From acc4eb0054a72c03a4d7bc49cbf257d1e864e236 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 5 Dec 2019 15:57:32 +0100 Subject: [PATCH] GitHub actions - run nextflow in a docker image --- .github/workflows/fastqc.yml | 3 ++- .github/workflows/samtools_index.yml | 3 ++- .github/workflows/samtools_sort.yml | 3 ++- .github/workflows/trim_galore.yml | 3 ++- tools/fastqc/test/main.nf | 14 +++++++++++++- tools/samtools/index/test/main.nf | 14 +++++++++++++- tools/samtools/sort/test/main.nf | 14 +++++++++++++- tools/trim_galore/test/main.nf | 14 +++++++++++++- 8 files changed, 60 insertions(+), 8 deletions(-) diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index 87726302..fb395797 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -15,4 +15,5 @@ jobs: - uses: actions/checkout@v1 # Test the module - - run: nextflow run ./tools/fastqc/test/ + - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 + run: nextflow run ./tools/fastqc/test/ diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 27df40d1..32719e5e 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -15,4 +15,5 @@ jobs: - uses: actions/checkout@v1 # Test the module - - run: nextflow run ./tools/samtools/index/test/ + - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 + run: nextflow run ./tools/samtools/index/test/ diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index ef066db8..46791408 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -15,4 +15,5 @@ jobs: - uses: actions/checkout@v1 # Test the module - - run: nextflow run ./tools/samtools/sort/test/ + - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 + run: nextflow run ./tools/samtools/sort/test/ diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml index 053408c4..48c93b5f 100644 --- a/.github/workflows/trim_galore.yml +++ b/.github/workflows/trim_galore.yml @@ -15,4 +15,5 @@ jobs: - uses: actions/checkout@v1 # Test the module - - run: nextflow run ./tools/trim_galore/test/ + - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 + run: nextflow run ./tools/trim_galore/test/ diff --git a/tools/fastqc/test/main.nf b/tools/fastqc/test/main.nf index 33242101..5fb89109 100644 --- a/tools/fastqc/test/main.nf +++ b/tools/fastqc/test/main.nf @@ -1 +1,13 @@ -/* A mini pipeline to test FastQC here */ +#!/usr/bin/env nextflow +echo true + +cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola' + +process sayHello { + input: + val x from cheers + script: + """ + echo '$x world!' + """ +} diff --git a/tools/samtools/index/test/main.nf b/tools/samtools/index/test/main.nf index 2e9ae0f5..5fb89109 100644 --- a/tools/samtools/index/test/main.nf +++ b/tools/samtools/index/test/main.nf @@ -1 +1,13 @@ -/* A mini pipeline to test samtools index here */ +#!/usr/bin/env nextflow +echo true + +cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola' + +process sayHello { + input: + val x from cheers + script: + """ + echo '$x world!' + """ +} diff --git a/tools/samtools/sort/test/main.nf b/tools/samtools/sort/test/main.nf index 6e0055e2..5fb89109 100644 --- a/tools/samtools/sort/test/main.nf +++ b/tools/samtools/sort/test/main.nf @@ -1 +1,13 @@ -/* A mini pipeline to test samtools sort here */ +#!/usr/bin/env nextflow +echo true + +cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola' + +process sayHello { + input: + val x from cheers + script: + """ + echo '$x world!' + """ +} diff --git a/tools/trim_galore/test/main.nf b/tools/trim_galore/test/main.nf index 33242101..5fb89109 100644 --- a/tools/trim_galore/test/main.nf +++ b/tools/trim_galore/test/main.nf @@ -1 +1,13 @@ -/* A mini pipeline to test FastQC here */ +#!/usr/bin/env nextflow +echo true + +cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola' + +process sayHello { + input: + val x from cheers + script: + """ + echo '$x world!' + """ +}