Mercurial > repos > kkonganti > cfsan_cronology

changeset 14:9e80528263c4

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 17:32:05 -0400
parents 1e6a6e88db16
children 7c0407ebbdf3
files 0.2.0/modules/download_ref_genome/main.nf
diffstat 1 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/0.2.0/modules/download_ref_genome/main.nf	Mon Jul 15 16:26:46 2024 -0400
+++ b/0.2.0/modules/download_ref_genome/main.nf	Mon Jul 15 17:32:05 2024 -0400
@@ -5,8 +5,8 @@
     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
     conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.10.4' :
-        'quay.io/biocontainers/python:3.10.4' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-datasets-pylib:15.31.1--pyhdfd78af_0' :
+        'staphb/ncbi-datasets:15.31.1' }"
 
     input:
         val meta
@@ -23,6 +23,8 @@
         def args = task.ext.args ?: ''
         prefix   = task.ext.prefix ?: "${meta.id}"
         """
+        [ -e /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE=/usr/local/ssl/cacert.pem
+
         datasets download genome accession --assembly-version latest --include genome,gff3 ${meta.id}
 
         unzip ncbi_dataset.zip