Tool       | Previous version | New version |
+| ---------- | ---------------- | ----------- |
+| Centrifuge | 1.0.4_beta       | 1.0.4.1     |
+
+### `Deprecated`
+
+## v1.1.4 - Augmented Akita Patch [2024-01-24]
+
+### `Added`
+
+### `Fixed`
+
+- [#431](https://github.com/nf-core/modules/pull/4781#event-11555493525) Updated kaiju2table module to report taxon names (fix by @Joon-Klaps)
+- [#430](https://github.com/nf-core/taxprofiler/pull/430) Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)
+
+### `Dependencies`
+
+| Tool  | Previous version | New version |
+| ----- | ---------------- | ----------- |
+| kaiju | 1.8.2            | 1.10.0      |
+
+### `Deprecated`
+
+## v1.1.3 - Augmented Akita Patch [2024-01-12]
+
+### `Added`
+
+- [#424](https://github.com/nf-core/taxprofiler/pull/424) Updated to nf-core pipeline template v2.11.1 (added by @LilyAnderssonLee & @sofstam)
+
+### `Fixed`
+
+- [#419](https://github.com/nf-core/taxprofiler/pull/419) Added improved syntax highlighting for tables in documentation (fix by @mashehu)
+- [#421](https://github.com/nf-core/taxprofiler/pull/421) Updated the krakenuniq/preloadedkrakenuniq module that contained a fix for saving the output reads (❤️ to @SannaAb for reporting, fix by @Midnighter)
+- [#427](https://github.com/nf-core/taxprofiler/pull/427) Fixed preprint information in the recommended methods text (fix by @jfy133)
+
+### `Dependencies`
+
+| Tool          | Previous version | New version |
+| ------------- | ---------------- | ----------- |
+| multiqc       | 1.15             | 1.19        |
+| fastqc        | 11.9             | 12.1        |
+| nf-validation | unpinned         | 1.1.3       |
+
+## v1.1.2 - Augmented Akita Patch [2023-10-27]
+
+### `Added`
+
+- [#408](https://github.com/nf-core/taxprofiler/pull/408) Added preprint citation information to README and manifest (added by @jfy133)
+
+### `Fixed`
+
+- [#405](https://github.com/nf-core/taxprofiler/pull/405) Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#406](https://github.com/nf-core/taxprofiler/pull/406) Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
+- [#409](https://github.com/nf-core/taxprofiler/pull/409) Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)
+
+### `Dependencies`
+
+| Tool           | Previous version | New version |
+| -------------- | ---------------- | ----------- |
+| megan/rma2info | 6.21.7           | 6.24.20     |
+
+### `Deprecated`
+
+## v1.1.1 - Augmented Akita Patch [2023-10-11]
+
+### `Added`
+
+- [#379](https://github.com/nf-core/taxprofiler/pull/379) Added support for previously missing Bracken-corrected Kraken2 report as output (added by @hkaspersen & @jfy133 )
+- [#380](https://github.com/nf-core/taxprofiler/pull/380) Updated to nf-core pipeline template v2.10 (added by @LilyAnderssonLee & @sofstam)
+- [#393](https://github.com/nf-core/taxprofiler/pull/383) Add validation check for a taxpasta taxonomy directory if --taxpasta*add*\* parameters requested (♥️ to @alimalrashed for reporting, added by @jfy133)
+
+### `Fixed`
+
+- [#383](https://github.com/nf-core/taxprofiler/pull/383) Update the module of KrakenUniq to the latest to account for edge case bugs where FASTQ input was mis-detected as wrong format (❤️ to @asafpr for reporting and solution, fixed by @LilyAnderssonLee)
+- [#392](https://github.com/nf-core/taxprofiler/pull/392) Update the module of Taxpasta to support adding taxa information to results (❤️ to @SannaAb for reporting, fixed by @Midnighter)
+
+### `Dependencies`
+
+| Tool       | Previous version | New version |
+| ---------- | ---------------- | ----------- |
+| KrakenUniq | 1.0.2            | 1.0.4       |
+| taxpasta   | 0.6.0            | 0.6.1       |
+
+### `Deprecated`
+
+## v1.1.0 - Augmented Akita [2023-09-19]
+
+### `Added`
+
+- [#298](https://github.com/nf-core/taxprofiler/pull/298) **New classifier** [ganon](https://pirovc.github.io/ganon/) (added by @jfy133)
+- [#312](https://github.com/nf-core/taxprofiler/pull/312) **New classifier** [KMCP](https://github.com/shenwei356/kmcp) (added by @sofstam)
+- [#318](https://github.com/nf-core/taxprofiler/pull/318) **New classifier** [MetaPhlAn4](https://github.com/biobakery/MetaPhlAn) (MetaPhlAn3 support remains) (added by @LilyAnderssonLee)
+- [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing (added by @Midnighter)
+- [#272](https://github.com/nf-core/taxprofiler/pull/272) Add saving of final 'analysis-ready-reads' to dedicated directory (❤️ to @alexhbnr for request, added by @jfy133)
+- [#303](https://github.com/nf-core/taxprofiler/pull/303) Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for request, added by @jfy133)
+- [#308](https://github.com/nf-core/taxprofiler/pull/308) Add citations and bibliographic information to the MultiQC methods text of tools used in a given pipeline run (added by @jfy133)
+- [#315](https://github.com/nf-core/taxprofiler/pull/315) Updated to nf-core pipeline template v2.9 (added by @sofstam & @jfy133)
+- [#321](https://github.com/nf-core/taxprofiler/pull/321) Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
+- [#325](https://github.com/nf-core/taxprofiler/pull/325) Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
+- [#345](https://github.com/nf-core/taxprofiler/pull/345) Add simple tutorial to explain how to get up and running with an nf-core/taxprofiler run (added by @jfy133)
+- [#355](https://github.com/nf-core/taxprofiler/pull/355) Add support for TAXPASTA's `--add-rank-lineage` to output (❤️ to @MajoroMask for request, added by @Midnighter, @sofstam, @jfy133)
+- [#368](https://github.com/nf-core/taxprofiler/pull/368/) Add the ability to ignore profile errors caused by empty profiles and other validation errors when merging multiple profiles using TAXPASTA (added by @Midnighter and @LilyAnderssonLee)
+
+### `Fixed`
+
+- [#271](https://github.com/nf-core/taxprofiler/pull/271) Improved standardised table generation documentation for mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
+- [#269](https://github.com/nf-core/taxprofiler/pull/269) Reduced output files in AWS full test output due to very large files (fix by @jfy133)
+- [#270](https://github.com/nf-core/taxprofiler/pull/270) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
+- [#274](https://github.com/nf-core/taxprofiler/pull/274) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
+- [#275](https://github.com/nf-core/taxprofiler/pull/275) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
+- [#285](https://github.com/nf-core/taxprofiler/pull/285) Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
+- [#286](https://github.com/nf-core/taxprofiler/pull/286) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
+- [#289](https://github.com/nf-core/taxprofiler/pull/289) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
+- [#290](https://github.com/nf-core/taxprofiler/pull/290) Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
+- [#305](https://github.com/nf-core/taxprofiler/pull/305) Fix docker/podman registry definition for tower compatibility (fix by @adamrtalbot, @jfy133)
+- [#304](https://github.com/nf-core/taxprofiler/pull/304) Correct mistake in kaiju2table documentation, only single rank can be supplied (♥ to @artur-matysik for reporting, fix by @jfy133)
+- [#307](https://github.com/nf-core/taxprofiler/pull/307) Fix databases being sometimes associated with the wrong tool (e.g. Kaiju) (fix by @jfy133, @Midnighter and @LilyAnderssonLee)
+- [#313](https://github.com/nf-core/taxprofiler/pull/313) Fix pipeline not providing error when database sheet does not have a header (♥ to @noah472 for reporting, fix by @jfy133)
+- [#330](https://github.com/nf-core/taxprofiler/pull/330) Added better tagging to allow disambiguation of Kraken2 steps of Kraken2 vs Bracken (♥ to @MajoroMask for requesting, added by @jfy133)
+- [#334](https://github.com/nf-core/taxprofiler/pull/334) Increase the memory of the FALCO process to 4GB (fix by @LilyAnderssonLee)
+- [#332](https://github.com/nf-core/taxprofiler/pull/332) Improved meta map stability for more robust pipeline resuming (fix by @jfy133)
+- [#338](https://github.com/nf-core/taxprofiler/pull/338) Fixed wrong file 'out' file going to `centrifuge kreport` module (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
+- [#342](https://github.com/nf-core/taxprofiler/pull/342) Fixed docs/usage to correctly list the required database files for Bracken and tips to obtain Kraken2 databases (fix by @husensofteng)
+- [#350](https://github.com/nf-core/taxprofiler/pull/350) Reorganize the CI tests into separate profiles in preparation for implementation of nf-test (fix by @LilyAnderssonLee)
+- [#364](https://github.com/nf-core/taxprofiler/pull/364) Add autoMounts to apptainer profile in nextflow.config (♥ to @hkaspersen for reporting, fix by @LilyAnderssonLee)
+- [#372](https://github.com/nf-core/taxprofiler/pull/372) Update modules to use quay.io nf-core mirrored containers (♥ to @maxulysse for pointing out, fix by @LilyAnderssonLee and @jfy133)
+
+### `Dependencies`
+
+| Tool      | Previous version | New version |
+| --------- | ---------------- | ----------- |
+| MultiQC   | 1.13             | 1.15        |
+| TAXPASTA  | 0.2.3            | 0.6.0       |
+| MetaPhlAn | 3.0.12           | 4.0.6       |
+| fastp     | 0.23.2           | 0.23.4      |
+| samtools  | 1.16.1           | 1.17        |
+
+### `Deprecated`
+
+- [#338](https://github.com/nf-core/taxprofiler/pull/338) Updated Centrifuge module to not generate (undocumented) SAM alignments by default if --save_centrifuge_reads supplied, due to a Centrifuge bug modifying profile header. SAM alignments can still be generated if `--out-fmt` supplied in `database.csv` (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
+
+## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
+
+### `Added`
+
+### `Fixed`
+
+- [#291](https://github.com/nf-core/taxprofiler/pull/291) - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)
+
+## v1.0.0 - Dodgy Dachshund [2023-03-13]
+>>>>>>> dev
 
 Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.
 
+- Add read quality control (sequencing QC, adapter removal and merging)
+- Add read complexity filtering
+- Add host-reads removal step
+- Add run merging
+- Add taxonomic classification
+- Add taxon table standardisation
+- Add post-classification visualisation
+
 ### `Added`
 
 ### `Fixed`