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Refactor ext args as pipeline params
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Signed-off-by: Ben Sherman <[email protected]>
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@bentsherman
bentsherman committed Oct 16, 2023
1 parent 0e34e31 commit 143af87
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Showing 8 changed files with 90 additions and 25 deletions.
70 changes: 64 additions & 6 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,74 @@
----------------------------------------------------------------------------------------
*/

def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []

//
// General configuration options
//

process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

params {

//
// Genome preparation options
//

prepare_genome_untar_args = '--no-same-owner'
prepare_genome_gffread_args = '--keep-exon-attrs -F -T'
prepare_genome_rsem_args = '--star'
prepare_genome_bbsplit_args = 'build=1'

//
// Read subsampling and strand inferring options
//

subsample_fq_args = '--record-count 1000000 --seed 1'
subsample_salmon_args = '--skipQuant'

//
// Read QC and trimming options
//

fastqc_args = '--quiet'

//
// Contaminant removal options
//

bbsplit_args = 'build=1 ambiguous2=all maxindel=150000'
sortmerna_args = '--num_alignments 1 -v'

//
// General alignment options
//

picard_args = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
bedtools_args = '-split -du'

//
// STAR Salmon alignment options
//

samtools_sort_args = '-n'

//
// STAR RSEM alignment options
//

//
// HISAT2 alignment options
//

//
// Post-alignment QC options
//

preseq_lcextrap_args = '-verbose -bam -seed 1 -seg_len 100000000'

//
// Salmon pseudo-alignment options
//

}
7 changes: 7 additions & 0 deletions lib/Utils.groovy
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Expand Up @@ -44,4 +44,11 @@ class Utils {
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
}
}

public static Map publishDir(def params, String subPath, Map opts=[:]) {
final defaults = [
mode: params.publish_dir_mode
]
return defaults + [path: "${params.outdir}/${subPath}"] + opts
}
}
16 changes: 8 additions & 8 deletions subworkflows/local/prepare_genome.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ workflow PREPARE_GENOME {
ch_gff = Channel.value(file(gff))
}

GFFREAD.config.ext.args = '--keep-exon-attrs -F -T'
GFFREAD.config.ext.args = params.prepare_genome_gffread_args
GFFREAD.config.publishDir = genome_publish_dir
ch_gtf = GFFREAD ( ch_gff ).gtf
ch_versions = ch_versions.mix(GFFREAD.out.versions)
Expand Down Expand Up @@ -184,7 +184,7 @@ workflow PREPARE_GENOME {
if ('bbsplit' in prepare_tool_indices) {
if (bbsplit_index) {
if (bbsplit_index.endsWith('.tar.gz')) {
UNTAR_BBSPLIT_INDEX.config.ext.args2 = '--no-same-owner'
UNTAR_BBSPLIT_INDEX.config.ext.args2 = params.prepare_genome_untar_args
UNTAR_BBSPLIT_INDEX.config.publishDir = genome_index_publish_dir
ch_bbsplit_index = UNTAR_BBSPLIT_INDEX ( [ [:], bbsplit_index ] ).untar.map { it[1] }
ch_versions = ch_versions.mix(UNTAR_BBSPLIT_INDEX.out.versions)
Expand All @@ -201,7 +201,7 @@ workflow PREPARE_GENOME {
.collect { [ it ] } // Collect entries as a list to pass as "tuple val(short_names), path(path_to_fasta)" to module
.set { ch_bbsplit_fasta_list }

BBMAP_BBSPLIT.config.ext.args = 'build=1'
BBMAP_BBSPLIT.config.ext.args = params.prepare_genome_bbsplit_args
BBMAP_BBSPLIT.config.publishDir = genome_index_publish_dir
ch_bbsplit_index = BBMAP_BBSPLIT ( [ [:], [] ], [], ch_fasta, ch_bbsplit_fasta_list, true ).index
ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions)
Expand All @@ -215,7 +215,7 @@ workflow PREPARE_GENOME {
if ('star_salmon' in prepare_tool_indices) {
if (star_index) {
if (star_index.endsWith('.tar.gz')) {
UNTAR_STAR_INDEX.config.ext.args2 = '--no-same-owner'
UNTAR_STAR_INDEX.config.ext.args2 = params.prepare_genome_untar_args
UNTAR_STAR_INDEX.config.publishDir = genome_index_publish_dir
ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map { it[1] }
ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
Expand All @@ -242,15 +242,15 @@ workflow PREPARE_GENOME {
if ('star_rsem' in prepare_tool_indices) {
if (rsem_index) {
if (rsem_index.endsWith('.tar.gz')) {
UNTAR_RSEM_INDEX.config.ext.args2 = '--no-same-owner'
UNTAR_RSEM_INDEX.config.ext.args2 = params.prepare_genome_untar_args
UNTAR_RSEM_INDEX.config.publishDir = genome_index_publish_dir
ch_rsem_index = UNTAR_RSEM_INDEX ( [ [:], rsem_index ] ).untar.map { it[1] }
ch_versions = ch_versions.mix(UNTAR_RSEM_INDEX.out.versions)
} else {
ch_rsem_index = Channel.value(file(rsem_index))
}
} else {
RSEM_PREPAREREFERENCE_GENOME.config.ext.args = '--star'
RSEM_PREPAREREFERENCE_GENOME.config.ext.args = params.prepare_genome_rsem_args
RSEM_PREPAREREFERENCE_GENOME.config.publishDir = genome_index_publish_dir
ch_rsem_index = RSEM_PREPAREREFERENCE_GENOME ( ch_fasta, ch_gtf ).index
ch_versions = ch_versions.mix(RSEM_PREPAREREFERENCE_GENOME.out.versions)
Expand All @@ -272,7 +272,7 @@ workflow PREPARE_GENOME {
}
if (hisat2_index) {
if (hisat2_index.endsWith('.tar.gz')) {
UNTAR_HISAT2_INDEX.config.ext.args2 = '--no-same-owner'
UNTAR_HISAT2_INDEX.config.ext.args2 = params.prepare_genome_untar_args
UNTAR_HISAT2_INDEX.config.publishDir = genome_index_publish_dir
ch_hisat2_index = UNTAR_HISAT2_INDEX ( [ [:], hisat2_index ] ).untar.map { it[1] }
ch_versions = ch_versions.mix(UNTAR_HISAT2_INDEX.out.versions)
Expand All @@ -292,7 +292,7 @@ workflow PREPARE_GENOME {
ch_salmon_index = Channel.empty()
if (salmon_index) {
if (salmon_index.endsWith('.tar.gz')) {
UNTAR_SALMON_INDEX.config.ext.args2 = '--no-same-owner'
UNTAR_SALMON_INDEX.config.ext.args2 = params.prepare_genome_untar_args
UNTAR_SALMON_INDEX.config.publishDir = genome_index_publish_dir
ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], salmon_index ] ).untar.map { it[1] }
ch_versions = ch_versions.mix(UNTAR_SALMON_INDEX.out.versions)
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/nf-core/bam_markduplicates_picard/main.nf
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4 changes: 2 additions & 2 deletions subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
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4 changes: 2 additions & 2 deletions subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
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10 changes: 5 additions & 5 deletions workflows/rnaseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -350,7 +350,7 @@ workflow RNASEQ {
// MODULE: Remove genome contaminant reads
//
if (!params.skip_bbsplit) {
BBMAP_BBSPLIT.config.ext.args = 'build=1 ambiguous2=all maxindel=150000'
BBMAP_BBSPLIT.config.ext.args = params.bbsplit_args
BBMAP_BBSPLIT.config.publishDir = [
[
path: "${params.outdir}/bbsplit",
Expand Down Expand Up @@ -383,7 +383,7 @@ workflow RNASEQ {
if (params.remove_ribo_rna) {
ch_sortmerna_fastas = Channel.from(ch_ribo_db.readLines()).map { row -> file(row, checkIfExists: true) }.collect()

SORTMERNA.config.ext.args = '--num_alignments 1 -v'
SORTMERNA.config.ext.args = params.sortmerna_args
SORTMERNA.config.publishDir = [
[
path: "${params.outdir}/sortmerna",
Expand Down Expand Up @@ -548,7 +548,7 @@ workflow RNASEQ {
)

// Name sort BAM before passing to Salmon
SAMTOOLS_SORT.config.ext.args = '-n'
SAMTOOLS_SORT.config.ext.args = params.samtools_sort_args
SAMTOOLS_SORT.config.ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
SAMTOOLS_SORT.config.publishDir = [
path: "${params.outdir}/${params.aligner}",
Expand Down Expand Up @@ -780,7 +780,7 @@ workflow RNASEQ {
//
ch_preseq_multiqc = Channel.empty()
if (!params.skip_alignment && !params.skip_qc && !params.skip_preseq) {
PRESEQ_LCEXTRAP.config.ext.args = '-verbose -bam -seed 1 -seg_len 100000000'
PRESEQ_LCEXTRAP.config.ext.args = params.preseq_lcextrap_args
PRESEQ_LCEXTRAP.config.publishDir = [
[
path: "${params.outdir}/${params.aligner}/preseq",
Expand Down Expand Up @@ -895,7 +895,7 @@ workflow RNASEQ {
//
if (!params.skip_alignment && !params.skip_bigwig) {

BEDTOOLS_GENOMECOV.config.ext.args = '-split -du'
BEDTOOLS_GENOMECOV.config.ext.args = params.bedtools_args
BEDTOOLS_GENOMECOV.config.publishDir = [
path: { "${params.outdir}/bedtools/${meta.id}" },
enabled: false
Expand Down

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