[Tiptoft] Deprecate Tiptoft

docs/workflows/genomic_characterization/theiacov.md

@@ -371,17 +371,6 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | 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 |

docs/workflows/genomic_characterization/theiaprok.md

@@ -279,9 +279,6 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | export_taxon_tables | **theiaprok_illumina_se_version** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, ONT, PE |
 | export_taxon_tables | **theiaprok_ont_analysis_date** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, PE, SE |
 | export_taxon_tables | **theiaprok_ont_version** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, PE, SE |
-| export_taxon_tables | **tiptoft_plasmid_replicon_fastq** | File | Internal component, do not modify |  | Do not modify, Optional | FASTA, PE, SE |
-| export_taxon_tables | **tiptoft_plasmid_replicon_genes** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, PE, SE |
-| export_taxon_tables | **tiptoft_version** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, PE, SE |
 | export_taxon_tables | **trimmomatic_version** | String | Internal component, do not modify |  | Do not modify, Optional | FASTA, ONT |
 | gambit | **cpu** | Int | Number of CPUs to allocate to the task | 8 | Optional | FASTA, ONT, PE, SE |
 | gambit | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | FASTA, ONT, PE, SE |
@@ -571,17 +568,6 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | 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 |
@@ -838,7 +824,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 
     **Read subsampling:** Samples are automatically randomly subsampled to 150X coverage using `RASUSA`.
 
-    **Plasmid prediction:** `tiptoft`  is used to predict plasmid sequences directly from uncorrected long-read data. Plasmids are identified using replicon sequences used for typing from [PlasmidFinder](https://cge.food.dtu.dk/services/PlasmidFinder/).
+    **Plasmid prediction:** Plasmids are identified using replicon sequences used for typing from [PlasmidFinder](https://cge.food.dtu.dk/services/PlasmidFinder/).
 
     **Read filtering:** Reads are filtered by length and quality using `nanoq`. By default, sequences with less than 500 basepairs and quality score lower than 10 are filtered out to improve assembly accuracy.
 
@@ -849,9 +835,9 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
         | Workflow | **TheiaProk_ONT** |
         | --- | --- |
         | Sub-workflow | [wf_read_QC_trim_ont.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_read_QC_trim_ont.wdl) |
-        | Tasks | [task_nanoplot.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/basic_statistics/task_nanoplot.wdl) [task_fastq_scan.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/basic_statistics/task_fastq_scan.wdl) [task_rasusa.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/utilities/task_rasusa.wdl) [task_nanoq.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/read_filtering/task_nanoq.wdl) [task_tiptoft.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/gene_typing/plasmid_detection/task_tiptoft.wdl) |
-        | Software Source Code | [fastq-scan](https://github.com/rpetit3/fastq-scan), [NanoPlot](https://github.com/wdecoster/NanoPlot), [RASUSA](https://github.com/mbhall88/rasusa), [tiptoft](https://github.com/andrewjpage/tiptoft), [nanoq](https://github.com/esteinig/nanoq) |
-        | Original Publication(s) | [NanoPlot paper](https://academic.oup.com/bioinformatics/article/39/5/btad311/7160911)<br>[RASUSA paper](https://doi.org/10.21105/joss.03941)<br>[Nanoq Paper](https://doi.org/10.21105/joss.02991)<br>[Tiptoft paper](https://doi.org/10.21105/joss.01021) |
+        | Tasks | [task_nanoplot.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/basic_statistics/task_nanoplot.wdl) [task_fastq_scan.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/basic_statistics/task_fastq_scan.wdl) [task_rasusa.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/utilities/task_rasusa.wdl) [task_nanoq.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/quality_control/read_filtering/task_nanoq.wdl)
+        | Software Source Code | [fastq-scan](https://github.com/rpetit3/fastq-scan), [NanoPlot](https://github.com/wdecoster/NanoPlot), [RASUSA](https://github.com/mbhall88/rasusa), [nanoq](https://github.com/esteinig/nanoq) |
+        | Original Publication(s) | [NanoPlot paper](https://academic.oup.com/bioinformatics/article/39/5/btad311/7160911)<br>[RASUSA paper](https://doi.org/10.21105/joss.03941)<br>[Nanoq Paper](https://doi.org/10.21105/joss.02991)<br> |
 
 ??? task "`dragonflye`: _De novo_ Assembly"
     !!! techdetails "dragonflye Technical Details"
@@ -2103,9 +2089,6 @@ The TheiaProk workflows automatically activate taxa-specific sub-workflows after
 | theiaprok_illumina_se_version | String | Version of TheiaProk SE workflow execution | SE |
 | theiaprok_ont_analysis_date | String | Date of TheiaProk ONT workflow execution | ONT |
 | theiaprok_ont_version | String | Version of TheiaProk ONT workflow execution | ONT |
-| tiptoft_plasmid_replicon_fastq | File | File produced by tiptoft that contains reads containing plasmid rep/inc genes | ONT |
-| tiptoft_plasmid_replicon_genes | String | Rep/inc genes found in sample | ONT |
-| tiptoft_version | String | Version of tiptoft used for analysis | ONT |
 | trimmomatic_docker | String | Docker image used for trimmomatic | PE, SE |
 | trimmomatic_version | String | Version of trimmomatic used | PE, SE |
 | ts_mlst_allelic_profile | String | Profile of MLST loci and allele numbers predicted by MLST | FASTA, ONT, PE, SE |

tasks/utilities/data_export/task_broad_terra_tools.wdl

@@ -81,9 +81,6 @@ task export_taxon_tables {
     Float? nanoplot_r1_median_q_clean
     Float? nanoplot_r1_est_coverage_clean
     String? rasusa_version
-    File? tiptoft_plasmid_replicon_fastq
-    String? tiptoft_plasmid_replicon_genes
-    String? tiptoft_version
     File? assembly_fasta
     File? contigs_gfa
     String? dragonflye_version
@@ -497,9 +494,6 @@ task export_taxon_tables {
       "nanoplot_r1_median_q_clean": "~{nanoplot_r1_median_q_clean}",
       "nanoplot_r1_est_coverage_clean": "~{nanoplot_r1_est_coverage_clean}",
       "rasusa_version": "~{rasusa_version}",
-      "tiptoft_plasmid_replicon_fastq": "~{tiptoft_plasmid_replicon_fastq}",
-      "tiptoft_plasmid_replicon_genes": "~{tiptoft_plasmid_replicon_genes}",
-      "tiptoft_version": "~{tiptoft_version}",
       "assembly_fasta": "~{assembly_fasta}",
       "contigs_gfa": "~{contigs_gfa}",
       "dragonflye_version": "~{dragonflye_version}",

tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml

@@ -512,7 +512,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl
       md5sum: 64caaaff5910ac0036e2659434500962
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
-      md5sum: 8c97c5bd65e2787239f12ef425d479ae
+      md5sum: 59e18911ba07c16e01df38abe0e70477
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
       md5sum: 9b8e2da62c8572a369c786a9bbc3a36e
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl

tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml

@@ -483,7 +483,7 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl
       md5sum: 64caaaff5910ac0036e2659434500962
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
-      md5sum: 8c97c5bd65e2787239f12ef425d479ae
+      md5sum: 59e18911ba07c16e01df38abe0e70477
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
       md5sum: 02dc0075bf28d557d7b81aa2dc61feab
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl

workflows/theiaprok/wf_theiaprok_ont.wdl

@@ -276,9 +276,6 @@ workflow theiaprok_ont {
               nanoplot_r1_median_q_clean = nanoplot_clean.median_q,
               nanoplot_r1_est_coverage_clean = nanoplot_clean.est_coverage,
               rasusa_version = read_qc_trim.rasusa_version,
-              tiptoft_plasmid_replicon_fastq = read_qc_trim.tiptoft_plasmid_replicon_fastq,
-              tiptoft_plasmid_replicon_genes = read_qc_trim.tiptoft_plasmid_replicon_genes,
-              tiptoft_version = read_qc_trim.tiptoft_version,
               assembly_fasta = dragonflye.assembly_fasta,
               contigs_gfa = dragonflye.contigs_gfa,
               dragonflye_version = dragonflye.dragonflye_version,
@@ -589,10 +586,6 @@ workflow theiaprok_ont {
     String? kraken_docker = read_qc_trim.kraken_docker
     # Read QC - rasusa outputs
     String? rasusa_version = read_qc_trim.rasusa_version
-    # Read QC - tiptoft outputs
-    File? tiptoft_plasmid_replicon_fastq = read_qc_trim.tiptoft_plasmid_replicon_fastq
-    String? tiptoft_plasmid_replicon_genes = read_qc_trim.tiptoft_plasmid_replicon_genes
-    String? tiptoft_version = read_qc_trim.tiptoft_version
     # Assembly - dragonflye outputs
     File? assembly_fasta = dragonflye.assembly_fasta
     File? contigs_gfa = dragonflye.contigs_gfa

workflows/utilities/wf_read_QC_trim_ont.wdl

@@ -1,6 +1,5 @@
 version 1.0
 
-import "../../tasks/gene_typing/plasmid_detection/task_tiptoft.wdl" as tiptoft_task
 import "../../tasks/quality_control/read_filtering/task_artic_guppyplex.wdl" as artic_guppyplex
 import "../../tasks/quality_control/read_filtering/task_nanoq.wdl" as nanoq_task
 import "../../tasks/quality_control/read_filtering/task_ncbi_scrub.wdl" as ncbi_scrub
@@ -9,7 +8,7 @@ import "../../tasks/utilities/task_rasusa.wdl" as rasusa_task
 
 workflow read_QC_trim_ont {
   meta {
-    description: "Runs basic QC on Oxford Nanopore (ONT) reads with nanoplot, rasusa downsampling, tiptoft plasmid detection, and nanoq filtering"
+    description: "Runs basic QC on Oxford Nanopore (ONT) reads with nanoplot, rasusa downsampling, and nanoq filtering"
   }
   input {
     String samplename
@@ -59,19 +58,6 @@ workflow read_QC_trim_ont {
     Float? rasusa_fraction_of_reads
     Int? rasusa_number_of_reads
 
-    # tiptoft inputs
-    Int? tiptoft_cpu
-    Int? tiptoft_disk_size
-    String? tiptoft_docker
-    Int? tiptoft_memory
-    Int? tiptoft_kmer_size
-    Int? tiptoft_max_gap
-    Int? tiptoft_margin
-    Int? tiptoft_min_block_size
-    Int? tiptoft_min_fasta_hits
-    Int? tiptoft_min_kmers_for_onex_pass
-    Int? tiptoft_min_perc_coverage
-
     # nanoq inputs
     Int? nanoq_cpu
     Int? nanoq_disk_size
@@ -179,23 +165,6 @@ workflow read_QC_trim_ont {
         seed = rasusa_seed
 
     }
-    # tiptoft for plasmid detection
-    call tiptoft_task.tiptoft {
-      input:
-        read1 = read1,
-        samplename = samplename,
-        cpu = tiptoft_cpu,
-        disk_size = tiptoft_disk_size,
-        docker = tiptoft_docker,
-        kmer_size = tiptoft_kmer_size,
-        margin = tiptoft_margin,
-        max_gap = tiptoft_max_gap,
-        memory = tiptoft_memory,
-        min_block_size = tiptoft_min_block_size,
-        min_fasta_hits = tiptoft_min_fasta_hits,
-        min_kmers_for_onex_pass = tiptoft_min_kmers_for_onex_pass,
-        min_perc_coverage = tiptoft_min_perc_coverage
-    }  
     # nanoq/filtlong (default min length 500)
     call nanoq_task.nanoq {
       input:
@@ -239,11 +208,5 @@ workflow read_QC_trim_ont {
 
     # rasusa outputs
     String? rasusa_version = rasusa.rasusa_version  
-
-    # tiptoft outputs
-    File? tiptoft_plasmid_replicon_fastq = tiptoft.tiptoft_plasmid_replicon_fastq
-    File? tiptoft_result_tsv = tiptoft.tiptoft_tsv
-    String? tiptoft_plasmid_replicon_genes = tiptoft.plasmid_replicon_genes
-    String? tiptoft_version = tiptoft.tiptoft_version
   }
 }