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GitHub actions - run nextflow in a docker image

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This commit is contained in:
Phil Ewels 2019-12-05 15:57:32 +01:00
parent af766a9cc7
commit acc4eb0054
8 changed files with 60 additions and 8 deletions
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3
.github/workflows/fastqc.yml vendored
View file

@ -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/

3
.github/workflows/samtools_index.yml vendored
View file

@ -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/

3
.github/workflows/samtools_sort.yml vendored
View file

@ -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/

3
.github/workflows/trim_galore.yml vendored
View file

@ -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/

14
tools/fastqc/test/main.nf
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@ -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!'
"""
}

14
tools/samtools/index/test/main.nf
View file

@ -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!'
"""
}

14
tools/samtools/sort/test/main.nf
View file

@ -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!'
"""
}

14
tools/trim_galore/test/main.nf
View file

@ -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!'
"""
}