[RASUSA] update from 0.7.0 -> 2.1.0 (#731)

* update rasusa container, stage for testing * [Update] Change rasusa Docker container version to 2.1.0 in documentation * use new version subcommands and fail hard * conform to rasusa update argument standards * update last know changes * update last know changes for rasusa * remove space for fomatting * ambiguous version to enable future update * fix broken link * stage rasusa for next version update --------- Co-authored-by: xonq <[email protected]>
theiagen · Jan 29, 2025 · 5a7c9ab · 5a7c9ab
1 parent 4f9bb14
commit 5a7c9ab
Show file tree

Hide file tree

Showing 8 changed files with 19 additions and 16 deletions.
diff --git a/docs/workflows/genomic_characterization/theiacov.md b/docs/workflows/genomic_characterization/theiacov.md
@@ -366,7 +366,7 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | read_QC_trim | **rasusa_bases** | String | Internal component, do not modify | | Optional | ONT | |
 | read_QC_trim | **rasusa_cpu** | Int | Internal component, do not modify | 4 | Optional | ONT | |
 | read_QC_trim | **rasusa_disk_size** | Int | Internal component, do not modify | 100 | Optional | ONT | |
-| read_QC_trim | **rasusa_docker** | String | Internal component, do not modify | "us-docker.pkg.dev/general-theiagen/staphb/rasusa:0.7.0" | Optional | ONT | |
+| read_QC_trim | **rasusa_docker** | String | Internal component, do not modify | "us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0" | Optional | ONT | |
 | read_QC_trim | **rasusa_fraction_of_reads** | Float | Internal component, do not modify | | Optional | ONT | |
 | read_QC_trim | **rasusa_memory** | Int | Internal component, do not modify | 8 | Optional | ONT | |
 | read_QC_trim | **rasusa_number_of_reads** | Int | Internal component, do not modify | | Optional | ONT | |

diff --git a/docs/workflows/genomic_characterization/theiaeuk.md b/docs/workflows/genomic_characterization/theiaeuk.md
@@ -117,7 +117,7 @@ All input reads are processed through "core tasks" in each workflow. The core ta
 | rasusa_task | **bases** | String | Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB |  | Optional |
 | rasusa_task | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional |
 | rasusa_task | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
-| rasusa_task | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/rasusa:0.7.0 | Optional |
+| rasusa_task | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0 | Optional |
 | rasusa_task | **frac** | Float | Subsample to a fraction of the reads |  | Optional |
 | rasusa_task | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional |
 | rasusa_task | **num** | Int | Subsample to a specific number of reads |  | Optional |

diff --git a/docs/workflows/genomic_characterization/theiaprok.md b/docs/workflows/genomic_characterization/theiaprok.md
@@ -562,7 +562,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | read_QC_trim | **rasusa_bases** | String | Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB. If this option is given, --coverage and --genome-size are ignored | | Optional | ONT |
 | read_QC_trim | **rasusa_cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT |
 | read_QC_trim | **rasusa_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT |
-| read_QC_trim | **rasusa_docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/rasusa:0.7.0" | Optional | ONT |
+| read_QC_trim | **rasusa_docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0" | Optional | ONT |
 | read_QC_trim | **rasusa_fraction_of_reads** | Float | Subsample to a fraction of the reads - e.g., 0.5 samples half the reads | | Optional | ONT |
 | read_QC_trim | **rasusa_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | ONT |
 | read_QC_trim | **rasusa_number_of_reads** | Int | Subsample to a specific number of reads | | Optional | ONT |

diff --git a/docs/workflows/standalone/rasusa.md b/docs/workflows/standalone/rasusa.md
@@ -4,7 +4,7 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.0.0 | Yes | Sample-level |
+| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB vX.X.X | Yes | Sample-level |
 
 ## RASUSA_PHB
 
@@ -39,7 +39,7 @@ RASUSA functions to randomly downsample the number of raw reads to a user-define
 | rasusa_task | **bases** | String | Explicitly define the number of bases required in the downsampled reads in quotations; when used, genome size and coverage are ignored; acceptable metric suffixes include: `b`, `k`, `m`, `g`, and `t` for base, kilo, mega, giga, and tera, respectively | | Optional |
 | rasusa_task | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional |
 | rasusa_task | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
-| rasusa_task | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/rasusa:0.7.0" | Optional |
+| rasusa_task | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0" | Optional |
 | rasusa_task | **frac** | Float | Explicitly define the fraction of reads to keep in the subsample; when used, genome size and coverage are ignored; acceptable inputs include whole numbers and decimals, e.g. 50.0 will leave 50% of the reads in the subsample | | Optional |
 | rasusa_task | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional |
 | rasusa_task | **num** | Int | Optional: explicitly define the number of reads in the subsample; when used, genome size and coverage are ignored; acceptable metric suffixes include: `b`, `k`, `m`, `g`, and `t` for base, kilo, mega, giga, and tera, respectively | | Optional |

diff --git a/docs/workflows_overview/workflows_alphabetically.md b/docs/workflows_overview/workflows_alphabetically.md
@@ -32,7 +32,7 @@ title: Alphabetical Workflows
 | [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
 | [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
 | [**Pangolin_Update**](../workflows/genomic_characterization/pangolin_update.md) | Update Pangolin assignments | SARS-CoV-2, Viral | Sample-level | Yes | v2.0.0 | [Pangolin_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Pangolin_Update_PHB:main?tab=info) |
-| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
+| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | vX.X.X | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
 | [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
 | [**Samples_to_Ref_Tree**](../workflows/phylogenetic_placement/samples_to_ref_tree.md)| Use Nextclade to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Samples_to_Ref_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Samples_to_Ref_Tree_PHB:main?tab=info) |
 | [**Snippy_Streamline**](../workflows/phylogenetic_construction/snippy_streamline.md)| Implementation of Snippy workflows for phylogenetic analysis from reads, with optional dynamic reference selection | Bacteria | Set-level | Yes | vX.X.X | [Snippy_Streamline_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Streamline_PHB:main?tab=info) |

diff --git a/docs/workflows_overview/workflows_kingdom.md b/docs/workflows_overview/workflows_kingdom.md
@@ -21,7 +21,7 @@ title: Workflows by Kingdom
 | [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-level | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
 | [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | vX.X.X | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info), [Kraken2_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_ONT_PHB:main?tab=info) |
 | [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
-| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
+| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | vX.X.X | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
 | [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
 | [**SRA_Fetch**](../workflows/data_import/sra_fetch.md)| Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info) |
 | [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | vX.X.X | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |

diff --git a/docs/workflows_overview/workflows_type.md b/docs/workflows_overview/workflows_type.md
@@ -104,7 +104,7 @@ title: Workflows by Type
 | [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | vX.X.X | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info), [Kraken2_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_ONT_PHB:main?tab=info) |
 | [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
 | [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
-| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
+| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | vX.X.X | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
 | [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
 | [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.3.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?tab=info) |
 | [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |

diff --git a/tasks/utilities/task_rasusa.wdl b/tasks/utilities/task_rasusa.wdl
@@ -9,7 +9,7 @@ task rasusa {
     File read1
     File? read2
     String samplename
-    String docker = "us-docker.pkg.dev/general-theiagen/staphb/rasusa:0.7.0"
+    String docker = "us-docker.pkg.dev/general-theiagen/staphb/rasusa:2.1.0"
     Int disk_size = 100
     Int cpu = 4
     Int memory = 8
@@ -28,28 +28,31 @@ task rasusa {
     Int? num 
   }
   command <<<
+    # fail hard
+    set -euo pipefail
     rasusa --version | tee VERSION
     # set single-end or paired-end outputs
     if [ -z "~{read2}" ]; then
-      OUTPUT_FILES="~{samplename}_subsampled_R1.fastq.gz"
+      OUTPUT_FILES="-o ~{samplename}_subsampled_R1.fastq.gz"
     else
-      OUTPUT_FILES="~{samplename}_subsampled_R1.fastq.gz ~{samplename}_subsampled_R2.fastq.gz"
+      OUTPUT_FILES="-o ~{samplename}_subsampled_R1.fastq.gz -o ~{samplename}_subsampled_R2.fastq.gz"
     fi
-    # ignore coverage values if frac input provided
+    # ignore coverage and genome length if frac input provided
     if [ -z "~{frac}" ]; then
       COVERAGE="--coverage ~{coverage} --genome-size ~{genome_length}"
     else
       COVERAGE=""
     fi
-    # run rasusa
-    rasusa \
-      -i ~{read1} ~{read2} \
+
+    # run rasusa for read sampling
+    rasusa reads \
       ${COVERAGE} \
       ~{'--seed ' + seed} \
       ~{'--bases ' + bases} \
       ~{'--frac ' + frac} \
       ~{'--num ' + num} \
-      -o ${OUTPUT_FILES}
+      ${OUTPUT_FILES} \
+      ~{read1} ~{read2}
   >>>
   output {
     File read1_subsampled = "~{samplename}_subsampled_R1.fastq.gz"