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[read_QC_trim_ONT] add additional inputs for user modification (#702)
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* expose optional inputs for all the things

* ugh documentation is not the funnest activity

* fix multiple declarations

* update docs accordingly

* standardize the capitalization

* fix that broken header finally
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@sage-wright
sage-wright authored Jan 6, 2025
1 parent 604cdf2 commit dd7d021
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49 changes: 43 additions & 6 deletions docs/workflows/genomic_characterization/theiacov.md
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| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
|---|---|---|---|---|
| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.3.0 | Yes, some optional features incompatible | Sample-level |
| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB vX.X.X | Yes, some optional features incompatible | Sample-level |

## TheiaCoV Workflows

Expand Down Expand Up @@ -110,7 +110,7 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)

<div class="searchable-table" markdown="1">

| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |* | **Organism** |
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | **Workflow** | **Organism** |
|---|---|---|---|---|---|---|---|
| theiacov_clearlabs | **primer_bed** | File | The bed file containing the primers used when sequencing was performed | | Required | CL | sars-cov-2 |
| theiacov_clearlabs | **read1** | File | Read data produced by the Clear Dx platform from ClearLabs | | Required | CL | sars-cov-2 |
Expand Down Expand Up @@ -336,15 +336,52 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
| raw_check_reads | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| raw_check_reads | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/bactopia/gather_samples:2.0.2 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| raw_check_reads | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 2 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **artic_guppyplex_cpu** | Int | Number of CPUs to allocate to the task | 8 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **artic_guppyplex_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **artic_guppyplex_docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **artic_guppyplex_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 16 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **bbduk_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **call_kraken** | Boolean | True/False variable that determines if the Kraken2 task should be called. | FALSE | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **call_kraken** | Boolean | True/False variable that determines if the Kraken2 task should be called. | FALSE | Optional | PE, SE, ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **call_midas** | Boolean | True/False variable that determines if the MIDAS task should be called. | TRUE | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **downsampling_coverage** | Float | The desired coverage to sub-sample the reads to with RASUSA | 150 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **fastp_args** | String | Additional fastp task arguments | --detect_adapter_for_pe -g -5 20 -3 20 | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_db** | File | The database used to run Kraken2. Must contain viral and human sequences. | "gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz" | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_db** | File | The database used to run Kraken2. Must contain viral and human sequences. | "gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz" | Optional | ONT, PE, SE, ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_docker_image** | Int | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db" | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **kraken_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **midas_db** | File | The database used by the MIDAS task | gs://theiagen-public-files-rp/terra/theiaprok-files/midas/midas_db_v1.2.tar.gz | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1" | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_max_read_length** | Int | The maximum read length to keep after trimming | 100000 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_max_read_qual** | Int | The maximum read quality to keep after trimming | 40 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 2 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_min_read_length** | Int | The minimum read length to keep after trimming | 500 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **nanoq_min_read_qual** | Int | The minimum read quality to keep after trimming | 10 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **ncbi_scrub_cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **ncbi_scrub_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **ncbi_scrub_docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1" | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **ncbi_scrub_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| 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_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 | |
| read_QC_trim | **rasusa_seed** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **tiptoft_cpu** | Int | Internal component, do not modify | 2 | Optional | ONT | |
| read_QC_trim | **tiptoft_disk_size** | Int | Internal component, do not modify | 100 | Optional | ONT | |
| read_QC_trim | **tiptoft_docker** | String | Internal component, do not modify | "us-docker.pkg.dev/general-theiagen/staphb/tiptoft:1.0.2" | Optional | ONT | |
| read_QC_trim | **tiptoft_kmer_size** | String | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **tiptoft_margin** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **tiptoft_max_gap** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **tiptoft_memory** | Int | Internal component, do not modify | 8 | Optional | ONT | |
| read_QC_trim | **tiptoft_min_block_size** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **tiptoft_min_fasta_hits** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC-trim | **tiptoft_min_kmers_for_onex_pass** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **tiptoft_min_perc_coverage** | Int | Internal component, do not modify | | Optional | ONT | |
| read_QC_trim | **read_processing** | String | The name of the tool to perform basic read processing; options: "trimmomatic" or "fastp" | trimmomatic | Optional | PE, SE | |
| read_QC_trim | **read_qc** | String | The tool used for quality control (QC) of reads. Options are fastq_scan and fastqc | fastq_scan | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
| read_QC_trim | **target_organism** | String | Organism to search for in Kraken | | Optional | PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
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40 changes: 38 additions & 2 deletions docs/workflows/genomic_characterization/theiaprok.md
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Expand Up @@ -4,7 +4,7 @@

| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
|---|---|---|---|---|
| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.3.0 | Yes, some optional features incompatible | Sample-level |
| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB vX.X.X | Yes, some optional features incompatible | Sample-level |

## TheiaProk Workflows

Expand Down Expand Up @@ -524,6 +524,10 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
| raw_check_reads | **organism** | String | Internal component, do not modify | | Do not modify, Optional | ONT, PE, SE |
| raw_check_reads | **workflow_series** | String | Internal component, do not modify | | Do not modify, Optional | ONT, PE, SE |
| read_QC_trim | **adapters** | File | A file containing the sequence of the adapters used during library preparation, used in the BBDuk task | | Optional | PE, SE |
| read_QC_trim | **artic_guppyplex_cpu** | Int | Internal component, do not modify| 8 | Optional | ONT |
| read_QC_trim | **artic_guppyplex_disk_size** | Int | Internal component, do not modify| 100 | Optional | ONT |
| read_QC_trim | **artic_guppyplex_docker** | String | Internal component, do not modify| us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3 | Optional | ONT |
| read_QC_trim | **artic_guppyplex_memory** | Int | Internal component, do not modify| 16 | Optional | ONT |
| read_QC_trim | **bbduk_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | PE, SE |
| read_QC_trim | **call_kraken** | Boolean | Set to true to launch Kraken2; if true, you must provide a kraken_db | FALSE | Optional | ONT, PE, SE |
| read_QC_trim | **call_midas** | Boolean | Set to true to launch Midas | TRUE | Optional | PE, SE |
Expand All @@ -533,15 +537,47 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
| read_QC_trim | **kraken_cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT, PE, SE |
| read_QC_trim | **kraken_db** | File | Kraken2 database file; must be provided in call_kraken is true | | Optional | ONT, PE, SE |
| read_QC_trim | **kraken_disk_size** | Int | GB of storage to request for VM used to run the kraken2 task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database) | 100 | Optional | ONT, PE, SE |
| read_QC_trim | **kraken_docker_image** | Int | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db" | Optional | ONT |
| read_QC_trim | **kraken_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | ONT, PE, SE |
| read_QC_trim | **max_length** | Int | Internal component, do not modify | | Do not modify, Optional | ONT |
| read_QC_trim | **midas_db** | File | Midas database file | gs://theiagen-large-public-files-rp/terra/theiaprok-files/midas/midas_db_v1.2.tar.gz | Optional | PE, SE |
| read_QC_trim | **min_length** | Int | Internal component, do not modify | | Do not modify, Optional | ONT |
| read_QC_trim | **midas_db** | File | Midas database file | gs://theiagen-large-public-files-rp/terra/theiaprok-files/midas/midas_db_v1.2.tar.gz | Optional | PE, SE |
| read_QC_trim | **phix** | File | A file containing the phix used during Illumina sequencing; used in the BBDuk task | | Optional | PE, SE |
| read_QC_trim | **nanoq_cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional | ONT |
| read_QC_trim | **nanoq_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT |
| read_QC_trim | **nanoq_docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/biocontainers/nanoq:0.9.0--hec16e2b_1" | Optional | ONT |
| read_QC_trim | **nanoq_max_read_length** | Int | The maximum read length to keep after trimming | 100000 | Optional | ONT |
| read_QC_trim | **nanoq_max_read_qual** | Int | The maximum read quality to keep after trimming | 40 | Optional | ONT |
| read_QC_trim | **nanoq_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 2 | Optional | ONT |
| read_QC_trim | **nanoq_min_read_length** | Int | The minimum read length to keep after trimming | 500 | Optional | ONT |
| read_QC_trim | **nanoq_min_read_qual** | Int | The minimum read quality to keep after trimming | 10 | Optional | ONT |
| read_QC_trim | **ncbi_scrub_cpu** | Int | Internal component, do not modify| 4 | Optional | ONT |
| read_QC_trim | **ncbi_scrub_disk_size** | Int | Internal component, do not modify| 100 | Optional | ONT |
| read_QC_trim | **ncbi_scrub_docker** | String | Internal component, do not modify| "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1" | Optional | ONT |
| read_QC_trim | **ncbi_scrub_memory** | Int | Internal component, do not modify| 8 | Optional | ONT |
| 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_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 |
| read_QC_trim | **rasusa_seed** | Int | Random seed to use | | Optional | ONT |
| read_QC_trim | **read_processing** | String | Read trimming software to use, either "trimmomatic" or "fastp" | trimmomatic | Optional | PE, SE |
| read_QC_trim | **read_qc** | String | Allows the user to decide between fastq_scan (default) and fastqc for the evaluation of read quality. | fastq_scan | Optional | PE, SE |
| read_QC_trim | **run_prefix** | String | Internal component, do not modify | | Do not modify, Optional | ONT |
| read_QC_trim | **target_organism** | String | This string is searched for in the kraken2 outputs to extract the read percentage | | Optional | ONT, PE, SE |
| read_QC_trim | **tiptoft_cpu** | Int | Number of CPUs to allocate to the task | 2 | Optional | ONT |
| read_QC_trim | **tiptoft_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT |
| read_QC_trim | **tiptoft_docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/staphb/tiptoft:1.0.2" | Optional | ONT |
| read_QC_trim | **tiptoft_kmer_size** | String | The kmer size | | Optional | ONT |
| read_QC_trim | **tiptoft_margin** | Int | Flanking region around a block to use for mapping | | Optional | ONT |
| read_QC_trim | **tiptoft_max_gap** | Int | Maximum gap for blocks to be contiguous, measured in multiples of the kmer size | | Optional | ONT |
| read_QC_trim | **tiptoft_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | ONT |
| read_QC_trim | **tiptoft_min_block_size** | Int | Minimum block size in bases | | Optional | ONT |
| read_QC_trim | **tiptoft_min_fasta_hits** | Int | Minimum number of kmers matching a read | | Optional | ONT
| read_QC-trim | **tiptoft_min_kmers_for_onex_pass** | Int | Minimum number of kmers matching a read in 1st pass | | Optional | ONT |
| read_QC_trim | **tiptoft_min_perc_coverage** | Int | Minimum percentage ocoverage o typing sequence to report | | Optional | ONT |
| read_QC_trim | **trimmomatic_args** | String | Additional arguments to pass to trimmomatic. "-phred33" specifies the Phred Q score encoding which is almost always phred33 with modern sequence data. | -phred33 | Optional | PE, SE |
| resfinder_task | **acquired** | Boolean | Set to true to tell ResFinder to identify acquired resistance genes | TRUE | Optional | FASTA, ONT, PE, SE |
| resfinder_task | **call_pointfinder** | Boolean | Set to true to enable detection of point mutations. | FALSE | Optional | FASTA, ONT, PE, SE |
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