Merge pull request #583 from nf-core/dev

v1.2.3 - Bouncy Basenji Patch PR

Author: jfy133

.github/workflows/ci.yml

@@ -57,6 +57,8 @@ 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/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

@@ -1,4 +1,4 @@
-nf_core_version: 3.1.1
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li,
@@ -12,4 +12,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 1.2.2
+  version: 1.2.3

.pre-commit-config.yaml

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

CHANGELOG.md

@@ -3,6 +3,27 @@
 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).
 
+## v1.2.3 - Bouncy Basenji Patch [2024-03-13]
+
+### `Added`
+
+- [#576](https://github.com/nf-core/taxprofiler/pull/576) Sort input to krakenuniq to enable retrieval of cached batch tasks (❤️ to @muniheart for reporting and fix)
+- [#569](https://github.com/nf-core/taxprofiler/pull/569) Updated to nf-core pipeline template v3.1.2 (added by @sofstam)
+- [#571](https://github.com/nf-core/taxprofiler/pull/571) Updated to nf-core pipeline template v3.2.0 (added by @sofstam)
+-
+
+### `Fixed`
+
+- [#580](https://github.com/nf-core/taxprofiler/pull/580) Minor documentation typo fixes (❤️ to @AlexHoratio for reporting and fix)
+- [#573](https://github.com/nf-core/taxprofiler/pull/573) Improved help messages and documentation to state many of the taxpasta related params require taxonomy files to be input (❤️ to @alexhbnr for reporting, fix by @jfy133)
+- [#578](https://github.com/nf-core/taxprofiler/pull/578) Fixed incorrect keyword in nextflow_schema.json (fix by @mashehu)
+- [#585](https://github.com/nf-core/taxprofiler/pull/585) Fixed code blocks (fix by @masheshu)
+- [#586](https://github.com/nf-core/taxprofiler/pull/586) Fixed wrong argument name for saving analysis reads (fix by @epstein6)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.2.2 - Bouncy Basenji Patch [2024-01-15]
 
 ### `Added`

README.md

@@ -7,6 +7,7 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/taxprofiler/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7728364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7728364)
+
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
@@ -58,9 +59,7 @@
 
 First, prepare a samplesheet with your input data that looks as follows:
 
-`samplesheet.csv`:
-
-```csv
+```csv title="samplesheet.csv"
 sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
 2612,run1,ILLUMINA,2612_run1_R1.fq.gz,,
 2612,run2,ILLUMINA,2612_run2_R1.fq.gz,,
@@ -71,9 +70,7 @@ Each row represents a fastq file (single-end), a pair of fastq files (paired end
 
 Additionally, you will need a database sheet that looks as follows:
 
-`databases.csv`:
-
-```csv
+```csv title="databases.csv"
 tool,db_name,db_params,db_path
 kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
 metaphlan,db1,,/<path>/<to>/metaphlan/metaphlan_database/
@@ -123,6 +120,8 @@ We thank the following people for their contributions to the development of this
 - [Jianhong Ou](https://github.com/jianhong)
 - [Rafal Stepien](https://github.com/rafalstepien)
 - [Mahwash Jamy](https://github.com/mjamy)
+- [Alex Caswell](https://github.com/AlexHoratio)
+- [Aidan Epstein](https://github.com/epstein6)
 
 ### Acknowledgments
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.2.2"
+  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.2.3"
   target="_blank">nf-core/taxprofiler</a> analysis pipeline. For information about
-  how to interpret these results, please see the <a href="https://nf-co.re/taxprofiler/1.2.2/docs/output"
+  how to interpret these results, please see the <a href="https://nf-co.re/taxprofiler/1.2.3/docs/output"
   target="_blank">documentation</a>.
 report_section_order:
   "nf-core-taxprofiler-methods-description":

assets/nf-core-taxprofiler_logo_light.png

@@ -603,6 +603,7 @@ process {
     }
 
     withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
+        tag = { "${meta.db_name}|${task.index}" }
         ext.args = { "${meta.db_params}" }
         // one run with multiple samples, so fix ID to just db name to ensure clean log name
         ext.prefix = { "${meta.db_name}.krakenuniq" }