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Fix redundant containers #11276

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Fix redundant containers #11276

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28d895d
Fix redundant containers
SPPearce Apr 23, 2026
d01c75f
Merge branch 'master' into adjust_repeated_containers
SPPearce Apr 23, 2026
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4 changes: 1 addition & 3 deletions modules/nf-core/clair3/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,7 @@ process CLAIR3 {
label 'process_high'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'docker.io/hkubal/clair3:v2.0.0' :
'docker.io/hkubal/clair3:v2.0.0' }"
container "docker.io/hkubal/clair3:v2.0.0"

input:
tuple val(meta), path(bam), path(bai), val(packaged_model), path(user_model), val(platform)
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1 change: 0 additions & 1 deletion modules/nf-core/traitar/pfamget/environment.yml
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@@ -1,6 +1,5 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
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2 changes: 1 addition & 1 deletion modules/nf-core/traitar/pfamget/main.nf
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Expand Up @@ -4,7 +4,7 @@ process TRAITAR_PFAMGET {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' :
'oras://community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:9b929a08d061b63d' :
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@famosab famosab Apr 23, 2026

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should this be swapped to https?

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@SPPearce SPPearce Apr 23, 2026

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I couldn't figure out how to get that from the wave-cli :|
We have a lot of oras links in the repository already.

'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' }"

output:
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2 changes: 1 addition & 1 deletion modules/nf-core/traitar/run/main.nf
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Expand Up @@ -4,7 +4,7 @@ process TRAITAR {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' :
'oras://community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:9b929a08d061b63d' :
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@famosab famosab Apr 23, 2026

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same here

'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' }"

input:
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