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chore: bump images and point to branch build
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adthrasher committed Jan 31, 2025
1 parent 5deaa18 commit e0f765d
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Showing 14 changed files with 27 additions and 27 deletions.
2 changes: 1 addition & 1 deletion data_structures/flag_filter.wdl
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Expand Up @@ -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
}
}
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4 changes: 2 additions & 2 deletions data_structures/read_group.wdl
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Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
8 changes: 4 additions & 4 deletions tools/bwa.wdl
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Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
2 changes: 1 addition & 1 deletion tools/estimate.wdl
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Expand Up @@ -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
}
}
2 changes: 1 addition & 1 deletion tools/htseq.wdl
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Expand Up @@ -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
}
}
2 changes: 1 addition & 1 deletion tools/md5sum.wdl
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Expand Up @@ -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
}
}
4 changes: 2 additions & 2 deletions tools/star.wdl
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Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
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12 changes: 6 additions & 6 deletions tools/util.wdl
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Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
Expand Down Expand Up @@ -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
}
}
2 changes: 1 addition & 1 deletion workflows/dnaseq/dnaseq-standard-fastq.wdl
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Expand Up @@ -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
}
}
2 changes: 1 addition & 1 deletion workflows/dnaseq/dnaseq-standard.wdl
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Expand Up @@ -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
}
}
8 changes: 4 additions & 4 deletions workflows/methylation/methylation-cohort.wdl
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Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion workflows/methylation/methylation-preprocess.wdl
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion workflows/qc/quality-check-standard.wdl
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Expand Up @@ -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
}
}
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2 changes: 1 addition & 1 deletion workflows/rnaseq/rnaseq-standard.wdl
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Expand Up @@ -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
}
}

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