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Merge pull request #486 from atrigila/csvtk_replace
Replace `CSVTK_JOIN` to improve processing in large amount of files
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Original file line number | Diff line number | Diff line change |
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#!/usr/bin/env Rscript | ||
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library(optparse) | ||
library(tidyr) | ||
library(vroom) | ||
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option_list <- list( | ||
make_option(c("--input"), type = "character", help = "Input TSV file", metavar = "character"), | ||
make_option(c("--output"), type = "character", help = "Output CSV file", metavar = "character") | ||
) | ||
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opt_parser <- OptionParser(option_list = option_list) | ||
opt <- parse_args(opt_parser) | ||
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# Read CSV with vroom | ||
data <- vroom::vroom(opt$input, delim = "\t", col_types = c(.default = "c")) | ||
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last_col <- names(data)[ncol(data)] | ||
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# Convert from wide to long format | ||
long_data <- data %>% | ||
pivot_longer( | ||
cols = last_col, | ||
names_to = "Sample_ID", | ||
values_to = "Counts" | ||
) | ||
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vroom_write(long_data, opt$output, delim = ",") | ||
|
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,32 @@ | ||
#!/usr/bin/env Rscript | ||
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library(optparse) | ||
library(tidyr) | ||
library(vroom) | ||
library(dplyr) | ||
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option_list <- list( | ||
make_option(c("--input"), type = "character", help = "Input CSV file in long format", metavar = "character"), | ||
make_option(c("--output"), type = "character", help = "Output CSV file in wide format", metavar = "character") | ||
) | ||
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opt_parser <- OptionParser(option_list = option_list) | ||
opt <- parse_args(opt_parser) | ||
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# Read CSV with vroom | ||
long_data <- vroom::vroom(opt$input, delim = ",", | ||
col_types = c( | ||
Counts = "d", | ||
.default = "c" | ||
)) | ||
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# Transform to wide format | ||
wide_data <- long_data %>% | ||
pivot_wider( | ||
names_from = Sample_ID, | ||
values_from = Counts, | ||
values_fill = 0 | ||
) | ||
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# Export wide format | ||
vroom_write(wide_data, opt$output, delim = "\t") |
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Original file line number | Diff line number | Diff line change |
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channels: | ||
- conda-forge | ||
dependencies: | ||
- conda-forge::r-optparse | ||
- conda-forge::r-tidyverse |
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Original file line number | Diff line number | Diff line change |
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process PIVOT_LONGER { | ||
tag"$meta.id" | ||
label 'process_single' | ||
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conda "${moduleDir}/environment.yml" | ||
container "community.wave.seqera.io/library/r-optparse_r-tidyverse_r-vroom:3cbb224fea84a0e1" | ||
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input: | ||
tuple val(meta), path(tsv) | ||
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output: | ||
tuple val(meta), path("*_long.csv") , emit: csv | ||
path "versions.yml" , emit: versions | ||
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script: | ||
""" | ||
pivot_longer.R \\ | ||
--input ${tsv} \\ | ||
--output ${meta.id}_long.csv | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') | ||
tidyr: \$(Rscript -e "library(tidyr); cat(as.character(packageVersion('tidyr')))") | ||
optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))") | ||
END_VERSIONS | ||
""" | ||
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} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,5 @@ | ||
channels: | ||
- conda-forge | ||
dependencies: | ||
- conda-forge::r-optparse | ||
- conda-forge::r-tidyverse |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,35 @@ | ||
process PIVOT_WIDER { | ||
tag"$meta.id" | ||
label 'process_high' | ||
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conda "${moduleDir}/environment.yml" | ||
container "community.wave.seqera.io/library/r-optparse_r-tidyverse_r-vroom:3cbb224fea84a0e1" | ||
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input: | ||
tuple val(meta), path(csvs) | ||
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output: | ||
tuple val(meta), path("*joined_samples_mirtop.tsv") , emit: csv | ||
path "versions.yml" , emit: versions | ||
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script: | ||
""" | ||
awk 'NR == 1 || FNR > 1' ${csvs.join(' ')} > final_long_results_temp.csv | ||
pivot_wider.R \\ | ||
--input final_long_results_temp.csv \\ | ||
--output ${meta.id}_concatenated_temp.csv | ||
sort -t\$'\t' -k1,1 ${meta.id}_concatenated_temp.csv > joined_samples_mirtop.tsv | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') | ||
tidyr: \$(Rscript -e "library(tidyr); cat(as.character(packageVersion('tidyr')))") | ||
dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") | ||
optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))") | ||
vroom: \$(Rscript -e "library(vroom); cat(as.character(packageVersion('vroom')))") | ||
END_VERSIONS | ||
""" | ||
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} |
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