From 93f7b26aa228c1dc517ba8b6d606bb79cbe54c10 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 6 Dec 2019 09:24:33 +0100 Subject: [PATCH] Use submodules for test data --- .github/workflows/fastqc.yml | 1 + .github/workflows/samtools_index.yml | 1 + .github/workflows/samtools_sort.yml | 1 + .github/workflows/trim_galore.yml | 1 + tools/fastqc/test/main.nf | 7 ++++--- 5 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index d4034576..9cfcfa55 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -12,6 +12,7 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + submodules: true - name: Install Nextflow run: | diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index c49bbec6..302e0b6d 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -12,6 +12,7 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + submodules: true - name: Install Nextflow run: | diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index f6e0ac4c..cc9ce4f8 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -12,6 +12,7 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + submodules: true - name: Install Nextflow run: | diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml index 033ae6ec..d914313e 100644 --- a/.github/workflows/trim_galore.yml +++ b/.github/workflows/trim_galore.yml @@ -12,6 +12,7 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + submodules: true - name: Install Nextflow run: | diff --git a/tools/fastqc/test/main.nf b/tools/fastqc/test/main.nf index 6ab43b7b..f24a81da 100644 --- a/tools/fastqc/test/main.nf +++ b/tools/fastqc/test/main.nf @@ -5,9 +5,10 @@ include '../main.nf' params(params) // Define input channels readPaths = [ - ['SRR389222_sub1', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz']], - ['SRR389222_sub2', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']], - ['SRR389222_sub3', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz']] + ['SRR4238351', ['../../../test-datasets/tools/fastqc/input/SRR4238351_subsamp.fastq.gz']], + ['SRR4238355', ['../../../test-datasets/tools/fastqc/input/SRR4238355_subsamp.fastq.gz']], + ['SRR4238359', ['../../../test-datasets/tools/fastqc/input/SRR4238359_subsamp.fastq.gz']], + ['SRR4238379', ['../../../test-datasets/tools/fastqc/input/SRR4238379_subsamp.fastq.gz']] ] Channel .from(readPaths)