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Seqera containers: POC 5 #47

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Seqera containers: POC 5 #47

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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
2499af7
POC 5 - includeCondig in script alongside include
ewels Jun 18, 2024
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1 change: 0 additions & 1 deletion modules/local/plot_run_gantt/main.nf
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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 @@ -6,4 +6,11 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}

profiles {
docker { process.withName: 'PLOT_RUN_GANTT' { container = 'community.wave.seqera.io/library/click_pandas_plotly_express_typing:21adb9e2d1b605a5' } }
docker_arm64 { process.withName: 'PLOT_RUN_GANTT' { container = 'community.wave.seqera.io/library/click_pandas_plotly_express_typing:2e5e17c7ed2d1115' } }
singularity { process.withName: 'PLOT_RUN_GANTT' { container = 'oras://community.wave.seqera.io/library/click_pandas_plotly_express_typing:a4af841350996386' } }
Comment on lines +12 to +15
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We don't need withName selectors

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This file is being loaded by the top level pipeline, as part of the regular pipeline config. So I think we do?

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yeah, that's why I asked for module config, otherwise this is almost the same as proposal 4

singularity_arm64 { process.withName: 'PLOT_RUN_GANTT' { container = 'oras://community.wave.seqera.io/library/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 @@ -9,3 +9,10 @@ process {
]
}
}

profiles {
docker { process.withName: 'SEQERA_RUNS_DUMP' { container = 'community.wave.seqera.io/library/tower-cli:0.9.2--dc544a7e574ab73b' } }
docker_arm64 { process.withName: 'SEQERA_RUNS_DUMP' { container = 'community.wave.seqera.io/library/tower-cli:0.9.2--104eab7c00912b48' } }
singularity { process.withName: 'SEQERA_RUNS_DUMP' { container = 'oras://community.wave.seqera.io/library/tower-cli:0.9.2--810270aea7c40770' } }
singularity_arm64 { process.withName: 'SEQERA_RUNS_DUMP' { container = 'oras://community.wave.seqera.io/library/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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12 changes: 3 additions & 9 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 @@ -103,7 +100,7 @@ profiles {
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 Down Expand Up @@ -184,9 +181,6 @@ env {
TOWER_ACCESS_TOKEN = "$TOWER_ACCESS_TOKEN"
}

// Load Nextflow config for nf_aggregate workflow
includeConfig 'workflows/nf_aggregate/nextflow.config'

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

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4 changes: 4 additions & 0 deletions workflows/nf_aggregate/main.nf
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Expand Up @@ -3,8 +3,12 @@
//

include { SEQERA_RUNS_DUMP } from '../../modules/local/seqera_runs_dump'
includeConfig '../../modules/local/seqera_runs_dump/nextflow.config'
include { PLOT_RUN_GANTT } from '../../modules/local/plot_run_gantt'
includeConfig '../../modules/local/plot_run_gantt/nextflow.config'
include { MULTIQC } from '../../modules/nf-core/multiqc'
includeConfig '../../modules/nf-core/multiqc/nextflow.config'

Comment on lines +6 to +11
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Are you proposing this new syntax? It is not currently supported

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Hah, not intentionally

include { paramsSummaryMultiqc } from '../../subworkflows/local/utils_nf_aggregate'
include { getProcessVersions } from '../../subworkflows/local/utils_nf_aggregate'
include { getWorkflowVersions } from '../../subworkflows/local/utils_nf_aggregate'
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3 changes: 0 additions & 3 deletions workflows/nf_aggregate/nextflow.config
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