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Use submodules for test data

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This commit is contained in:
Phil Ewels 2019-12-06 09:24:33 +01:00
parent 36df850298
commit 93f7b26aa2
5 changed files with 8 additions and 3 deletions
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1
.github/workflows/fastqc.yml vendored
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@ -12,6 +12,7 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
submodules: true
- name: Install Nextflow - name: Install Nextflow
run: | run: |

1
.github/workflows/samtools_index.yml vendored
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@ -12,6 +12,7 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
submodules: true
- name: Install Nextflow - name: Install Nextflow
run: | run: |

1
.github/workflows/samtools_sort.yml vendored
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@ -12,6 +12,7 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
submodules: true
- name: Install Nextflow - name: Install Nextflow
run: | run: |

1
.github/workflows/trim_galore.yml vendored
View file

@ -12,6 +12,7 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
submodules: true
- name: Install Nextflow - name: Install Nextflow
run: | run: |

7
tools/fastqc/test/main.nf
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@ -5,9 +5,10 @@ include '../main.nf' params(params)
// Define input channels // Define input channels
readPaths = [ readPaths = [
['SRR389222_sub1', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz']], ['SRR4238351', ['../../../test-datasets/tools/fastqc/input/SRR4238351_subsamp.fastq.gz']],
['SRR389222_sub2', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']], ['SRR4238355', ['../../../test-datasets/tools/fastqc/input/SRR4238355_subsamp.fastq.gz']],
['SRR389222_sub3', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz']] ['SRR4238359', ['../../../test-datasets/tools/fastqc/input/SRR4238359_subsamp.fastq.gz']],
['SRR4238379', ['../../../test-datasets/tools/fastqc/input/SRR4238379_subsamp.fastq.gz']]
] ]
Channel Channel
.from(readPaths) .from(readPaths)