diff --git a/docs/workflows/standalone/dorado_basecalling.md b/docs/workflows/standalone/dorado_basecalling.md index 3b7726295..30a9d2d5c 100644 --- a/docs/workflows/standalone/dorado_basecalling.md +++ b/docs/workflows/standalone/dorado_basecalling.md @@ -27,6 +27,21 @@ Automatic Detection: When set to sup, hac, or fast, Dorado will automatically se - `dna_r10.4.1_e8.2_400bps_hac@v4.2.0` - `dna_r10.4.1_e8.2_400bps_fast@v4.2.0` +??? Info "Supported Kit Names" + + Ensure you use an accepted kit name in the `kit_name` parameter. The following kit names are supported in Dorado: + + ``` + EXP-NBD103, EXP-NBD104, EXP-NBD114, EXP-NBD114-24, EXP-NBD196, EXP-PBC001, EXP-PBC096, + SQK-16S024, SQK-16S114-24, SQK-LWB001, SQK-MLK111-96-XL, SQK-MLK114-96-XL, SQK-NBD111-24, + SQK-NBD111-96, SQK-NBD114-24, SQK-NBD114-96, SQK-PBK004, SQK-PCB109, SQK-PCB110, SQK-PCB111-24, + SQK-PCB114-24, SQK-RAB201, SQK-RAB204, SQK-RBK001, SQK-RBK004, SQK-RBK110-96, SQK-RBK111-24, + SQK-RBK111-96, SQK-RBK114-24, SQK-RBK114-96, SQK-RLB001, SQK-RPB004, SQK-RPB114-24, + TWIST-16-UDI, TWIST-96A-UDI, VSK-PTC001, VSK-VMK001, VSK-VMK004, VSK-VPS001 + ``` + + Select from these options to avoid input errors. + ### Inputs | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | diff --git a/mkdocs.yml b/mkdocs.yml index 2bd8e7d19..18ff9f3a9 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -52,7 +52,7 @@ nav: - Zip_Column_Content: workflows/data_export/zip_column_content.md - Standalone: - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md - - Dorado_Bsecalling: workflows/standalone/dorado_basecalling.md + - Dorado_Basecalling: workflows/standalone/dorado_basecalling.md - GAMBIT_Query: workflows/standalone/gambit_query.md - Kraken2: workflows/standalone/kraken2.md - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md diff --git a/tasks/basecalling/task_dorado_basecall.wdl b/tasks/basecalling/task_dorado_basecall.wdl index 631984c99..424a9d644 100644 --- a/tasks/basecalling/task_dorado_basecall.wdl +++ b/tasks/basecalling/task_dorado_basecall.wdl @@ -12,7 +12,7 @@ task basecall { } command <<< - set -e + set -euo pipefail # Create output directory for SAM files sam_output="output/sam/" @@ -48,4 +48,6 @@ task basecall { disk: disk_size + " GB" gpuCount: 1 gpuType: "nvidia-tesla-t4" } + preemptible: 0 + maxRetries: 1 } diff --git a/tasks/basecalling/task_dorado_demux.wdl b/tasks/basecalling/task_dorado_demux.wdl index cfb62c8a7..af4855f1c 100644 --- a/tasks/basecalling/task_dorado_demux.wdl +++ b/tasks/basecalling/task_dorado_demux.wdl @@ -7,12 +7,12 @@ task dorado_demux { String fastq_file_name Int cpu = 4 Int memory = 16 - Int disk_size = 50 + Int disk_size = 100 String docker = "us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.0" } command <<< - set -e + set -euo pipefail echo "### Starting Dorado demux ###" date @@ -90,5 +90,7 @@ task dorado_demux { cpu: cpu memory: "~{memory} GB" disks: "local-disk ~{disk_size} SSD" + preemptible: 0 + maxRetries: 1 } } diff --git a/tasks/basecalling/task_samtools_convert.wdl b/tasks/basecalling/task_samtools_convert.wdl index 83a3a6d4f..7e1dc184b 100644 --- a/tasks/basecalling/task_samtools_convert.wdl +++ b/tasks/basecalling/task_samtools_convert.wdl @@ -10,7 +10,7 @@ task samtools_convert { } command <<< - set -e + set -euo pipefail bam_output="output/bam/" mkdir -p $bam_output @@ -20,7 +20,7 @@ task samtools_convert { bam_file="${bam_output}/${base_name}.bam" echo "Converting SAM to BAM: $sam_file -> $bam_file" - samtools view -bS "$sam_file" > "$bam_file" || { echo "ERROR: samtools failed to convert $sam_file to BAM" >&2; exit 1; } + samtools view -@ ~{cpu} -bS "$sam_file" > "$bam_file" || { echo "ERROR: samtools failed to convert $sam_file to BAM" >&2; exit 1; } echo "Conversion successful: $bam_file" done @@ -36,6 +36,6 @@ task samtools_convert { docker: docker cpu: cpu memory: "~{memory} GB" - disks: "local-disk ~{disk_size} HDD" + disks: "local-disk ~{disk_size} SSD" } } diff --git a/workflows/utilities/data_import/wf_update_srr_metadata.wdl b/workflows/utilities/data_import/wf_update_srr_metadata.wdl new file mode 100644 index 000000000..9a62c9619 --- /dev/null +++ b/workflows/utilities/data_import/wf_update_srr_metadata.wdl @@ -0,0 +1,22 @@ +version 1.0 + +import "../../../tasks/utilities/data_handling/task_fetch_srr_metadata.wdl" as srr_task + +workflow wf_retrieve_srr { + meta { + description: "This workflow retrieves the Sequence Read Archive (SRA) accession (SRR) associated with a given sample accession. It uses the fastq-dl tool to fetch metadata from SRA and outputs the SRR accession that can be used for downstream analysis." + } + input { + String sample_accession + String retrieve_srr_docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0" + } + + call srr_task.fetch_srr_metadata { + input: + sample_accession = sample_accession, + docker = retrieve_srr_docker + } + output { + String srr_accession = fetch_srr_metadata.srr_accession + } +} \ No newline at end of file