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export DADA2 QC svg #521

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merged 1 commit into from
Jan 13, 2023
Merged

export DADA2 QC svg #521

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#521](https://github.com/nf-core/ampliseq/pull/521) - Export svg in addition to pdf files for quality plots from DADA2

### `Changed`

### `Fixed`
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6 changes: 6 additions & 0 deletions bin/novaseq_err_pe.r
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Expand Up @@ -32,10 +32,16 @@ saveRDS(errR.md.full, paste0(run_id, "_2.md.err.rds"))
pdf(paste0(run_id, "_1.md.err.pdf"))
plotErrors(errF.md.full, nominalQ = TRUE)
dev.off()
svg(paste0(run_id, "_1.md.err.svg"))
plotErrors(errF.md.full, nominalQ = TRUE)
dev.off()

pdf(paste0(run_id, "_2.md.err.pdf"))
plotErrors(errR.md.full, nominalQ = TRUE)
dev.off()
svg(paste0(run_id, "_2.md.err.svg"))
plotErrors(errR.md.full, nominalQ = TRUE)
dev.off()

sink(file = paste0(run_id, "_1.md.err.convergence.txt"))
dada2:::checkConvergence(errF.md.full)
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3 changes: 3 additions & 0 deletions bin/novaseq_err_se.r
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Expand Up @@ -24,6 +24,9 @@ saveRDS(errF.md.full, paste0(run_id, ".md.err.rds"))
pdf(paste0(run_id, ".md.err.pdf"))
plotErrors(errF.md.full, nominalQ = TRUE)
dev.off()
svg(paste0(run_id, ".md.err.svg"))
plotErrors(errF.md.full, nominalQ = TRUE)
dev.off()

sink(file = paste0(run_id, ".md.err.convergence.txt"))
dada2:::checkConvergence(errF.md.full)
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28 changes: 25 additions & 3 deletions conf/modules.config
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Expand Up @@ -125,6 +125,11 @@ process {
mode: params.publish_dir_mode,
pattern: "*{.pdf,plotQualityProfile.txt}"
],
[
path: { "${params.outdir}/dada2/QC/svg" },
mode: params.publish_dir_mode,
pattern: "*{.svg}"
],
[
path: { "${params.outdir}/dada2/args" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -168,6 +173,11 @@ process {
mode: params.publish_dir_mode,
pattern: "*{.pdf}"
],
[
path: { "${params.outdir}/dada2/QC/svg" },
mode: params.publish_dir_mode,
pattern: "*{.svg}"
],
[
path: { "${params.outdir}/dada2/args" },
mode: params.publish_dir_mode,
Expand All @@ -188,6 +198,11 @@ process {
mode: params.publish_dir_mode,
pattern: "*{.pdf,convergence.txt}"
],
[
path: { "${params.outdir}/dada2/QC/svg" },
mode: params.publish_dir_mode,
pattern: "*{.svg}"
],
[
path: { "${params.outdir}/dada2/args" },
mode: params.publish_dir_mode,
Expand All @@ -203,9 +218,16 @@ process {

withName: NOVASEQ_ERR {
publishDir = [
path: { "${params.outdir}/dada2/QC" },
mode: params.publish_dir_mode,
pattern: "*{.pdf,convergence.txt}"
[
path: { "${params.outdir}/dada2/QC" },
mode: params.publish_dir_mode,
pattern: "*{.pdf,convergence.txt}"
],
[
path: { "${params.outdir}/dada2/QC/svg" },
mode: params.publish_dir_mode,
pattern: "*{.svg}"
]
]
}

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10 changes: 10 additions & 0 deletions modules/local/dada2_err.nf
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Expand Up @@ -13,6 +13,7 @@ process DADA2_ERR {
output:
tuple val(meta), path("*.err.rds"), emit: errormodel
tuple val(meta), path("*.err.pdf"), emit: pdf
tuple val(meta), path("*.err.svg"), emit: svg
tuple val(meta), path("*.err.log"), emit: log
tuple val(meta), path("*.err.convergence.txt"), emit: convergence
path "versions.yml" , emit: versions
Expand Down Expand Up @@ -43,10 +44,16 @@ process DADA2_ERR {
pdf("${meta.run}_1.err.pdf")
plotErrors(errF, nominalQ = TRUE)
dev.off()
svg("${meta.run}_1.err.svg")
plotErrors(errF, nominalQ = TRUE)
dev.off()

pdf("${meta.run}_2.err.pdf")
plotErrors(errR, nominalQ = TRUE)
dev.off()
svg("${meta.run}_2.err.svg")
plotErrors(errR, nominalQ = TRUE)
dev.off()

sink(file = "${meta.run}_1.err.convergence.txt")
dada2:::checkConvergence(errF)
Expand Down Expand Up @@ -75,6 +82,9 @@ process DADA2_ERR {
pdf("${meta.run}.err.pdf")
plotErrors(errF, nominalQ = TRUE)
dev.off()
svg("${meta.run}.err.svg")
plotErrors(errF, nominalQ = TRUE)
dev.off()

sink(file = "${meta.run}.err.convergence.txt")
dada2:::checkConvergence(errF)
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6 changes: 5 additions & 1 deletion modules/local/dada2_quality.nf
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Expand Up @@ -11,7 +11,8 @@ process DADA2_QUALITY {
tuple val(meta), path(reads)

output:
path "*_qual_stats.pdf" , emit: pdf
path "*_qual_stats.pdf" , emit: pdf
path "*_qual_stats.svg" , emit: svg
tuple val(meta), path("*_qual_stats.tsv"), emit: tsv
path "versions.yml" , emit: versions
path "*.args.txt" , emit: args
Expand Down Expand Up @@ -65,6 +66,9 @@ process DADA2_QUALITY {
pdf(paste0("${prefix}_qual_stats",".pdf"))
plot
dev.off()
svg(paste0("${prefix}_qual_stats",".svg"))
plot
dev.off()

write.table(paste0('plotQualityProfile\t$args\nmax_files\t',max_files), file = "${prefix}_plotQualityProfile.args.txt", row.names = FALSE, col.names = FALSE, quote = FALSE, na = '')
writeLines(c("\\"${task.process}\\":", paste0(" R: ", paste0(R.Version()[c("major","minor")], collapse = ".")),paste0(" dada2: ", packageVersion("dada2")),paste0(" ShortRead: ", packageVersion("ShortRead")) ), "versions.yml")
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1 change: 1 addition & 0 deletions modules/local/novaseq_err.nf
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Expand Up @@ -12,6 +12,7 @@ process NOVASEQ_ERR {
output:
tuple val(meta), path("*.md.err.rds"), emit: errormodel
tuple val(meta), path("*.md.err.pdf"), emit: pdf
tuple val(meta), path("*.md.err.svg"), emit: svg
tuple val(meta), path("*.md.err.convergence.txt"), emit: convergence
path "versions.yml" , emit: versions

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