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Merge pull request #139 from Plant-Food-Research-Open/dev
Candidate for 2.1.1
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Original file line number | Diff line number | Diff line change |
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@@ -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: ${{ matrix.NXF_VER }} | ||
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||
- name: Install nf-test | ||
uses: nf-core/[email protected] | ||
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- name: Run nf-tests | ||
run: | | ||
nf-test \ | ||
test \ | ||
--verbose \ | ||
tests |
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@@ -10,3 +10,7 @@ testing* | |
# PFR files | ||
*.stdout | ||
*.stderr | ||
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# nf-test files | ||
.nf-test/ | ||
.nf-test.log |
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@@ -3,6 +3,25 @@ | |
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | ||
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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## v2.1.1 - [20-Sep-2024] | ||
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### `Added` | ||
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1. Configured nf-test for function testing | ||
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### `Fixed` | ||
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1. Made the `hic` param pattern more flexible as `^SR\w+$|^\S+\{1,2\}[\w\.]*\.f(ast)?q\.gz$` [#130](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/130) | ||
2. Fixed flowchart syntax to remove '\n' [#132](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/132) | ||
3. Updated modules to remove Bioconda `defaults` channel [#135](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/135) | ||
4. Now gff files for circular molecules can have end coordinates greater than the sequence length [#129](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/129) | ||
5. Fixed the branch protection GitHub action | ||
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### `Dependencies` | ||
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1. Nextflow!>=23.04.0 | ||
2. [email protected] | ||
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## v2.1.0 - [31-July-2024] | ||
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### `Added` | ||
|
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@@ -9,3 +9,7 @@ do | |
rm -rf "work/$i" | ||
done | ||
echo "Cleaned work..." | ||
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rm -f .nf-test.log | ||
rm -rf .nf-test | ||
echo "Cleaned nf-test..." |
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