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Minor fixes #78

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merged 3 commits into from
Mar 24, 2023
Merged

Minor fixes #78

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a9e10a9
Changes to pep file naming and mem for some jobs
DLBPointon Mar 24, 2023
3d92489
Updates to get rid of multiple samtools faidx runs
DLBPointon Mar 24, 2023
13388f0
Added a missing versions statement
DLBPointon Mar 24, 2023
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6 changes: 3 additions & 3 deletions conf/base.config
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Expand Up @@ -23,14 +23,14 @@ process {

// RESOURCES: MEMORY INTENSIVE STEPS, SOFTWARE TO BE UPDATED TO COMBAT THIS
withName: '.*:.*:SELFCOMP:(SELFCOMP_ALIGNMENTBLOCKS|SELFCOMP_MAPIDS|SELFCOMP_MUMMER2BED|SELFCOMP_SPLITFASTA|BEDTOOLS_MERGE)' {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory') }
cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 100.GB * task.attempt, 'memory') }
time = { check_max( 8.h * task.attempt, 'time' ) }
}

// RESOURCES: CHANGES TO FREQUENT FAILURES BELOW THIS MEM POINT
withName: '(MINIPROT_ALIGN|MINIMAP2_ALIGN)' {
memory = { check_max( 50.GB * task.attempt, 'memory' ) }
memory = { check_max( 100.GB * task.attempt, 'memory' ) }
}

// 25GB * (task attempt * 2) = 50GB, 100GB, 150GB
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4 changes: 4 additions & 0 deletions subworkflows/local/gene_alignment.nf
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Expand Up @@ -17,6 +17,7 @@ workflow GENE_ALIGNMENT {
take:
dot_genome // Channel: [val(meta), [ datafile ]]
reference_tuple
reference_index
assembly_classT
alignment_datadir
alignment_genesets
Expand Down Expand Up @@ -78,16 +79,19 @@ workflow GENE_ALIGNMENT {
// SUBWORKFLOW: GENERATES GENE ALIGNMENTS FOR RNA, NUCLEAR AND COMPLEMENT_DNA DATA, EMITS BIGBED
//
GEN_ALIGNMENTS ( reference_tuple,
reference_index,
gen_files,
dot_genome,
intron_size )

CDS_ALIGNMENTS ( reference_tuple,
reference_index,
cds_files,
dot_genome,
intron_size )

RNA_ALIGNMENTS ( reference_tuple,
reference_index,
rna_files,
dot_genome,
intron_size )
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1 change: 1 addition & 0 deletions subworkflows/local/generate_genome.nf
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Expand Up @@ -34,6 +34,7 @@ workflow GENERATE_GENOME {

emit:
dot_genome = GENERATE_GENOME_FILE.out.dotgenome
ref_index = SAMTOOLS_FAIDX.out.fai
reference_tuple = to_samtools

versions = ch_versions.ifEmpty(null)
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11 changes: 3 additions & 8 deletions subworkflows/local/nuc_alignments.nf
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Expand Up @@ -9,6 +9,7 @@ include { UCSC_BEDTOBIGBED } from '../../modules/nf-core/ucsc/bedtobigbed/m
workflow NUC_ALIGNMENTS {
take:
reference_tuple
reference_index
nuc_files
dot_genome
intron_size
Expand Down Expand Up @@ -41,13 +42,6 @@ workflow NUC_ALIGNMENTS {
)
.set { formatted_input }

//
// MODULE: GENERATES FASTA INDEX OF REFERENCE
// EMITS FAIDX FILE
//
SAMTOOLS_FAIDX ( reference_tuple )
ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)

//
// MODULE: ALIGNS REFERENCE FAIDX TO THE GENE_ALIGNMENT QUERY FILE FROM NUC_FILES
// EMITS ALIGNED BAM FILE
Expand All @@ -71,7 +65,7 @@ workflow NUC_ALIGNMENTS {
tuple([id: meta.org, type: meta.type], file) }
.groupTuple( by: [0] )
.combine( reference_tuple )
.combine( SAMTOOLS_FAIDX.out.fai )
.combine( reference_index )
.multiMap { it ->
nuc_grouped: tuple( it[0], it[1] )
reference: it[-3]
Expand All @@ -93,6 +87,7 @@ workflow NUC_ALIGNMENTS {
// MODULE: CONVERTS THE ABOVE MERGED BAM INTO BED FORMAT
//
BEDTOOLS_BAMTOBED { SAMTOOLS_MERGE.out.bam }
ch_versions = ch_versions.mix(BEDTOOLS_BAMTOBED.out.versions)

//
// MODULE: SORTS THE ABOVE BED FILE
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2 changes: 1 addition & 1 deletion subworkflows/local/pep_alignments.nf
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Expand Up @@ -53,7 +53,7 @@ workflow PEP_ALIGNMENTS {
//
MINIPROT_ALIGN.out.gff
.map { it ->
tuple([ id: it[0].org,
tuple([ id: it[0].org + '_pep',
type: it[0].type
],
it[1] )
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1 change: 1 addition & 0 deletions workflows/treeval.nf
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Expand Up @@ -101,6 +101,7 @@ workflow TREEVAL {
//
GENE_ALIGNMENT ( GENERATE_GENOME.out.dot_genome,
GENERATE_GENOME.out.reference_tuple,
GENERATE_GENOME.out.ref_index,
YAML_INPUT.out.assembly_classT,
YAML_INPUT.out.align_data_dir,
YAML_INPUT.out.align_geneset,
Expand Down