From 31c0f617b985f4f743a5ba7ef2bcebea13605870 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sat, 11 Jul 2020 17:14:14 +0200 Subject: [PATCH] Fix up cutadapt tests --- .github/workflows/cutadapt.yml | 13 +++++++------ .github/workflows/fastqc.yml | 5 +++-- .github/workflows/samtools_index.yml | 5 +++-- .github/workflows/samtools_sort.yml | 5 +++-- .github/workflows/tcoffee.yml | 5 +++-- .github/workflows/trim_galore.yml | 5 +++-- software/cutadapt/test/main.nf | 21 ++++++++++----------- 7 files changed, 32 insertions(+), 27 deletions(-) diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml index dfb15238..7092e868 100644 --- a/.github/workflows/cutadapt.yml +++ b/.github/workflows/cutadapt.yml @@ -7,10 +7,11 @@ on: jobs: run_ci_test: runs-on: ubuntu-latest - + env: + NXF_ANSI_LOG: false steps: - # Check out the repository - uses: actions/checkout@v2 + - name: Checkout submodules shell: bash run: | @@ -25,10 +26,10 @@ jobs: - name: Test module with paired-end data run: | - cd software/cutadapt/test_paired/ - nextflow run . -ansi-log false + cd software/cutadapt/test/ + nextflow run . - name: Test module with single-end data run: | - cd software/cutadapt/test_single/ - nextflow run . -ansi-log false + cd software/cutadapt/test/ + nextflow run . --single_end diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index 4ddcbefe..6888bbc0 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -7,7 +7,8 @@ on: jobs: run_ci_test: runs-on: ubuntu-latest - + env: + NXF_ANSI_LOG: false steps: # Check out the repository @@ -20,4 +21,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./software/fastqc/test/ -ansi-log false + - run: nextflow run ./software/fastqc/test/ diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 260c868d..5b7c1cd5 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -7,7 +7,8 @@ on: jobs: run_ci_test: runs-on: ubuntu-latest - + env: + NXF_ANSI_LOG: false steps: # Check out the repository @@ -20,4 +21,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./software/samtools/index/test/ -ansi-log false + - run: nextflow run ./software/samtools/index/test/ diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index b020dfbd..bba7d578 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -7,7 +7,8 @@ on: jobs: run_ci_test: runs-on: ubuntu-latest - + env: + NXF_ANSI_LOG: false steps: # Check out the repository @@ -20,4 +21,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./software/samtools/sort/test/ -ansi-log false + - run: nextflow run ./software/samtools/sort/test/ diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/tcoffee.yml index 7ec3431e..582a1bb7 100644 --- a/.github/workflows/tcoffee.yml +++ b/.github/workflows/tcoffee.yml @@ -7,7 +7,8 @@ on: jobs: run_ci_test: runs-on: ubuntu-latest - + env: + NXF_ANSI_LOG: false steps: # Check out the repository @@ -27,4 +28,4 @@ jobs: # Test the module - run: | cd software/tcoffee/test/ - nextflow run . -ansi-log false + nextflow run . diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml index ae823971..b34f2ae6 100644 --- a/.github/workflows/trim_galore.yml +++ b/.github/workflows/trim_galore.yml @@ -7,7 +7,8 @@ on: jobs: run_ci_test: runs-on: ubuntu-latest - + env: + NXF_ANSI_LOG: false steps: # Check out the repository @@ -20,4 +21,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./software/trim_galore/test/ -ansi-log false + - run: nextflow run ./software/trim_galore/test/ diff --git a/software/cutadapt/test/main.nf b/software/cutadapt/test/main.nf index 2ab4529b..186af146 100644 --- a/software/cutadapt/test/main.nf +++ b/software/cutadapt/test/main.nf @@ -3,19 +3,18 @@ nextflow.preview.dsl = 2 include '../main.nf' params(params) // 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 -// But most of this module is not functional currently anyway.... -single_end_input = Channel.from([ - ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'], - ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'], - ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'], - ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz'] - ]).map { row -> [ row[0], [ file(row[1]) ] ] } +if(params.single_end){ + input_fastqs = Channel.from([ + ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'], + ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'], + ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'], + ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz'] + ]).map { row -> [ row[0], [ file(row[1]) ] ] } +} // Run the workflow workflow { - cutadapt(paired_end_input) - cutadapt(single_end_input) + cutadapt(input_fastqs) }