diff --git a/.gitignore b/.gitignore index b436d83..2e7ada0 100644 --- a/.gitignore +++ b/.gitignore @@ -20,5 +20,6 @@ tests/subset.bam nextflow_schema.json_old dockers smrtlink_dockers +slim_smrtlink_dockers bin/fix_rg_ids.py bin/fix_rg_ids.sh \ No newline at end of file diff --git a/README.md b/README.md index 7332788..c5f5821 100644 --- a/README.md +++ b/README.md @@ -45,7 +45,7 @@ All docker containers used in this pipeline are publicly available. - *multiqc*: quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0 - *python*: python:3.12-bookworm - *pandas*: quay.io/biocontainers/pandas:1.5.2 -- *smrttools*: seqwell/smrttools:26.1.0 (docker-only; used by `CREATE_XML` to run PacBio SMRT Tools' `dataset create` CLI) +- *smrttools*: seqwell/smrttools:26.1.0-slim (docker-only; used by `CREATE_XML` to run PacBio SMRT Tools' `dataset create` CLI) ## Conda Environment diff --git a/nextflow.config b/nextflow.config index ef06293..932243a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -155,7 +155,7 @@ process { withName: CREATE_XML { memory = '8.0G' cpus = 2 - container = 'seqwell/smrttools:26.1.0' + container = 'seqwell/smrttools:26.1.0-slim' } publishDir = [ path: { "${params.output}/${meta.pool_ID}/xml" },