From 652ac5de021c50761ae47035ed8e3a0b5fb75cec Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Wed, 12 Nov 2025 18:22:18 -0600 Subject: [PATCH 1/5] WIP --- tools/qualimap.wdl | 6 ++++-- workflows/qc/multiqc_config/multiqc_config.yaml | 2 ++ 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/tools/qualimap.wdl b/tools/qualimap.wdl index 67cd89d14..ef2002020 100755 --- a/tools/qualimap.wdl +++ b/tools/qualimap.wdl @@ -77,12 +77,14 @@ task rnaseq { rm "$gtf_name" tar -czf "~{out_tar_gz}" "~{prefix}" + + mv "~{prefix}/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" \ + coverage_profile_along_genes_total.txt >>> output { File raw_summary = "~{prefix}/rnaseq_qc_results.txt" - File raw_coverage - = "~{prefix}/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" + File raw_coverage = "coverage_profile_along_genes_total.txt" File results = out_tar_gz } diff --git a/workflows/qc/multiqc_config/multiqc_config.yaml b/workflows/qc/multiqc_config/multiqc_config.yaml index e3cca6e2d..c53aa15e5 100644 --- a/workflows/qc/multiqc_config/multiqc_config.yaml +++ b/workflows/qc/multiqc_config/multiqc_config.yaml @@ -185,5 +185,7 @@ sp: fn: "*.instrument.tsv" ngsderive/junction_annotation: fn: "*.junction_summary.tsv" + qualimap/rnaseq/coverage: + fn: "coverage_profile_along_genes_total.txt" samtools/flagstat: fn: "*.flagstat.txt" From 32e381cd4ec19210174ff839468808366644db4d Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Thu, 13 Nov 2025 15:32:54 -0600 Subject: [PATCH 2/5] perf: bump picard.mark_duplicates mem for small bams --- tools/picard.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/picard.wdl b/tools/picard.wdl index 07324ebe2..063099861 100755 --- a/tools/picard.wdl +++ b/tools/picard.wdl @@ -83,7 +83,7 @@ task mark_duplicates { } Float bam_size = size(bam, "GiB") - Int memory_gb = min(ceil(bam_size + 6), 50) + modify_memory_gb + Int memory_gb = min(ceil(bam_size + 10), 50) + modify_memory_gb Int disk_size_gb = ( ( if create_bam From 7b54a3c75913300facbdd3ab8c8a273fd99aa8ae Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Mon, 24 Nov 2025 13:00:10 -0600 Subject: [PATCH 3/5] Revert "WIP" This reverts commit 652ac5de021c50761ae47035ed8e3a0b5fb75cec. --- tools/qualimap.wdl | 6 ++---- workflows/qc/multiqc_config/multiqc_config.yaml | 2 -- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/tools/qualimap.wdl b/tools/qualimap.wdl index ef2002020..67cd89d14 100755 --- a/tools/qualimap.wdl +++ b/tools/qualimap.wdl @@ -77,14 +77,12 @@ task rnaseq { rm "$gtf_name" tar -czf "~{out_tar_gz}" "~{prefix}" - - mv "~{prefix}/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" \ - coverage_profile_along_genes_total.txt >>> output { File raw_summary = "~{prefix}/rnaseq_qc_results.txt" - File raw_coverage = "coverage_profile_along_genes_total.txt" + File raw_coverage + = "~{prefix}/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" File results = out_tar_gz } diff --git a/workflows/qc/multiqc_config/multiqc_config.yaml b/workflows/qc/multiqc_config/multiqc_config.yaml index c53aa15e5..e3cca6e2d 100644 --- a/workflows/qc/multiqc_config/multiqc_config.yaml +++ b/workflows/qc/multiqc_config/multiqc_config.yaml @@ -185,7 +185,5 @@ sp: fn: "*.instrument.tsv" ngsderive/junction_annotation: fn: "*.junction_summary.tsv" - qualimap/rnaseq/coverage: - fn: "coverage_profile_along_genes_total.txt" samtools/flagstat: fn: "*.flagstat.txt" From 3fe55e6abe04182e834e01702d596d6a56343e93 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Sat, 29 Nov 2025 14:47:09 -0600 Subject: [PATCH 4/5] perf: bump mem again --- tools/picard.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/picard.wdl b/tools/picard.wdl index 063099861..8f35947d1 100755 --- a/tools/picard.wdl +++ b/tools/picard.wdl @@ -83,7 +83,7 @@ task mark_duplicates { } Float bam_size = size(bam, "GiB") - Int memory_gb = min(ceil(bam_size + 10), 50) + modify_memory_gb + Int memory_gb = min(ceil(bam_size + 12), 50) + modify_memory_gb Int disk_size_gb = ( ( if create_bam From 1ca768a5d6aa09c1b63e35eeb3c8728a8cdba892 Mon Sep 17 00:00:00 2001 From: Ari Frantz Date: Tue, 9 Dec 2025 14:49:32 -0600 Subject: [PATCH 5/5] fix: bump fastp memory --- tools/fastp.wdl | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/tools/fastp.wdl b/tools/fastp.wdl index 62763b1ab..42b78e34e 100644 --- a/tools/fastp.wdl +++ b/tools/fastp.wdl @@ -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.", @@ -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") @@ -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"