diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl index 42e1c8af7..3f1f0826e 100644 --- a/data_structures/flag_filter.wdl +++ b/data_structures/flag_filter.wdl @@ -107,7 +107,7 @@ task validate_string_is_12bit_int { >>> runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/data_structures/read_group.wdl b/data_structures/read_group.wdl index 13238121c..eadb9edc1 100644 --- a/data_structures/read_group.wdl +++ b/data_structures/read_group.wdl @@ -138,7 +138,7 @@ task get_read_groups { runtime { disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -356,7 +356,7 @@ task validate_read_group { >>> runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -412,7 +412,7 @@ task inner_read_group_to_string { } runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/docker/python-plotting/Dockerfile b/docker/python-plotting/Dockerfile index dbb74f753..3b5a1b1c8 100644 --- a/docker/python-plotting/Dockerfile +++ b/docker/python-plotting/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.14.2-alpine +FROM python:3.14.3-alpine RUN apk add --no-cache bash diff --git a/docker/python-plotting/package.json b/docker/python-plotting/package.json index 1fc0df903..490c74a47 100644 --- a/docker/python-plotting/package.json +++ b/docker/python-plotting/package.json @@ -1,4 +1,4 @@ { "name": "python-plotting", - "version": "2.0.8" + "version": "2.0.9" } \ No newline at end of file diff --git a/docker/umap/Dockerfile b/docker/umap/Dockerfile index 452d55829..74b7d304c 100644 --- a/docker/umap/Dockerfile +++ b/docker/umap/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.14.2-alpine +FROM python:3.14.3-alpine # Downstream requires llvm20, but that is out-of-date # llvm20 installs with the -20 suffix, so we need to symlink diff --git a/docker/umap/package.json b/docker/umap/package.json index 71cfaf371..9d36e56c7 100644 --- a/docker/umap/package.json +++ b/docker/umap/package.json @@ -1,5 +1,5 @@ { "name": "umap", "version": "0.5.7", - "revision": "11" + "revision": "12" } \ No newline at end of file diff --git a/docker/util/package.json b/docker/util/package.json index a30115713..ac48e5fa7 100644 --- a/docker/util/package.json +++ b/docker/util/package.json @@ -1,4 +1,4 @@ { "name": "util", - "version": "3.0.2" + "version": "3.0.3" } \ No newline at end of file diff --git a/tools/htseq.wdl b/tools/htseq.wdl index c71d93260..6245c0077 100755 --- a/tools/htseq.wdl +++ b/tools/htseq.wdl @@ -190,7 +190,7 @@ task calc_tpm { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/tools/md5sum.wdl b/tools/md5sum.wdl index b63752891..9d11a34e4 100755 --- a/tools/md5sum.wdl +++ b/tools/md5sum.wdl @@ -35,7 +35,7 @@ task compute_checksum { runtime { disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/tools/util.wdl b/tools/util.wdl index db3b53cb3..0b081b65b 100644 --- a/tools/util.wdl +++ b/tools/util.wdl @@ -41,7 +41,7 @@ task download { runtime { disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -80,7 +80,7 @@ task split_string { } runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -128,7 +128,7 @@ task calc_feature_lengths { runtime { memory: "16 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -247,7 +247,7 @@ task unpack_tarball { runtime { disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -351,7 +351,7 @@ task global_phred_scores { runtime { memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -398,7 +398,7 @@ task check_fastq_and_rg_concordance { >>> runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } @@ -462,7 +462,7 @@ task split_fastq { cpu: ncpu memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl index 149e95c5d..3d4ff774a 100644 --- a/workflows/dnaseq/dnaseq-standard.wdl +++ b/workflows/dnaseq/dnaseq-standard.wdl @@ -158,7 +158,7 @@ task parse_input { >>> runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/workflows/methylation/methylation-cohort.wdl b/workflows/methylation/methylation-cohort.wdl index 54e55f033..946a41ba6 100644 --- a/workflows/methylation/methylation-cohort.wdl +++ b/workflows/methylation/methylation-cohort.wdl @@ -285,7 +285,7 @@ task generate_umap { } runtime { - container: "ghcr.io/stjudecloud/umap:0.5.7-11" + container: "ghcr.io/stjudecloud/umap:0.5.7-12" memory: "8 GB" cpu: 1 disks: "~{disk_size_gb} GB" @@ -325,7 +325,7 @@ task plot_umap { cpu: 1 memory: "4 GB" disks: "4 GB" - container: "ghcr.io/stjudecloud/python-plotting:2.0.8" + container: "ghcr.io/stjudecloud/python-plotting:2.0.9" maxRetries: 1 } } diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl index 9ae9d52f0..5115d3f90 100644 --- a/workflows/qc/quality-check-standard.wdl +++ b/workflows/qc/quality-check-standard.wdl @@ -547,7 +547,7 @@ task parse_input { } runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } } diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl index f138d2704..edac26733 100755 --- a/workflows/rnaseq/rnaseq-standard.wdl +++ b/workflows/rnaseq/rnaseq-standard.wdl @@ -181,7 +181,7 @@ task parse_input { >>> runtime { - container: "ghcr.io/stjudecloud/util:3.0.2" + container: "ghcr.io/stjudecloud/util:3.0.3" maxRetries: 1 } }