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2 changes: 2 additions & 0 deletions .github/workflows/pre-commit.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@ on:
push:
branches: [main]

env:
NXF_SYNTAX_PARSER: "v2"
jobs:
pre-commit:
runs-on: ubuntu-latest
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5 changes: 3 additions & 2 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,19 +9,20 @@ on:

env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
NFT_VER: "0.9.2"
NFT_VER: "0.9.3"
NFT_WORKDIR: "~"
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
NXF_SYNTAX_PARSER: "v2"
jobs:
test:
runs-on: ubuntu-latest
strategy:
matrix:
JAVA_VERSION: ["17", "21"]
NXF_VER:
- "24.10.5"
- "25.10.0"
- "latest-everything"

steps:
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14 changes: 7 additions & 7 deletions tests/filterNextflowOutput/main.nf
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
include { FASTQC } from './modules/local/fastqc'

params.failure = false
params.outdir = "results"
params.monochrome_logs = false
params {
failure : Boolean = false
outdir : String = "results"
monochrome_logs : Boolean = false
}

workflow {

colors = getColors(params.monochrome_logs)

input = channel.of(
def colors = getColors(params.monochrome_logs)
def input = channel.of(
'sample_1',
'sample_2',
'sample_3',
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1 change: 0 additions & 1 deletion tests/getAllFilesFromDir/main.nf
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
workflow {

def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

// stable_content
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1 change: 0 additions & 1 deletion tests/getRelativePath/main.nf
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
workflow {

def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

// stable_content
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1 change: 0 additions & 1 deletion tests/removeNextflowVersion/main.nf
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
workflow {

channel.of(
"""
Workflow:
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