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Docker #10

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merged 5 commits into from
Oct 25, 2023
Merged

Docker #10

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eaa643e
feat: build docker and push to hub
dnousome Oct 25, 2023
11d6156
fix: use SINCLAIR style for docker build
dnousome Oct 25, 2023
efecf3e
fix: update Dockers
dnousome Oct 25, 2023
5899742
fix: manifest update for docker
dnousome Oct 25, 2023
2d9a745
fix: change versioning
dnousome Oct 25, 2023
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57 changes: 42 additions & 15 deletions .github/workflows/docker.yaml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,24 +7,51 @@ on:
- 'docker'

jobs:
docker:
generate-matrix:
runs-on: ubuntu-latest
outputs:
matrix-metadata: ${{ steps.metadata.outputs.matrix }}
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
-
name: Login to Docker Hub
uses: docker/login-action@v3
- uses: hellofresh/action-changed-files@v3
id: metadata
with:
pattern: docker/(?P<image_dir>\w+)/.*
default-patterns: |
meta.yml
Dockerfile

update-docker:
needs: [generate-matrix]
strategy:
matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: pietrobolcato/[email protected]
id: metadata
with:
config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
- name: Get date
id: date
run: |
echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
- name: Login to DockerHub
#if: github.event_name != 'pull_request'
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
uses: docker/build-push-action@v5
- name: Build and push
uses: docker/build-push-action@v4
# only try building & pushing the container if parsing the metadata worked
if: ${{ steps.metadata.outputs['container'] != '' }}
with:
push: true
tags: user/app:latest
context: docker/${{ matrix.image_dir }}
# only push container to docker hub if not triggered from a PR
push: ${{ github.event_name != 'pull_request' }}
tags: ${{ steps.metadata.outputs['container'] }}
build-args: |
BUILD_DATE=${{ steps.date.outputs.DATE }}
BUILD_TAG=${{ steps.metadata.outputs['version'] }}
REPONAME=${{ steps.metadata.outputs['image_name'] }}
4 changes: 4 additions & 0 deletions docker/logan_base/meta.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
dockerhub_namespace: dnousome
image_name: ccbr_logan_base
version: v0.3.1
container: "$(dockerhub_namespace)/$(image_name):$(version)"
54 changes: 27 additions & 27 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ profiles {
process {
executor = 'local'
withName:fc_lane {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName:fastq_screen {
container= 'docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0'
Expand All @@ -69,7 +69,7 @@ profiles {
container= 'docker://nciccbr/ccbr_qualimap:v0.0.1'
}
withName: 'samtools_flagstats|vcftools|bcftools_stats|gatk_varianteval|snpeff|somalier_extract|somalier_analysis' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'multiqc' {
container= 'docker://nciccbr/ccbr_multiqc_1.9:v0.0.1'
Expand All @@ -78,22 +78,22 @@ profiles {
container= 'docker://nciccbr/ccbr_picard:v0.0.1'
}
withName: 'fastp|bwamem2|indelrealign|bqsr|gatherbqsr|samtoolsindex|applybqsr' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName:'mutect2|mutect2_t|mutect2_t_tonly|mutect2filter|mutect2filter_tonly|learnreadorientationmodel|learnreadorientationmodel_tonly|contamination_paired|contamination_tumoronly|pileup_paired_t|pileup_paired_n|pileup_paired_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'strelka_tn|vardict_tn|vardict_tonly|varscan_tn|varscan_tonly|combineVariants|combineVariants_strelka' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'annotvep_tn|annotvep_tonly' {
container= 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
}
withName: 'svaba_somatic|manta_somatic' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'sequenza' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}


Expand Down Expand Up @@ -152,88 +152,88 @@ profiles {
cpus=8
}
withName:fastp {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory=24.GB
time=24.h
cpus=4
}
withName:fc_lane {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName:bwamem2 {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory=200.GB
time=48.h
cpus=17
}
withName:indelrealign{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory=48.GB
time=72.h
cpus=16
}
withName:bqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 32.GB
time= 48.h
}
withName:gatherbqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 2.h
}
withName:applybqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
time= 48.h
}
withName:samtoolsindex{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
cpus= 4
}
withName: 'mutect2|mutect2_t|mutect2_t_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
cpus= 4
time= 72.h
}
withName: 'vardict_tn|vardict_tonly|varscan_tn|varscan_tonly|combineVariants|combineVariants_strelka' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 32.GB
cpus= 2
time= 72.h
}
withName: 'strelka_tn' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
cpus= 16
time= 72.h
}
withName:'mutect2filter|mutect2filter_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 24.GB
time= 24.h
cpus= 4
}
withName:'contamination_paired|contamination_tumoronly'{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 24.GB
time= 24.h
}
withName:'learnreadorientationmodel|learnreadorientationmodel_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
time= 24.h
}
withName:'mergemut2stats|mergemut2stats_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 24.h
}
withName:'pileup_paired_t|pileup_paired_n|pileup_paired_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
}
Expand Down Expand Up @@ -273,12 +273,12 @@ profiles {
scratch='/lscratch/$SLURM_JOB_ID/dv'
}
withName:'somalier_extract|somalier_analysis' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
}
withName:'gatk_varianteval' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
}
Expand All @@ -295,13 +295,13 @@ profiles {
cpus=16
}
withName:'svaba_somatic|manta_somatic' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 64.GB
time= 24.h
cpus=16
}
withName: 'sequenza' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 64.GB
time= 24.h
cpus=12
Expand Down
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