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Add options for saving intermediate files #314

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merged 5 commits into from
Feb 9, 2024
Merged

Add options for saving intermediate files #314

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0c7400f
add parameter to save aligned read optionally,
christopher-mohr Feb 8, 2024
9b19940
do not store aligned reads for test
christopher-mohr Feb 8, 2024
3faa16c
set save_merged to false for test profile
christopher-mohr Feb 9, 2024
598af94
add parameter for specifying whether to save
christopher-mohr Feb 9, 2024
7d0a749
do not store aligned reads from mirna quant
christopher-mohr Feb 9, 2024
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14 changes: 9 additions & 5 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ process {
path: { "${params.outdir}/cat_fastq" },
mode: params.publish_dir_mode,
pattern: '*.fastq',
// enabled: params.save_merged_fastq //TODO ? implement save_merged_fastq param
enabled: params.save_merged
]
}

Expand Down Expand Up @@ -230,7 +230,8 @@ process {
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/mature" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.save_aligned_mirna_quant
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:.*' {
Expand All @@ -245,7 +246,8 @@ process {
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/hairpin" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.save_aligned_mirna_quant
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:.*' {
Expand Down Expand Up @@ -274,7 +276,8 @@ process {
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/seqcluster" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.save_aligned_mirna_quant
]
}
withName: 'MIRTOP_QUANT' {
Expand Down Expand Up @@ -317,7 +320,8 @@ process {
publishDir = [
path: { "${params.outdir}/genome_quant/bam" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.save_aligned
]
}

Expand Down
8 changes: 5 additions & 3 deletions conf/test.config
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Expand Up @@ -24,8 +24,10 @@ params {
input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'

mirtrace_species = 'hsa'
protocol = 'illumina'
skip_mirdeep = true
mirtrace_species = 'hsa'
protocol = 'illumina'
skip_mirdeep = true
save_merged = false
save_aligned_mirna_quant = false

}
5 changes: 3 additions & 2 deletions nextflow.config
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Expand Up @@ -28,6 +28,8 @@ params {
mirgenedb_hairpin = null
mirgenedb_gff = null
mirgenedb_species = null
save_aligned = false
save_aligned_mirna_quant = true

// UMI handling
with_umi = false
Expand All @@ -46,7 +48,7 @@ params {
fastp_min_length = 17
fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa"
save_trimmed_fail = false
save_merged = false
save_merged = true
skip_fastqc = false
skip_multiqc = false
skip_mirdeep = false
Expand Down Expand Up @@ -83,7 +85,6 @@ params {
version = false

// Config options

custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
Expand Down
16 changes: 14 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -78,7 +78,8 @@
"skip_umi_extract": {
"type": "boolean",
"fa_icon": "fas fa-compress-alt",
"description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run."
"description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run.",
"default": true
},
"umitools_bc_pattern": {
"type": "string",
Expand Down Expand Up @@ -184,6 +185,16 @@
"help_text": "Saving generated references means that you can use them for future pipeline runs, reducing processing times.",
"fa_icon": "fas fa-save"
},
"save_aligned": {
"type": "boolean",
"fa_icon": "fas fa-download",
"description": "Save aligned reads in bam format."
},
"save_aligned_mirna_quant": {
"type": "boolean",
"default": true,
"description": "Save aligned reads in bam format of miRNA quant subworkflow."
},
"igenomes_ignore": {
"type": "boolean",
"description": "Do not load the iGenomes reference config.",
Expand Down Expand Up @@ -254,7 +265,8 @@
},
"save_merged": {
"type": "boolean",
"description": "Save merged reads."
"description": "Save merged reads.",
"default": true
}
}
},
Expand Down
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