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tweaks filtered fastq filenames and limits large file outputs #3

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tweaks filtered fastq filenames and limits large file outputs #3

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7989ac1
tweaks fastq filename format
mikeyweigand Dec 9, 2024
b0a4374
adds param to keep big bam and fastq files
mikeyweigand Dec 10, 2024
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49 changes: 42 additions & 7 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -51,15 +51,29 @@ process {
publishDir = [
path: { "${params.outdir}/mapping-bp" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename ->
if (filename.equals('versions.yml')){ null }
else if (filename.endsWith('.bam') || filename.endsWith('.bam.bai')){
if ( params.keep_big_files == true ) { filename }
else { null }
}
else { filename }
}
]
}
withName: SAMTOOLS_DEPTH {
ext.args = '-aa'
publishDir = [
path: { "${params.outdir}/mapping-bp" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename ->
if (filename.equals('versions.yml')){ null }
else if ( filename.endsWith('bp-depth.tsv') ){
if ( params.keep_big_files == true ) { filename }
else { null }
}
else { filename }
}
]
}
withName: HS_FLAGSTAT {
Expand All @@ -81,17 +95,24 @@ process {
withName: HS_FASTQ {
ext.args = '-N'
ext.suffix = 'hs-unmapped.'
ext.filt = 'hs-unmapped.'
ext.filt = 'hs-unmapped'
publishDir = [
path: { "${params.outdir}/mapping-hs" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename ->
if (filename.equals('versions.yml')){ null }
else if ( filename.endsWith('fastq.gz') ){
if ( params.keep_big_files == true ) { filename }
else { null }
}
else { filename }
}
]
}
withName: BP_FASTQ {
ext.args = '-N'
ext.suffix = 'bp-mapped.'
ext.filt = 'filtered.'
ext.filt = 'filtered'
publishDir = [
path: { "${params.outdir}/filteredreads" },
mode: params.publish_dir_mode,
Expand All @@ -111,15 +132,29 @@ process {
publishDir = [
path: { "${params.outdir}/mapping-hs" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename ->
if (filename.equals('versions.yml')){ null }
else if ( filename.endsWith('.bam') ){
if ( params.keep_big_files == true ) { filename }
else { null }
}
else { filename }
}
]
}
withName: BP_ALIGN {
ext.args = '--local'
publishDir = [
path: { "${params.outdir}/mapping-bp" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename ->
if (filename.equals('versions.yml')){ null }
else if (filename.endsWith('.bam')){
if ( params.keep_big_files == true ) { filename }
else { null }
}
else { filename }
}
]
}
withName: BLASTN_PAIRWISE {
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/modules/nf-core/samtools/fastq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ process SAMTOOLS_FASTQ {
val(interleave)

output:
tuple val(meta), path("*.R{1,2}.fastq.gz") , optional:true, emit: fastq
tuple val(meta), path("*_R{1,2}_*.fastq.gz") , optional:true, emit: fastq
tuple val(meta), path("*_interleaved.fastq.gz"), optional:true, emit: interleaved
tuple val(meta), path("*_singleton.fastq.gz") , optional:true, emit: singleton
tuple val(meta), path("*_other.fastq.gz") , optional:true, emit: other
Expand All @@ -28,7 +28,7 @@ process SAMTOOLS_FASTQ {
def filt = task.ext.filt ?: ''
def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq.gz" :
meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
"-1 ${prefix}.${filt}R1.fastq.gz -2 ${prefix}.${filt}R2.fastq.gz" // -s ${prefix}_singleton.fastq.gz"
"-1 ${prefix}_R1_${filt}.fastq.gz -2 ${prefix}_R2_${filt}.fastq.gz" // -s ${prefix}_singleton.fastq.gz"
"""
samtools sort -n --threads ${task.cpus-1} $input -o ${prefix}.${suffix}namesort.bam
samtools \\
Expand Down
1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -20,6 +20,7 @@ params {
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
keep_big_files = false // option to keep mapping results

// MultiQC options
multiqc_config = null
Expand Down
6 changes: 6 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -41,6 +41,12 @@
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
},
"keep_big_files": {
"type": "boolean",
"description": "Option to keep large intermediate *bam and *fastq files.",
"default": false,
"fa_icon": "fas fa-floppy-disk"
}
}
},
Expand Down