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Merge pull request #143 from nf-core/ci-fixes

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Get Singularity CI tests working
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Harshil Patel 2021-02-04 11:28:49 +00:00 committed by GitHub
commit 08d8443510
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6 changed files with 9 additions and 11 deletions
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4
.github/filters.yml vendored
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@ -3,7 +3,7 @@ bowtie_align:
- software/bowtie/build/** - software/bowtie/build/**
- tests/software/bowtie/align/** - tests/software/bowtie/align/**
bowtie_build: bowtie:
- software/bowtie/build/** - software/bowtie/build/**
- tests/software/bowtie/build/** - tests/software/bowtie/build/**
@ -12,7 +12,7 @@ bowtie2_align:
- software/bowtie2/build/** - software/bowtie2/build/**
- tests/software/bowtie2/align/** - tests/software/bowtie2/align/**
bowtie2_build: bowtie2:
- software/bowtie2/build/** - software/bowtie2/build/**
- tests/software/bowtie2/build/** - tests/software/bowtie2/build/**

6
.github/workflows/pytest-workflow.yml vendored
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@ -25,7 +25,7 @@ jobs:
matrix: matrix:
nxf_version: ['20.11.0-edge'] nxf_version: ['20.11.0-edge']
tags: ['${{ fromJson(needs.changes.outputs.modules) }}'] tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
profile: ['docker'] ## 'conda', 'singularity' profile: ['docker', 'singularity'] ## 'conda'
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:
@ -65,7 +65,7 @@ jobs:
if: matrix.profile == 'singularity' if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5 uses: eWaterCycle/setup-singularity@v5
with: with:
singularity-version: 3.5.3 singularity-version: 3.7.1
- name: Setup miniconda - name: Setup miniconda
if: matrix.profile == 'conda' if: matrix.profile == 'conda'
@ -80,7 +80,7 @@ jobs:
# Test the module # Test the module
- name: Run pytest-workflow - name: Run pytest-workflow
run: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof
- name: Upload logs on failure - name: Upload logs on failure
if: failure() if: failure()

3
tests/config/nextflow.config
View file

@ -2,13 +2,12 @@ params {
outdir = "output/" outdir = "output/"
publish_dir_mode = "copy" publish_dir_mode = "copy"
enable_conda = false enable_conda = false
singularity_pull_docker_container = true singularity_pull_docker_container = false
} }
if ("$PROFILE" == "singularity") { if ("$PROFILE" == "singularity") {
singularity.enabled = true singularity.enabled = true
singularity.autoMounts = true singularity.autoMounts = true
singularity.runOptions = '-B /tmp/'
} else if ("$PROFILE" == "conda") { } else if ("$PROFILE" == "conda") {
params.enable_conda = true params.enable_conda = true
} else { } else {

3
tests/software/bowtie/align/test.yml
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@ -42,6 +42,5 @@
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051 md5sum: f3c398bba5158f4039334a932d79c051
- path: output/bowtie/test.out - path: output/bowtie/test.out
md5sum: a23e9a2a76e949aeb3693bcfae41a615 md5sum: a81cb18024616415a6cec3108a36fccd
- path: output/bowtie/test.bam - path: output/bowtie/test.bam
should_exist: true

2
tests/software/bowtie/build/test.yml
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@ -15,4 +15,4 @@
- path: output/bowtie/bowtie/NC_010473.rev.1.ebwt - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
md5sum: 44f719c2fe42e1f35d54e798775846d1 md5sum: 44f719c2fe42e1f35d54e798775846d1
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051 md5sum: f3c398bba5158f4039334a932d79c051

2
tests/software/bowtie2/build/test.yml
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@ -15,4 +15,4 @@
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 4ccfee8857c3b1c69857e5ecdef597aa md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72