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Merge pull request #567 from d4straub/use-phylogenetic-placement-outp…
…ut-in-qiime use phylogenetic placement output in qiime
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| process FORMAT_PPLACETAX { | ||
| tag "${tax.baseName}" | ||
| label 'process_high' | ||
|
|
||
| conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : | ||
| 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(tax) | ||
|
|
||
| output: | ||
| path("*.per_query_unique.tsv"), emit: unique | ||
| path("*.taxonomy.tsv") , emit: tsv | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| """ | ||
| #!/usr/bin/env Rscript | ||
| tax = read.table("$tax", header = TRUE, sep = "\t", stringsAsFactors = FALSE, comment.char = '', quote = '') | ||
| df <- data.frame( | ||
| name=character(), | ||
| LWR=character(), | ||
| fract=character(), | ||
| aLWR=character(), | ||
| afract=character(), | ||
| taxopath=character(), | ||
| stringsAsFactors=FALSE) | ||
| for (asvid in unique(tax\$name)) { | ||
| # subset per ASV ID | ||
| temp = subset(tax, tax\$name == asvid) | ||
| maxLWR = max(temp\$LWR) | ||
| temp = subset(temp, temp\$LWR == maxLWR) | ||
| if ( nrow(temp) == 1 ) { | ||
| # STEP 1: if there is just 1 maximum, choose this row | ||
| print( paste ( asvid,"was added in STEP 1" ) ) | ||
| temp = temp[which.max(temp\$LWR),] | ||
| df <- rbind(df, temp) | ||
| } else { | ||
| # STEP2: be conservative, choose the taxonomy with less entries | ||
| # count number of entries in "taxopath", simplified: number of semicolons | ||
| temp\$taxlevels = nchar( temp\$taxopath ) - nchar(gsub(';', '', temp\$taxopath )) + 1 | ||
| minTaxlevels = min(temp\$taxlevels) | ||
| temp = subset(temp, temp\$taxlevels == minTaxlevels) | ||
| temp\$taxlevels = NULL | ||
| if ( nrow(temp) == 1 ) { | ||
| df <- rbind(df, temp) | ||
| print( paste ( asvid,"was added in STEP 2" ) ) | ||
| } else { | ||
| # STEP 3: if number of entries is same, remove last entry | ||
| # then, check if reduced entries are identical > if yes, choose any row, if no, repeat | ||
| # at that step the taxonomies have same length | ||
| print( paste ( asvid,"enters STEP 3" ) ) | ||
| list_taxonpath <- str_split( temp\$taxopath, ";") | ||
| df_taxonpath <- as.data.frame(do.call(rbind, list_taxonpath)) | ||
| for (i in ncol(df_taxonpath):0) { | ||
| # choose first column and change taxon to reduced overlap | ||
| if ( length(unique(df_taxonpath[,i])) == 1 ) { | ||
| if (i>1) { | ||
| temp\$taxopath <- apply(df_taxonpath[1,1:i], 1, paste, collapse=";")[[1]] | ||
| } else if (i==1) { | ||
| temp\$taxopath <- df_taxonpath[1,1] | ||
| } | ||
| df <- rbind(df, temp[1,]) | ||
| print( paste ( asvid,"was added with",temp\$taxopath[[1]],"in STEP 3a" ) ) | ||
| break | ||
| } else if (i==0) { | ||
| # if all fails, i.e. there is no consensus on any taxonomic level, use NA | ||
| temp\$taxopath <- "NA" | ||
| df <- rbind(df, temp[1,]) | ||
| print( paste ( asvid,"was added with",temp\$taxopath[[1]],"in STEP 3b" ) ) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| # output the cleaned, unified, unique taxonomic classification per ASV | ||
| write.table(df, file = "${meta.id}.taxonomy.per_query_unique.tsv", row.names = FALSE, col.names = TRUE, quote = FALSE, na = '', sep = "\\t") | ||
| # output ASV taxonomy table for QIIME2 | ||
| df_clean <- subset(df, select = c("name","taxopath")) | ||
| colnames(df_clean) <- c("ASV_ID","taxonomy") | ||
| write.table(df_clean, file = "${meta.id}.taxonomy.tsv", row.names = FALSE, col.names = TRUE, quote = FALSE, na = '', sep = "\\t") | ||
| writeLines(c("\\"${task.process}\\":", paste0(" R: ", paste0(R.Version()[c("major","minor")], collapse = ".")),paste0(" dada2: ", packageVersion("dada2")) ), "versions.yml") | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| process QIIME2_INTREE { | ||
| tag "${meta.id}:${meta.model}" | ||
| label 'process_low' | ||
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| container "quay.io/qiime2/core:2022.11" | ||
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| // Exit if running this module with -profile conda / -profile mamba | ||
| if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { | ||
| exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." | ||
| } | ||
|
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| input: | ||
| tuple val(meta), path(tree) | ||
|
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| output: | ||
| path("tree.qza") , emit: qza | ||
| path "versions.yml", emit: versions | ||
|
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| when: | ||
| task.ext.when == null || task.ext.when | ||
|
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| script: | ||
| """ | ||
| qiime tools import \\ | ||
| --type 'Phylogeny[Rooted]' \\ | ||
| --input-path $tree \\ | ||
| --output-path tree.qza | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| qiime2: \$( qiime --version | sed '1!d;s/.* //' ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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