Merge pull request #139 from Plant-Food-Research-Open/dev

Candidate for 2.1.1

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'plant-food-research-open/assemblyqc'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == plant-food-research-open/assemblyqc ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{ github.event.pull_request.head.repo.full_name }} == Plant-Food-Research-Open/assemblyqc ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/ci.yml

@@ -30,10 +30,13 @@ jobs:
           - invalid
           - stub
           - noltr
+          - hicparam
         include:
           - OPTION_STUB: ""
           - OPTION_STUB: "-stub"
             TEST_PARAMS: stub
+          - OPTION_STUB: "-stub"
+            TEST_PARAMS: hicparam
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -55,3 +58,31 @@ jobs:
             -params-file \
             ./tests/${{ matrix.TEST_PARAMS }}/params.json \
             ${{ matrix.OPTION_STUB }}
+
+  nf-test:
+    name: Run nf-tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'plant-food-research-open/assemblyqc') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ matrix.NXF_VER }}
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1.1.2
+
+      - name: Run nf-tests
+        run: |
+          nf-test \
+            test \
+            --verbose \
+            tests

.gitignore

@@ -10,3 +10,7 @@ testing*
 # PFR files
 *.stdout
 *.stderr
+
+# nf-test files
+.nf-test/
+.nf-test.log

CHANGELOG.md

@@ -3,6 +3,25 @@
 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).
 
+## v2.1.1 - [20-Sep-2024]
+
+### `Added`
+
+1. Configured nf-test for function testing
+
+### `Fixed`
+
+1. Made the `hic` param pattern more flexible as `^SR\w+$|^\S+\{1,2\}[\w\.]*\.f(ast)?q\.gz$` [#130](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/130)
+2. Fixed flowchart syntax to remove '\n' [#132](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/132)
+3. Updated modules to remove Bioconda `defaults` channel [#135](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/135)
+4. Now gff files for circular molecules can have end coordinates greater than the sequence length [#129](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/129)
+5. Fixed the branch protection GitHub action
+
+### `Dependencies`
+
+1. Nextflow!>=23.04.0
+2. nf-validation@1.1.3
+
 ## v2.1.0 - [31-July-2024]
 
 ### `Added`

CITATION.cff

@@ -25,7 +25,7 @@ authors:
   - family-names: "Deng"
     given-names: "Cecilia"
 title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
-version: 2.1.0
+version: 2.1.1
 date-released: 2024-07-30
 url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
 doi: 10.1093/bioinformatics/btae477

README.md

@@ -30,24 +30,24 @@
 flowchart LR
   forEachTag(Assembly) ==> VALIDATE_FORMAT[VALIDATE FORMAT]
 
-  VALIDATE_FORMAT ==> ncbiFCS[NCBI FCS\nADAPTOR]
+  VALIDATE_FORMAT ==> ncbiFCS[<span style="white-space: nowrap;">NCBI FCS ADAPTOR</span>]
   ncbiFCS ==> Check{Check}
 
-  VALIDATE_FORMAT ==> ncbiGX[NCBI FCS GX]
+  VALIDATE_FORMAT ==> ncbiGX[<span style="white-space: nowrap;">NCBI FCS GX</span>]
   ncbiGX ==> Check
   Check ==> |Clean|Run(Run)
 
   Check ==> |Contamination|Skip(Skip All)
   Skip ==> REPORT
 
-  VALIDATE_FORMAT ==> GFF_STATS[GENOMETOOLS GT STAT]
+  VALIDATE_FORMAT ==> GFF_STATS[<span style="white-space: nowrap;">GENOMETOOLS GT STAT</span>]
 
-  Run ==> ASS_STATS[ASSEMBLATHON STATS]
+  Run ==> ASS_STATS[<span style="white-space: nowrap;">ASSEMBLATHON STATS</span>]
   Run ==> BUSCO
   Run ==> TIDK
   Run ==> LAI
   Run ==> KRAKEN2
-  Run ==> HIC_CONTACT_MAP[HIC CONTACT MAP]
+  Run ==> HIC_CONTACT_MAP[<span style="white-space: nowrap;">HIC CONTACT MAP</span>]
   Run ==> MUMMER
   Run ==> MINIMAP2
   Run ==> MERQURY

cleanNXF.sh

@@ -9,3 +9,7 @@ do
     rm -rf "work/$i"
 done
 echo "Cleaned work..."
+
+rm -f .nf-test.log
+rm -rf .nf-test
+echo "Cleaned nf-test..."

docs/parameters.md

@@ -66,12 +66,12 @@ A Nextflow pipeline which evaluates assembly quality with multiple QC tools and
 
 ## HiC options
 
-| Parameter            | Description                                                                            | Type      | Default                                           | Required | Hidden |
-| -------------------- | -------------------------------------------------------------------------------------- | --------- | ------------------------------------------------- | -------- | ------ |
-| `hic`                | HiC reads path provided as a SRA ID or as paired reads with pattern '\*{1,2}.fastq.gz' | `string`  |                                                   |          |        |
-| `hic_skip_fastp`     | Skip HiC read trimming                                                                 | `boolean` |                                                   |          |        |
-| `hic_skip_fastqc`    | Skip HiC read QC                                                                       | `boolean` |                                                   |          |        |
-| `hic_fastp_ext_args` | Additional parameters for fastp trimming                                               | `string`  | --qualified_quality_phred 20 --length_required 50 |          |        |
+| Parameter            | Description                                                                              | Type      | Default                                           | Required | Hidden |
+| -------------------- | ---------------------------------------------------------------------------------------- | --------- | ------------------------------------------------- | -------- | ------ |
+| `hic`                | HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz' | `string`  |                                                   |          |        |
+| `hic_skip_fastp`     | Skip HiC read trimming                                                                   | `boolean` |                                                   |          |        |
+| `hic_skip_fastqc`    | Skip HiC read QC                                                                         | `boolean` |                                                   |          |        |
+| `hic_fastp_ext_args` | Additional parameters for fastp trimming                                                 | `string`  | --qualified_quality_phred 20 --length_required 50 |          |        |
 
 ## Synteny options
 

docs/usage.md

@@ -90,7 +90,7 @@ This section provides additional information for parameters. It does not list al
 
 ### HiC
 
-- `hic`: Path to reads provided as a SRA ID or as a path to paired reads with pattern '\*{1,2}.(fastq|fq).gz'. These reads are applied to each assembly listed by `input`.
+- `hic`: Path to reads provided as a SRA ID or as a path to paired reads such as 'hic_reads{1,2}.fastq.gz'. These reads are applied to each assembly listed by `input`.
 
 ### Synteny analysis