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Add singularity profile #89

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Add singularity profile #89

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cb78005
Add singularity profile
jennyfothergill Nov 18, 2023
e675cd4
Add singularity mounts
jennyfothergill Nov 18, 2023
c483ad9
Set paths for test dbs
jennyfothergill Nov 18, 2023
37c955a
Try adding container/conda to each process
jennyfothergill Nov 20, 2023
32ecebc
Remove container/conda lines
jennyfothergill Nov 20, 2023
0ca6f57
Try "mixed" profile, update blast container
jennyfothergill Nov 20, 2023
b5b5378
Remove unnecessary mixed profile
jennyfothergill Nov 20, 2023
00ca0bb
Return max_cpus to 2
jennyfothergill Nov 20, 2023
abdfb33
Remove added space
jennyfothergill Nov 20, 2023
75163de
Return docker enabled to true
jennyfothergill Nov 20, 2023
ed55fc9
Update docstring
jennyfothergill Nov 20, 2023
5a549fe
Add singularity profile to docs
jennyfothergill Nov 20, 2023
5170c8e
Fix docker consensus_classification container
jennyfothergill Nov 20, 2023
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Remove unnecessary mixed profile
@jennyfothergill
jennyfothergill committed Nov 20, 2023
commit b5b5378589888f44ed60b88972ad9a5ddbdf97ce
23 changes: 0 additions & 23 deletions nextflow.config
View file
Original file line number Diff line number Diff line change
@@ -131,29 +131,6 @@ profiles {
withName: output_documentation { container = 'docker://hecrp/nanoclust-output_documentation' }
}
}
mixed {
singularity.enabled = true
conda.enabled = true
singularity.autoMounts = true
process {
withName: demultiplex { container = 'docker://hecrp/nanoclust-demultiplex' }
withName: demultiplex_porechop { container = 'docker://hecrp/nanoclust-demultiplex_porechop' }
withName: QC { container = 'docker://hecrp/nanoclust-qc' }
withName: fastqc { container = 'docker://hecrp/nanoclust-fastqc' }
withName: multiqc { container = 'docker://hecrp/nanoclust-fastqc' }
withName: kmer_freqs { container = 'docker://hecrp/nanoclust-kmer_freqs' }
withName: read_clustering { container = 'docker://hecrp/nanoclust-read_clustering' }
withName: split_by_cluster { container = 'docker://hecrp/nanoclust-split_by_cluster' }
withName: read_correction { container = 'docker://hecrp/nanoclust-read_correction' }
withName: draft_selection { container = 'docker://hecrp/nanoclust-draft_selection' }
withName: racon_pass { container = 'docker://hecrp/nanoclust-racon_pass' }
withName: medaka_pass { container = 'docker://hecrp/nanoclust-medaka_pass' }
withName: consensus_classification { conda = "$baseDir/conda_envs/consensus_classification/environment.yml" }
withName: get_abundances { container = 'docker://hecrp/nanoclust-plot_abundances' }
withName: plot_abundances { container = 'docker://hecrp/nanoclust-plot_abundances' }
withName: output_documentation { container = 'docker://hecrp/nanoclust-output_documentation' }
}
}
}