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enable conda #120

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merged 2 commits into from
May 8, 2024
Merged

enable conda #120

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8453941
enable conda
tillenglert May 3, 2024
046772d
Merge branch 'dev' into enable-conda
tillenglert May 8, 2024
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2 changes: 1 addition & 1 deletion modules/local/plot_score_distribution.nf
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Expand Up @@ -2,7 +2,7 @@ process PLOT_SCORE_DISTRIBUTION {
label 'cache_lenient'
label 'process_medium_memory'

conda "bioconda::bioconductor-alphabeta:1.8.0"
conda "bioconda::bioconductor-alphabeta=1.8.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-alphabeta:1.8.0--r41hdfd78af_0' :
'biocontainers/bioconductor-alphabeta:1.8.0--r41hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -110,7 +110,7 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
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@skrakau skrakau May 3, 2024 •
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Why did this needed to be changed? It seemed at other locations it's still used as before?

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This seems to be a silent bug since dec 2022! I already posted this on slack: https://nfcore.slack.com/archives/CE5LG7WMB/p1714721754644179

Without the conda. it is not considered for the creation of the environment! This is probably also an issue in nf-core/epitopeprediction! @jonasscheid

conda.channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
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4 changes: 0 additions & 4 deletions subworkflows/local/utils_nfcore_metapep_pipeline/main.nf
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Expand Up @@ -133,10 +133,6 @@ workflow PIPELINE_COMPLETION {
// Check and validate pipeline parameters
//
def validateInputParameters() {
// Exit if running this pipeline with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "This pipeline does not support Conda. Please use a container engine such as Docker or Singularity instead."
}
// Exit if peptide length parameters are exchanged
if (params.min_pep_len > params.max_pep_len) {
error "The minimum peptide length needs to be smaller or equal than the maximum. See 'https://nf-co.re/metapep/dev/parameters' for more information."
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