From fedae7a31a0b9327098962c8a16f14b92105b816 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 3 May 2024 13:39:08 -0400 Subject: [PATCH 1/4] bugfix for exposing optional param for WDL 1.1 interp of optionals --- pipes/WDL/workflows/classify_single.wdl | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/workflows/classify_single.wdl b/pipes/WDL/workflows/classify_single.wdl index 42de1fac0..897267b6d 100644 --- a/pipes/WDL/workflows/classify_single.wdl +++ b/pipes/WDL/workflows/classify_single.wdl @@ -23,6 +23,9 @@ workflow classify_single { File kraken2_db_tgz File krona_taxonomy_db_kraken2_tgz + + Array[String] deplete_taxonomic_names = ["Vertebrata"] + Array[String] unwanted_taxonomic_names = ["Vertebrata", "other sequences", "Bacteria"] } parameter_meta { @@ -96,7 +99,7 @@ workflow classify_single { classified_reads_txt_gz = kraken2.kraken2_reads_report, ncbi_taxonomy_db_tgz = ncbi_taxdump_tgz, exclude_taxa = true, - taxonomic_names = ["Vertebrata"], + taxonomic_names = deplete_taxonomic_names, out_filename_suffix = "hs_depleted" } call reports.fastqc as fastqc_cleaned { @@ -108,7 +111,7 @@ workflow classify_single { classified_reads_txt_gz = kraken2.kraken2_reads_report, ncbi_taxonomy_db_tgz = ncbi_taxdump_tgz, exclude_taxa = true, - taxonomic_names = ["Vertebrata", "other sequences", "Bacteria"], + taxonomic_names = unwanted_taxonomic_names, out_filename_suffix = "acellular" } call read_utils.rmdup_ubam { From 1e7b2860f01a527bcda47c19a1ab79425f2b5be3 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 3 May 2024 13:42:55 -0400 Subject: [PATCH 2/4] rename new inputs to be consistent with the metagenomic_denovo workflow --- pipes/WDL/workflows/classify_single.wdl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pipes/WDL/workflows/classify_single.wdl b/pipes/WDL/workflows/classify_single.wdl index 897267b6d..fb950a16d 100644 --- a/pipes/WDL/workflows/classify_single.wdl +++ b/pipes/WDL/workflows/classify_single.wdl @@ -24,8 +24,8 @@ workflow classify_single { File kraken2_db_tgz File krona_taxonomy_db_kraken2_tgz - Array[String] deplete_taxonomic_names = ["Vertebrata"] - Array[String] unwanted_taxonomic_names = ["Vertebrata", "other sequences", "Bacteria"] + Array[String] taxa_to_dehost = ["Vertebrata"] + Array[String] taxa_to_avoid_assembly = ["Vertebrata", "other sequences", "Bacteria"] } parameter_meta { @@ -99,7 +99,7 @@ workflow classify_single { classified_reads_txt_gz = kraken2.kraken2_reads_report, ncbi_taxonomy_db_tgz = ncbi_taxdump_tgz, exclude_taxa = true, - taxonomic_names = deplete_taxonomic_names, + taxonomic_names = taxa_to_dehost, out_filename_suffix = "hs_depleted" } call reports.fastqc as fastqc_cleaned { @@ -111,7 +111,7 @@ workflow classify_single { classified_reads_txt_gz = kraken2.kraken2_reads_report, ncbi_taxonomy_db_tgz = ncbi_taxdump_tgz, exclude_taxa = true, - taxonomic_names = unwanted_taxonomic_names, + taxonomic_names = taxa_to_avoid_assembly, out_filename_suffix = "acellular" } call read_utils.rmdup_ubam { From 65dea0d63f4d3793e166989b3625312253016696 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 3 May 2024 13:46:54 -0400 Subject: [PATCH 3/4] push in an old parameterization --- pipes/WDL/tasks/tasks_read_utils.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl index 60bc8ded5..8847f07e3 100644 --- a/pipes/WDL/tasks/tasks_read_utils.wdl +++ b/pipes/WDL/tasks/tasks_read_utils.wdl @@ -173,10 +173,10 @@ task merge_and_reheader_bams { String out_basename = basename(in_bams[0], ".bam") String docker = "quay.io/broadinstitute/viral-core:2.3.1" + Int disk_size = 750 + Int machine_mem_gb = 4 } - Int disk_size = 750 - command <<< set -ex -o pipefail @@ -224,7 +224,7 @@ task merge_and_reheader_bams { runtime { docker: docker - memory: "3 GB" + memory: machine_mem_gb + " GB" cpu: 2 disks: "local-disk " + disk_size + " LOCAL" disk: disk_size + " GB" # TES From 48137287a2ae602d2d910d1008e0acd4d8eceed5 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 3 May 2024 14:15:16 -0400 Subject: [PATCH 4/4] attempt to fix build errors --- pipes/WDL/tasks/tasks_16S_amplicon.wdl | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pipes/WDL/tasks/tasks_16S_amplicon.wdl b/pipes/WDL/tasks/tasks_16S_amplicon.wdl index e68231da4..04089cf2b 100755 --- a/pipes/WDL/tasks/tasks_16S_amplicon.wdl +++ b/pipes/WDL/tasks/tasks_16S_amplicon.wdl @@ -9,7 +9,7 @@ task qiime_import_from_bam { Int memory_mb = 7000 Int cpu = 5 Int disk_size_gb = ceil(2*20) + 5 - String docker = "quay.io/broadinstitute/qiime2" + String docker = "quay.io/broadinstitute/qiime2:latest" } parameter_meta { reads_bam: { @@ -86,7 +86,7 @@ task trim_reads { Int memory_mb = 2000 Int cpu = 4 Int disk_size_gb = ceil(2*size(reads_qza, "GiB")) + 5 - String docker = "quay.io/broadinstitute/qiime2" + String docker = "quay.io/broadinstitute/qiime2:latest" } parameter_meta { reads_qza: { @@ -160,7 +160,7 @@ task join_paired_ends { Int memory_mb = 2000 Int cpu = 1 Int disk_size_gb = ceil(2*size(trimmed_reads_qza, "GiB")) + 50 - String docker = "quay.io/broadinstitute/qiime2" + String docker = "quay.io/broadinstitute/qiime2:latest" } parameter_meta{ trimmed_reads_qza: { @@ -210,7 +210,7 @@ task deblur { Int memory_mb = 2000 Int cpu = 1 Int disk_size_gb = ceil(2*size(joined_end_reads_qza, "GiB")) + 5 - String docker = "quay.io/broadinstitute/qiime2" + String docker = "quay.io/broadinstitute/qiime2:latest" } parameter_meta { joined_end_reads_qza: { @@ -288,7 +288,7 @@ task train_classifier { Int memory_mb = 2000 Int cpu = 1 Int disk_size_gb = ceil(2*size(otu_ref, "GiB")) + 5 - String docker = "quay.io/broadinstitute/qiime2" + String docker = "quay.io/broadinstitute/qiime2:latest" } parameter_meta{ otu_ref: { @@ -372,7 +372,7 @@ task tax_analysis { Int memory_mb = 5 Int cpu = 1 Int disk_size_gb = 375 - String docker = "quay.io/broadinstitute/qiime2" + String docker = "quay.io/broadinstitute/qiime2:latest" } parameter_meta{ trained_classifier: {