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Seqera containers: POC 4 #46

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Seqera containers: POC 4 #46

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5c351af
Strip out 'container' and tidy up config profiles
ewels Jun 17, 2024
e3f8ed9
Add container config to modules nextflow.config
ewels Jun 17, 2024
8a55332
Move registry prefix to pipeline nextflow.config
ewels Jun 19, 2024
a019b6b
Add docker_arm64 and singluarity_arm64 profiles to nextflow.config
ewels Jun 19, 2024
9abfdd7
Set container to docker x86 one by default
ewels Jun 19, 2024
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1 change: 0 additions & 1 deletion modules/local/plot_run_gantt/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ process PLOT_RUN_GANTT {
tag "$meta.id"

conda 'click=8.0.1 pandas=1.1.5 plotly_express=0.4.1 typing=3.10.0.0'
container 'seqeralabs/nf-aggregate:click-8.0.1_pandas-1.1.5_plotly_express-0.4.1_typing-3.10.0.0--ccea219dc6c3d6a1'

input:
tuple val(meta), path(run_dump)
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9 changes: 8 additions & 1 deletion modules/local/plot_run_gantt/nextflow.config
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Expand Up @@ -5,5 +5,12 @@ process {
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
container = 'click_pandas_plotly_express_typing:21adb9e2d1b605a5' }
}
}
}

profiles {
docker_arm64 { process.withName: 'PLOT_RUN_GANTT' { container = 'click_pandas_plotly_express_typing:2e5e17c7ed2d1115' } }
singularity { process.withName: 'PLOT_RUN_GANTT' { container = 'click_pandas_plotly_express_typing:a4af841350996386' } }
singularity_arm64 { process.withName: 'PLOT_RUN_GANTT' { container = 'click_pandas_plotly_express_typing:3fe674b9fa7b15b8' } }
}
1 change: 0 additions & 1 deletion modules/local/seqera_runs_dump/main.nf
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Expand Up @@ -3,7 +3,6 @@ include { getRunMetadata } from './functions'
process SEQERA_RUNS_DUMP {
tag "$meta.id"
conda 'tower-cli=0.9.2'
container 'seqeralabs/nf-aggregate:tower-cli-0.9.2--hdfd78af_1'

input:
val meta
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7 changes: 7 additions & 0 deletions modules/local/seqera_runs_dump/nextflow.config
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Expand Up @@ -7,5 +7,12 @@ process {
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.json') ? null : filename }
]
container = 'tower-cli:0.9.2--dc544a7e574ab73b'
}
}

profiles {
docker_arm64 { process.withName: 'SEQERA_RUNS_DUMP' { container = 'tower-cli:0.9.2--104eab7c00912b48' } }
singularity { process.withName: 'SEQERA_RUNS_DUMP' { container = 'tower-cli:0.9.2--810270aea7c40770' } }
singularity_arm64 { process.withName: 'SEQERA_RUNS_DUMP' { container = 'tower-cli:0.9.2--23fa648bc78102d6' } }
}
3 changes: 0 additions & 3 deletions modules/nf-core/multiqc/main.nf
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9 changes: 8 additions & 1 deletion modules/nf-core/multiqc/nextflow.config
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37 changes: 27 additions & 10 deletions nextflow.config
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Expand Up @@ -64,13 +64,10 @@ profiles {
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.build.repository = 'quay.io/seqeralabs/nf-aggregate'
seqera_containers {
wave.enabled = true
wave.freeze = true
wave.strategy = ['conda', 'container', 'dockerfile', 'spack']
wave.strategy = ['conda']
}
conda {
conda.enabled = true
Expand Down Expand Up @@ -102,8 +99,18 @@ profiles {
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
docker_arm64 { // Identical to above, but used by Seqera Containers config files at module level
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
process.arch = 'linux/arm64'
}
singularity {
singularity.enabled = true
Expand All @@ -115,6 +122,16 @@ profiles {
charliecloud.enabled = false
apptainer.enabled = false
}
singularity_arm64 { // Identical to above, but used by Seqera Containers config files at module level
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
Expand Down Expand Up @@ -162,10 +179,10 @@ profiles {
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
apptainer.registry = 'oras://community.wave.seqera.io/library'
docker.registry = 'community.wave.seqera.io/library'
podman.registry = 'community.wave.seqera.io/library'
singularity.registry = 'oras://community.wave.seqera.io/library'

// Nextflow plugins
plugins {
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