diff --git a/conf/podman.config b/conf/podman.config new file mode 100644 index 00000000..65490367 --- /dev/null +++ b/conf/podman.config @@ -0,0 +1,22 @@ +process { + + //---------------------------------------------- + // Custom containers for all deps. + //---------------------------------------------- + + withName: + 'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' { + container = "ghcr.io/torch-consortium/magma/magma-container-1:1.1.0" + } + + withName: + 'BWA.*|IQTREE.*|SNPDISTS.*|SNPSITES.*|BCFTOOLS.*|BGZIP.*|SAMTOOLS.*|SNPEFF.*|CLUSTERPICKER.*' { + container = "ghcr.io/torch-consortium/magma/magma-container-2:1.1.0" + } + +} + + +podman { + enabled = true +} diff --git a/nextflow.config b/nextflow.config index a83f443a..9f1ad15c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -57,6 +57,7 @@ profiles { // Package management specific settings conda_local { includeConfig 'conf/conda_local.config' } docker { includeConfig 'conf/docker.config' } + podman { includeConfig 'conf/podman.config' } // Executor specific settings pbs { includeConfig 'conf/pbs.config' }