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Seqera containers: POC 3 #45

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Seqera containers: POC 3 #45

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5c351af
Strip out 'container' and tidy up config profiles
ewels Jun 17, 2024
04e58bf
Add container URIs to module code
ewels Jun 17, 2024
1d769ed
Use base registry in nextflow.config
ewels Jun 17, 2024
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9 changes: 8 additions & 1 deletion modules/local/plot_run_gantt/main.nf
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Original file line number Diff line number Diff line change
@@ -1,8 +1,15 @@
def mod_container = switch([workflow.containerEngine, workflow.profile]) {
case {it[0] == 'singularity' && it[1].contains('arm')} -> 'click_pandas_plotly_express_typing:3fe674b9fa7b15b8'
case {it[0] == 'singularity'} -> 'click_pandas_plotly_express_typing:a4af841350996386'
case {it[1].contains('arm')} -> 'click_pandas_plotly_express_typing:2e5e17c7ed2d1115'
default -> 'click_pandas_plotly_express_typing:21adb9e2d1b605a5'
}
Comment on lines +1 to +6
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These mod_container definitions should be wrapped into functions, as currently the formal grammar does not support global variable definitions

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Also switch expressions are not currently supported, as I would like to leave room for us to eventually provide our own pattern matching syntax

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that's yet another horrible boilerplate code. -1

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@ewels can this be moved to a config file in the module directory? it would be easier to generate that way. and the pipeline config should include it under a profile

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Interesting idea - so a module config, but that is simply imported by the pipeline config. I like it! I'll whip up a POC No.4.

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I think one goal of the new config parser is to remove custom code from the config

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I think I should be able to do it with profiles - the same as POC No.1, but just split up into config files that are bundled with the module 🤔

Dinner now but I'll try later / tomorrow.

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@ewels ewels Jun 17, 2024 •
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@bentsherman - done in #46


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'
container mod_container

input:
tuple val(meta), path(run_dump)
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9 changes: 8 additions & 1 deletion modules/local/seqera_runs_dump/main.nf
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Original file line number Diff line number Diff line change
@@ -1,9 +1,16 @@
include { getRunMetadata } from './functions'

def mod_container = switch([workflow.containerEngine, workflow.profile]) {
case {it[0] == 'singularity' && it[1].contains('arm')} -> 'tower-cli:0.9.2--5198075f4b9d6343'
case {it[0] == 'singularity'} -> 'tower-cli:0.9.2--caeb70536524603e'
case {it[1].contains('arm')} -> 'tower-cli:0.9.2--a2fbb3505faf1193'
default -> 'tower-cli:0.9.2--28258d337ec30808'
}

process SEQERA_RUNS_DUMP {
tag "$meta.id"
conda 'tower-cli=0.9.2'
container 'seqeralabs/nf-aggregate:tower-cli-0.9.2--hdfd78af_1'
container mod_container

input:
val meta
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10 changes: 7 additions & 3 deletions modules/nf-core/multiqc/main.nf
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17 changes: 7 additions & 10 deletions nextflow.config
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Original file line number Diff line number Diff line change
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 @@ -162,10 +159,10 @@ 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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