diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl index 0b9d39ed..88f811f6 100644 --- a/data_structures/flag_filter.wdl +++ b/data_structures/flag_filter.wdl @@ -118,7 +118,7 @@ task validate_string_is_12bit_oct_dec_or_hex { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } diff --git a/data_structures/read_group.wdl b/data_structures/read_group.wdl index 94a655c4..c4461597 100644 --- a/data_structures/read_group.wdl +++ b/data_structures/read_group.wdl @@ -104,7 +104,7 @@ task read_group_to_string { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } @@ -441,7 +441,7 @@ task validate_read_group { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 0 } } diff --git a/tools/bwa.wdl b/tools/bwa.wdl index a9cdefc0..000f1680 100644 --- a/tools/bwa.wdl +++ b/tools/bwa.wdl @@ -86,7 +86,7 @@ task bwa_aln { cpu: ncpu memory: "5 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/bwa:0.7.17-2" + container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2" maxRetries: 1 } } @@ -187,7 +187,7 @@ task bwa_aln_pe { cpu: ncpu memory: "17 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/bwa:0.7.17-2" + container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2" maxRetries: 1 } } @@ -283,7 +283,7 @@ task bwa_mem { cpu: ncpu memory: "25 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/bwa:0.7.17-2" + container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2" maxRetries: 1 } } @@ -334,7 +334,7 @@ task build_bwa_db { runtime { memory: "5 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/bwa:0.7.17-2" + container: "ghcr.io/stjudecloud/bwa:branch-update_images-0.7.17-2" maxRetries: 1 } } diff --git a/tools/estimate.wdl b/tools/estimate.wdl index e49bea44..62c7b5ca 100644 --- a/tools/estimate.wdl +++ b/tools/estimate.wdl @@ -51,7 +51,7 @@ task run_estimate { runtime { memory: "~{memory_gb} GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/estimate:2.0.0" + container: "ghcr.io/stjudecloud/estimate:branch-update_images-2.0.0" maxRetries: max_retries } } diff --git a/tools/htseq.wdl b/tools/htseq.wdl index fccdfe2a..1cafc101 100755 --- a/tools/htseq.wdl +++ b/tools/htseq.wdl @@ -209,7 +209,7 @@ task calc_tpm { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } diff --git a/tools/md5sum.wdl b/tools/md5sum.wdl index 0aa70ae9..912c157f 100755 --- a/tools/md5sum.wdl +++ b/tools/md5sum.wdl @@ -36,7 +36,7 @@ task compute_checksum { runtime { memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } diff --git a/tools/star.wdl b/tools/star.wdl index b088263c..99b25ff8 100755 --- a/tools/star.wdl +++ b/tools/star.wdl @@ -127,7 +127,7 @@ task build_star_db { cpu: ncpu memory: "~{memory_gb} GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:2.7.11b-5" + container: "ghcr.io/stjudecloud/star:branch-update_images-2.7.11b-5" maxRetries: 1 } } @@ -833,7 +833,7 @@ task alignment { cpu: ncpu memory: "50 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:2.7.11b-5" + container: "ghcr.io/stjudecloud/star:branch-update_images-2.7.11b-5" maxRetries: 1 } } diff --git a/tools/util.wdl b/tools/util.wdl index 4a203f5c..67bf828a 100644 --- a/tools/util.wdl +++ b/tools/util.wdl @@ -42,7 +42,7 @@ task download { runtime { memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } @@ -139,7 +139,7 @@ task split_string { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } @@ -363,7 +363,7 @@ task unpack_tarball { runtime { memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } @@ -683,7 +683,7 @@ task global_phred_scores { runtime { memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } @@ -761,7 +761,7 @@ task qc_summary { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } @@ -822,7 +822,7 @@ task split_fastq { cpu: ncpu memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:2.0.0" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } diff --git a/workflows/dnaseq/dnaseq-standard-fastq.wdl b/workflows/dnaseq/dnaseq-standard-fastq.wdl index 26e88c47..40d97f15 100644 --- a/workflows/dnaseq/dnaseq-standard-fastq.wdl +++ b/workflows/dnaseq/dnaseq-standard-fastq.wdl @@ -159,7 +159,7 @@ task parse_input { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 0 } } diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl index 5e39d9c6..abda03a0 100644 --- a/workflows/dnaseq/dnaseq-standard.wdl +++ b/workflows/dnaseq/dnaseq-standard.wdl @@ -136,7 +136,7 @@ task parse_input { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 0 } } diff --git a/workflows/methylation/methylation-cohort.wdl b/workflows/methylation/methylation-cohort.wdl index 43c490e4..85fd7754 100644 --- a/workflows/methylation/methylation-cohort.wdl +++ b/workflows/methylation/methylation-cohort.wdl @@ -124,7 +124,7 @@ task combine_data { } runtime { - container: "ghcr.io/stjudecloud/pandas:2.2.1-3" + container: "ghcr.io/stjudecloud/pandas:branch-update_images-2.2.1-3" memory: "~{memory_gb} GB" cpu: 1 disks: "~{disk_size_gb} GB" @@ -170,7 +170,7 @@ task filter_probes { } runtime { - container: "ghcr.io/stjudecloud/pandas:2.2.1-3" + container: "ghcr.io/stjudecloud/pandas:branch-update_images-2.2.1-3" memory: "8 GB" cpu: 1 disks: "~{disk_size_gb} GB" @@ -209,7 +209,7 @@ task generate_umap { } runtime { - container: "ghcr.io/stjudecloud/umap:0.5.7-4" + container: "ghcr.io/stjudecloud/umap:branch-update_images-0.5.7-4" memory: "8 GB" cpu: 1 disks: "~{disk_size_gb} GB" @@ -244,7 +244,7 @@ task plot_umap { } runtime { - container: "ghcr.io/stjudecloud/python-plotting:2.0.0" + container: "ghcr.io/stjudecloud/python-plotting:branch-update_images-2.0.0" memory: "4 GB" cpu: 1 disks: "4 GB" diff --git a/workflows/methylation/methylation-preprocess.wdl b/workflows/methylation/methylation-preprocess.wdl index 9d0477a9..6f08920f 100644 --- a/workflows/methylation/methylation-preprocess.wdl +++ b/workflows/methylation/methylation-preprocess.wdl @@ -53,7 +53,7 @@ task process_raw_idats { } runtime { - container: "ghcr.io/stjudecloud/minfi:1.48.0-2" + container: "ghcr.io/stjudecloud/minfi:branch-update_images-1.48.0-2" memory: "8 GB" cpu: 1 disks: "~{disk_size_gb} GB" diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl index 4bb01a97..61d37f71 100644 --- a/workflows/qc/quality-check-standard.wdl +++ b/workflows/qc/quality-check-standard.wdl @@ -557,7 +557,7 @@ task parse_input { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } } diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl index ae87e045..bc1bade4 100755 --- a/workflows/rnaseq/rnaseq-standard.wdl +++ b/workflows/rnaseq/rnaseq-standard.wdl @@ -179,7 +179,7 @@ task parse_input { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.5.1" + container: "ghcr.io/stjudecloud/util:branch-update_images-2.0.0" maxRetries: 1 } }