Merge branch 'CW-7265' into 'dev'
Bambu always 1 thread [CW-7265] Closes CW-7265 See merge request epi2melabs/workflows/wf-transcriptomes!285
This commit is contained in:
Sarah Griffiths
commit
d520a7635b
@ -64,14 +64,6 @@ bambu_arg_spec <- function() {
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default = "discover",
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choices = c("discover", "fixed_annotation")
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),
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list(
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name = "threads",
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flag = "--threads",
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help = "Number of worker threads.",
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type = "integer",
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default = 1L,
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min = 1L
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),
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list(
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name = "ndr",
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flag = "--ndr",
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@ -258,11 +250,13 @@ bambu_discovery_enabled <- function(args) {
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}
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bambu_build_args <- function(args, reads, annotation_obj, discovery, quant) {
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# Pin bambu to ncore=1 in all modes to avoid parallel worker instability.
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ncore <- 1L
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bambu_args <- list(
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reads = reads,
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annotations = annotation_obj,
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genome = args$genome,
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ncore = as.integer(args$threads),
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ncore = ncore,
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discovery = discovery,
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quant = quant,
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lowMemory = TRUE,
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@ -301,25 +295,6 @@ bambu_message_ndr <- function(args) {
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message(sprintf(" Current NDR = %.3f balances precision and recall", args$ndr))
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}
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}
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bambu_effective_threads <- function(args, bam_count) {
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# bambu's low-memory mode can have issues with multiple BAMs and
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# parallel threads due to BiocFileCache writes,
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# so we enforce single-threading in that case.
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threads <- as.integer(args$threads)
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if (bam_count > 1 && threads > 1L) {
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warning(
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paste(
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"Low-memory mode with multiple BAMs can fail in bambu due to",
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"parallel BiocFileCache writes; forcing threads=1."
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),
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call. = FALSE
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)
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return(1L)
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}
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threads
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}
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bambu_normalise_rc_file_list <- function(rc_files, aliases = NULL) {
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if (!is.list(rc_files)) {
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rc_files <- list(rc_files)
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@ -409,13 +384,12 @@ bambu_write_discovery_outputs <- function(out_dir, rc_files, discovered_annotati
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bambu_run_discover_mode <- function(args, analysis_fn, prepare_annotations_fn, bamfile_list_ctor) {
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inputs <- bambu_resolve_inputs(args, bamfile_list_ctor = bamfile_list_ctor)
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args$threads <- bambu_effective_threads(args, length(inputs$bam_paths))
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annotation_obj <- prepare_annotations_fn(args$annotation)
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if (length(inputs$bam_paths) > 1) {
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message(sprintf("Using BamFileList yieldSize = %d", bambu_default_yield_size))
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}
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message(sprintf("Running bambu discover setup with threads = %d", args$threads))
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message("Running bambu discover setup with ncore = 1")
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message("Generating bambu rcFiles...")
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rc_files <- bambu_call_analysis(
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analysis_fn,
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@ -101,11 +101,6 @@ testthat::test_that("invalid discovery settings rejected", {
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testthat::expect_silent(workflow_glue_r_normalise_args(args, bambu_arg_spec()))
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args$ndr <- 1
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testthat::expect_silent(workflow_glue_r_normalise_args(args, bambu_arg_spec()))
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args$ndr <- NULL
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args$threads <- "2"
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normalised <- workflow_glue_r_normalise_args(args, bambu_arg_spec())
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testthat::expect_identical(normalised$threads, 2L)
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})
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# Fail fast if --bams is empty rather than passing empty input to bambu.
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@ -259,7 +254,6 @@ testthat::test_that("bambu args include requested discovery and quant flags", {
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args <- list(
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genome = "genome.fa",
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threads = 3L,
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transcriptome_mode = "discover",
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ndr = 0.2
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)
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@ -273,7 +267,7 @@ testthat::test_that("bambu args include requested discovery and quant flags", {
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testthat::expect_true(discover$discovery)
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testthat::expect_false(discover$quant)
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testthat::expect_equal(discover$NDR, 0.2)
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testthat::expect_equal(discover$ncore, 3L)
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testthat::expect_equal(discover$ncore, 1L)
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testthat::expect_true(discover$lowMemory)
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testthat::expect_equal(discover$yieldSize, 250000L)
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@ -376,8 +370,7 @@ testthat::test_that("discover mode writes chunked rc outputs", {
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aliases = "sampleA,sampleB",
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sample_sheet = sample_sheet,
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transcriptome_mode = "discover",
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ndr = 0.25,
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threads = 2
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ndr = 0.25
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),
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bambu_arg_spec()
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)
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@ -497,8 +490,7 @@ testthat::test_that("quant mode writes chunk quantification outputs", {
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chunk_rds = chunk_rds,
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discovered_annotation_rds = discovered_annotation_rds,
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transcriptome_mode = "discover",
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ndr = NULL,
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threads = 2
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ndr = NULL
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),
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bambu_arg_spec()
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)
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@ -562,8 +554,7 @@ testthat::test_that("quant mode skips chunks with no discovered annotations on t
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chunk_rds = chunk_rds,
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discovered_annotation_rds = discovered_annotation_rds,
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transcriptome_mode = "discover",
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ndr = NULL,
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threads = 2
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ndr = NULL
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),
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bambu_arg_spec()
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)
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@ -1000,7 +991,6 @@ testthat::test_that("CLI discover writes reusable chunk artifacts", {
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"--annotation", annotation,
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"--genome", reference,
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"--transcriptome_mode", "fixed_annotation",
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"--threads", "1",
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"--out_dir", out_dir
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)
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)
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@ -1064,7 +1054,6 @@ testthat::test_that("CLI quant consumes a discover chunk", {
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"--annotation", annotation,
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"--genome", reference,
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"--transcriptome_mode", "fixed_annotation",
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"--threads", "1",
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"--out_dir", discover_out_dir
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)
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)
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@ -1089,7 +1078,6 @@ testthat::test_that("CLI quant consumes a discover chunk", {
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"--chunk_rds", manifest$rds_path[[1]],
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"--discovered_annotation_rds", file.path(discover_out_dir, "bambu_discovered_annotations.rds"),
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"--genome", reference,
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"--threads", "1",
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"--out_dir", out_dir
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)
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)
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@ -1147,7 +1135,6 @@ testthat::test_that("CLI collate consumes quant chunk directories", {
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"--annotation", annotation,
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"--genome", reference,
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"--transcriptome_mode", "fixed_annotation",
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"--threads", "1",
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"--out_dir", discover_out_dir
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)
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)
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@ -1172,7 +1159,6 @@ testthat::test_that("CLI collate consumes quant chunk directories", {
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"--chunk_rds", manifest$rds_path[[1]],
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"--discovered_annotation_rds", file.path(discover_out_dir, "bambu_discovered_annotations.rds"),
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"--genome", reference,
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"--threads", "1",
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"--out_dir", chunk_out_dir
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)
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)
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@ -5,11 +5,7 @@ OPTIONAL_FILE = file("$projectDir/data/OPTIONAL_FILE")
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process bambuDiscover {
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label "wf_transcriptomes"
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cpus {
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int requested = (params.threads ?: 4) as int
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int sampleCount = aliases instanceof Collection ? aliases.size() : 1
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sampleCount > 1 ? requested : 1
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}
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cpus 1
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memory "60 GB"
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input:
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tuple val(meta), val(aliases), path(bams, stageAs: "bams/??.bam"), path(bais, stageAs: "bams/??.bam.bai"), path(sample_sheet)
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@ -32,7 +28,6 @@ process bambuDiscover {
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--annotation "${annotation}" \
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--genome "${reference}" \
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--transcriptome_mode "${params.transcriptome_mode}" \
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--threads ${task.cpus} \
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${ndr_arg} \
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--out_dir discover
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"""
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@ -41,11 +36,7 @@ process bambuDiscover {
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process bambuQuant {
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label "wf_transcriptomes"
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cpus {
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int requested = (params.threads ?: 4) as int
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boolean isJoint = meta instanceof Map && meta.alias == 'cohort'
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isJoint ? requested : 1
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}
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cpus 1
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memory { ["8.GB", "16.GB", "48.GB"][task.attempt - 1] }
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maxRetries 2
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errorStrategy 'retry'
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@ -60,7 +51,6 @@ process bambuQuant {
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--chunk_rds "${chunk_rds}" \
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--discovered_annotation_rds "${discovered_annotation}" \
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--genome "${reference}" \
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--threads ${task.cpus} \
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--out_dir "${chunk_id}"
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"""
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}
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