From 8a59468ac70ae84ee5ccd7cb5969f6f14852dbbc Mon Sep 17 00:00:00 2001 From: mbdabrowska1 Date: Wed, 13 Mar 2024 15:06:02 +0000 Subject: [PATCH] Updates all Singularity containers --- conf/modules.config | 1 + modules/local/draft_selection/main.nf | 2 +- modules/local/full_classification.nf | 2 +- modules/local/get_abundance/main.nf | 2 +- modules/local/join_results.nf | 2 +- modules/local/kmer_freqs/main.nf | 2 +- modules/local/medaka_pass.nf | 2 +- modules/local/racon_pass.nf | 2 +- modules/local/read_clustering/main.nf | 3 ++- modules/local/samplesheet_check.nf | 2 +- modules/local/split_clusters.nf | 2 +- 11 files changed, 12 insertions(+), 10 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 1c58ebc..07de064 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -75,6 +75,7 @@ process { "--min_cluster_size ${params.min_cluster_size}", "--cluster_sel_epsilon ${params.cluster_sel_epsilon}" ].join(' ').trim() + containerOptions = "--env NUMBA_CACHE_DIR=/tmp" } withName: CANU_CORRECTION { diff --git a/modules/local/draft_selection/main.nf b/modules/local/draft_selection/main.nf index e3ef15c..9fbe65e 100755 --- a/modules/local/draft_selection/main.nf +++ b/modules/local/draft_selection/main.nf @@ -4,7 +4,7 @@ process DRAFT_SELECTION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://quay.io/biocontainers/fastani:1.34--h4dfc31f_1' : 'biocontainers/fastani:1.34--h4dfc31f_1' }" input: diff --git a/modules/local/full_classification.nf b/modules/local/full_classification.nf index 4fa2ebf..1522dce 100644 --- a/modules/local/full_classification.nf +++ b/modules/local/full_classification.nf @@ -3,7 +3,7 @@ process FULL_CLASSIFICATION { conda "bioconda::kraken2 rdptools blast" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://mbdabrowska1/full-classification:1.0' : 'docker.io/mbdabrowska1/full-classification:1.0' }" input: diff --git a/modules/local/get_abundance/main.nf b/modules/local/get_abundance/main.nf index 41d7a95..b0d17f3 100644 --- a/modules/local/get_abundance/main.nf +++ b/modules/local/get_abundance/main.nf @@ -4,7 +4,7 @@ process GET_ABUNDANCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://mbdabrowska1/get-abundance:1.0' : 'docker.io/mbdabrowska1/get-abundance:1.0' }" input: diff --git a/modules/local/join_results.nf b/modules/local/join_results.nf index c65493a..0f8df02 100644 --- a/modules/local/join_results.nf +++ b/modules/local/join_results.nf @@ -4,7 +4,7 @@ process JOIN_RESULTS { conda "bioconda::grep=3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://ubuntu' : 'docker.io/ubuntu' }" input: diff --git a/modules/local/kmer_freqs/main.nf b/modules/local/kmer_freqs/main.nf index f09658e..479acdb 100644 --- a/modules/local/kmer_freqs/main.nf +++ b/modules/local/kmer_freqs/main.nf @@ -3,7 +3,7 @@ process KMER_FREQS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://mbdabrowska1/kmer_freqs:1.0' : 'docker.io/mbdabrowska1/kmer_freqs:1.0' }" input: diff --git a/modules/local/medaka_pass.nf b/modules/local/medaka_pass.nf index 652faf2..2cb1bf4 100644 --- a/modules/local/medaka_pass.nf +++ b/modules/local/medaka_pass.nf @@ -3,7 +3,7 @@ process MEDAKA_PASS { conda "bioconda::medaka=1.4.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://quay.io/biocontainers/medaka:1.4.4--py38h130def0_0' : 'biocontainers/medaka:1.4.4--py38h130def0_0' }" input: diff --git a/modules/local/racon_pass.nf b/modules/local/racon_pass.nf index 8518c7b..a8d295c 100644 --- a/modules/local/racon_pass.nf +++ b/modules/local/racon_pass.nf @@ -3,7 +3,7 @@ process RACON_PASS { conda "bioconda::minimap2 racon" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://mbdabrowska1/racon-pass:1.0' : 'docker.io/mbdabrowska1/racon-pass:1.0' }" input: diff --git a/modules/local/read_clustering/main.nf b/modules/local/read_clustering/main.nf index 1f41ec1..1b97f23 100644 --- a/modules/local/read_clustering/main.nf +++ b/modules/local/read_clustering/main.nf @@ -4,7 +4,7 @@ process READ_CLUSTERING { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://mbdabrowska1/read-clustering:1.0' : 'docker.io/mbdabrowska1/read-clustering:1.0' }" input: @@ -20,6 +20,7 @@ process READ_CLUSTERING { def args = task.ext.args ?: '' """ + echo "starting clustering" umap_hdbscan.py \\ --infile ${freqs} \\ --outfile ${prefix}_hdbscan_output \\ diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index be070af..e192fb0 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -4,7 +4,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.8.3 pandas openpyxl pathlib" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : + 'docker://mbdabrowska1/samplesheet-check:1.0.2' : 'docker.io/mbdabrowska1/samplesheet-check:1.0.2' }" input: diff --git a/modules/local/split_clusters.nf b/modules/local/split_clusters.nf index dff3255..fd739b6 100644 --- a/modules/local/split_clusters.nf +++ b/modules/local/split_clusters.nf @@ -4,7 +4,7 @@ process SPLIT_CLUSTERS { conda "bioconda::seqtk" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/grep:3.4--hf43ccf4_4' : + 'docker://quay.io/biocontainers/seqtk:1.4--he4a0461_1' : 'biocontainers/seqtk:1.4--he4a0461_1' }" input: