Updates all Singularity containers

sheffield-bioinformatics-core · Mar 13, 2024 · 8a59468 · 8a59468
1 parent 7774cb3
commit 8a59468
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Showing 11 changed files with 12 additions and 10 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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: