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fix: bump fastp memory requirements #284

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fix: bump fastp memory requirements #284

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652ac5d
WIP
a-frantz Nov 13, 2025
32e381c
perf: bump picard.mark_duplicates mem for small bams
a-frantz Nov 13, 2025
7b54a3c
Revert "WIP"
a-frantz Nov 24, 2025
3fe55e6
perf: bump mem again
a-frantz Nov 29, 2025
1ca768a
fix: bump fastp memory
a-frantz Dec 9, 2025
c11ddcb
Merge branch 'main' into sprocket-work
a-frantz Dec 9, 2025
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16 changes: 8 additions & 8 deletions tools/fastp.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ task fastp {
first_n_reads: "Only process the first `n` reads. `first_n_reads = 0` for processing entire input."
duplicate_accuracy: {
description: "Accuracy level to calculate duplication.",
help: "Value must be between 1 and 6 inclusive. Higher levels use more memory (by default: 2 GB, 4 GB, 6 GB, 12 GB, 20 GB, 32 GB).",
help: "Value must be between 1 and 6 inclusive. Higher levels use more memory (by default: 4 GB, 6 GB, 8 GB, 14 GB, 22 GB, 34 GB).",
}
n_base_limit: {
description: "If one read's number of N base(s) is `>n_base_limit`, then this read/pair is discarded.",
Expand Down Expand Up @@ -137,12 +137,12 @@ task fastp {
}

Map[Int, String] dup_acc_to_mem = {
1: "2 GB",
2: "4 GB",
3: "6 GB",
4: "12 GB",
5: "20 GB",
6: "32 GB",
1: "4 GB",
2: "6 GB",
3: "8 GB",
4: "14 GB",
5: "22 GB",
6: "34 GB",
}

Float input_size = size(read_one_fastq, "GB") + size(read_two_fastq, "GB")
Expand Down Expand Up @@ -221,7 +221,7 @@ task fastp {
cpu: ncpu
memory: (
if disable_duplicate_eval
then "2 GB"
then "4 GB"
else dup_acc_to_mem[duplicate_accuracy]
)
disks: "~{disk_size_gb} GB"
Expand Down
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