-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- bin summary script and module
- Add parameter for GTDBTk mash db
- remove AA bins as they didn't meaningfully speed up downstream
processes
- Fix linting
- Add descriptions in json schema for all parameters and groups
- switch DASTOOL fastatocontig2bin to local module (faster)
- patch checkm2/predict module to rename output tsv file
- refactor bin refinement subwf to remove duplicated steps- Loading branch information
Jim Downie
committed
Dec 13, 2024
1 parent
674b4ad
commit 4cac07b
Showing
33 changed files
with
486 additions
and
588 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| #!/usr/bin/env Rscript | ||
|
|
||
| library(optparse) | ||
| library(tidyverse) | ||
|
|
||
| parser <- OptionParser() | ||
| parser <- add_option( | ||
| object = parser, | ||
| opt_str = c("-s", "--stats"), | ||
| type = "character", | ||
| action = "store", | ||
| default = NULL, | ||
| help = "Comma-separated list of TSV files output by seqkit stats", | ||
| metavar="filename" | ||
| ) | ||
|
|
||
| parser <- add_option( | ||
| object = parser, | ||
| opt_str = c("-c", "--checkm2"), | ||
| type = "character", | ||
| action = "store", | ||
| default = NULL, | ||
| help = "Comma-separated list of TSV files output by checkm2 predict", | ||
| metavar="filename" | ||
| ) | ||
|
|
||
| parser <- add_option( | ||
| object = parser, | ||
| opt_str = c("-t", "--taxonomy"), | ||
| type = "character", | ||
| action = "store", | ||
| default = NULL, | ||
| help = "Comma-separated list of TSV files output by GTDB-Tk", | ||
| metavar="filename" | ||
| ) | ||
|
|
||
| parser <- add_option( | ||
| object = parser, | ||
| opt_str = c("-o", "--prefix"), | ||
| type = "character", | ||
| action = "store", | ||
| default = "output", | ||
| help = "Output file prefix", | ||
| metavar="filename" | ||
| ) | ||
|
|
||
| parser <- add_option( | ||
| object = parser, | ||
| opt_str = c("-x", "--completeness_score"), | ||
| type = "numeric", | ||
| action = "store", | ||
| default = 5, | ||
| help = "Output file prefix", | ||
| metavar="filename" | ||
| ) | ||
|
|
||
| parser <- add_option( | ||
| object = parser, | ||
| opt_str = c("-y", "--contam_score"), | ||
| type = "numeric", | ||
| action = "store", | ||
| default = 1, | ||
| help = "Output file prefix", | ||
| metavar="filename" | ||
| ) | ||
|
|
||
| input <- parse_args(parser) | ||
|
|
||
| read_stats <- function(file) { | ||
| df <- read_tsv(file) |> | ||
| mutate( | ||
| file = str_extract(file, "(.*)\\.fa", group = 1), | ||
| assembler = str_split(file, "[\\.|_]", simplify = TRUE)[,2], | ||
| binner = str_split(file, "[\\.|_]", simplify = TRUE)[,3] | ||
| ) |> | ||
| select(bin = file, assembler, binner, num_seqs, sum_len, min_len, max_len, N50, L50 = N50_num, GC = `GC(%)`) | ||
|
|
||
| return(df) | ||
| } | ||
|
|
||
| read_checkm <- function(file) { | ||
| df <- read_tsv(file) |> | ||
| select(bin = Name, | ||
| completeness = Completeness, | ||
| contamination = Contamination, | ||
| checkm2_model = Completeness_Model_Used | ||
| ) | ||
|
|
||
| return(df) | ||
| } | ||
|
|
||
| read_taxonomy <- function(file) { | ||
| df <- read_tsv(file) | ||
| if(ncol(df) > 3) { | ||
| df <- select(df, | ||
| bin = `Genome ID`, | ||
| gtdb_classification = `GTDB classification`, | ||
| ncbi_classification = `Majority vote NCBI classification`) | ||
| } else { | ||
| df <- select(df, | ||
| bin = `Genome ID`, | ||
| gtdb_classification = `GTDB classification`, | ||
| ncbi_classification = `Majority vote NCBI classification`, | ||
| taxid) | ||
| } | ||
|
|
||
| return(df) | ||
| } | ||
|
|
||
| data <- list() | ||
| if(rlang::has_name(input, "stats")) { | ||
| stats_files <- unlist(str_split(input$stats, ",")) | ||
| stats_df <- map(stats_files, read_stats) |> list_rbind() | ||
| data <- c(data, list(stats_df)) | ||
| } else { | ||
| stop("Error: no stats file provided!") | ||
| } | ||
|
|
||
| if(rlang::has_name(input, "checkm2")) { | ||
| checkm_files <- unlist(str_split(input$checkm2, ",")) | ||
| checkm_df <- map(checkm_files, read_checkm) |> list_rbind() | ||
| data <- c(data, list(checkm_df)) | ||
| } | ||
|
|
||
| if(rlang::has_name(input, "taxonomy")) { | ||
| tax_files <- unlist(str_split(input$taxonomy, ",")) | ||
| tax_df <- map(tax_files, read_taxonomy) |> list_rbind() | ||
| data <- c(data, list(tax_df)) | ||
| } | ||
|
|
||
| summary <- reduce(data, \(x, y) left_join(x, y, by = "bin")) | ||
|
|
||
| write_tsv(summary, glue::glue("{input$prefix}.bin_summary.tsv")) | ||
|
|
||
| writeLines( | ||
| c("BIN_SUMMARY:", | ||
| paste0(" R: ", paste0(R.Version()[c("major","minor")], collapse = ".")), | ||
| paste0(" tidyverse: ", packageVersion("tidyverse")) | ||
| ), | ||
| "versions.yml" | ||
| ) |
Empty file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
Oops, something went wrong.