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Merge pull request #38 from ewels/master

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Fix up cutadapt tests
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Phil Ewels 2020-07-11 17:16:26 +02:00 committed by GitHub
commit 8155270653
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7 changed files with 32 additions and 27 deletions
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13
.github/workflows/cutadapt.yml vendored
View file

@ -7,10 +7,11 @@ on:
jobs: jobs:
run_ci_test: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps: steps:
# Check out the repository
- uses: actions/checkout@v2 - uses: actions/checkout@v2
- name: Checkout submodules - name: Checkout submodules
shell: bash shell: bash
run: | run: |
@ -25,10 +26,10 @@ jobs:
- name: Test module with paired-end data - name: Test module with paired-end data
run: | run: |
cd software/cutadapt/test_paired/ cd software/cutadapt/test/
nextflow run . -ansi-log false nextflow run .
- name: Test module with single-end data - name: Test module with single-end data
run: | run: |
cd software/cutadapt/test_single/ cd software/cutadapt/test/
nextflow run . -ansi-log false nextflow run . --single_end

5
.github/workflows/fastqc.yml vendored
View file

@ -7,7 +7,8 @@ on:
jobs: jobs:
run_ci_test: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps: steps:
# Check out the repository # Check out the repository
@ -20,4 +21,4 @@ jobs:
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
# Test the module # Test the module
- run: nextflow run ./software/fastqc/test/ -ansi-log false - run: nextflow run ./software/fastqc/test/

5
.github/workflows/samtools_index.yml vendored
View file

@ -7,7 +7,8 @@ on:
jobs: jobs:
run_ci_test: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps: steps:
# Check out the repository # Check out the repository
@ -20,4 +21,4 @@ jobs:
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
# Test the module # Test the module
- run: nextflow run ./software/samtools/index/test/ -ansi-log false - run: nextflow run ./software/samtools/index/test/

5
.github/workflows/samtools_sort.yml vendored
View file

@ -7,7 +7,8 @@ on:
jobs: jobs:
run_ci_test: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps: steps:
# Check out the repository # Check out the repository
@ -20,4 +21,4 @@ jobs:
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
# Test the module # Test the module
- run: nextflow run ./software/samtools/sort/test/ -ansi-log false - run: nextflow run ./software/samtools/sort/test/

5
.github/workflows/tcoffee.yml vendored
View file

@ -7,7 +7,8 @@ on:
jobs: jobs:
run_ci_test: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps: steps:
# Check out the repository # Check out the repository
@ -27,4 +28,4 @@ jobs:
# Test the module # Test the module
- run: | - run: |
cd software/tcoffee/test/ cd software/tcoffee/test/
nextflow run . -ansi-log false nextflow run .

5
.github/workflows/trim_galore.yml vendored
View file

@ -7,7 +7,8 @@ on:
jobs: jobs:
run_ci_test: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps: steps:
# Check out the repository # Check out the repository
@ -20,4 +21,4 @@ jobs:
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
# Test the module # Test the module
- run: nextflow run ./software/trim_galore/test/ -ansi-log false - run: nextflow run ./software/trim_galore/test/

11
software/cutadapt/test/main.nf
View file

@ -3,19 +3,18 @@ nextflow.preview.dsl = 2
include '../main.nf' params(params) include '../main.nf' params(params)
// Define input channels // Define input channels
paired_end_input = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' ) input_fastqs = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
// TODO: params.single_end is set to false in nextflow config if(params.single_end){
// But most of this module is not functional currently anyway.... input_fastqs = Channel.from([
single_end_input = Channel.from([
['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'], ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'], ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'], ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz'] ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
]).map { row -> [ row[0], [ file(row[1]) ] ] } ]).map { row -> [ row[0], [ file(row[1]) ] ] }
}
// Run the workflow // Run the workflow
workflow { workflow {
cutadapt(paired_end_input) cutadapt(input_fastqs)
cutadapt(single_end_input)
} }