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larger genome alignment should go to basement for now #258

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merged 9 commits into from
Feb 16, 2024
Merged

larger genome alignment should go to basement for now #258

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0fa0f1b
larger genome alignment should go to basement for now
yumisims Feb 16, 2024
62b39c0
larger genome alignment should go to basement for now
yumisims Feb 16, 2024
ecdccaf
removed one bedsort
yumisims Feb 16, 2024
facc97c
test
yumisims Feb 16, 2024
4950791
test
yumisims Feb 16, 2024
5a299f7
removed imports no longer in use
yumisims Feb 16, 2024
a6607d5
change minimap2 run time
yumisims Feb 16, 2024
0751e4c
change minimap2 run time
yumisims Feb 16, 2024
024216d
Update base.config
DLBPointon Feb 16, 2024
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7 changes: 4 additions & 3 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ process {
time = { check_max( 12.h * task.attempt, 'time' ) }
}

// def counted = {x, y ->
// def counted = {x, y ->
// To avoid calculating the countLines multiple times
// Cant use countlines directly on the file otherwise raises a java.nio.file.ProviderMismatchError
// return (x**2) * Math.log(y)
Expand All @@ -128,15 +128,16 @@ process {

withName: '.*:.*:GENE_ALIGNMENT:.*:MINIPROT_INDEX' {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 1.GB * ( Math.ceil( ( fasta.size() / 1e+9 ) * 30 ) * Math.ceil( task.attempt * 1 ) ) , 'memory' ) }
memory = { check_max( 1.GB * ( Math.ceil( ( fasta.size() / 1e+9 ) * 10 ) * Math.ceil( task.attempt * 1 ) ) , 'memory' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}

// Standard parameters, covers most insecta
withName: '.*:.*:READ_COVERAGE:MINIMAP2_ALIGN' {
cpus = { check_max( 20 * 1, 'cpus' ) }
memory = { check_max( 50.GB * task.attempt, 'memory' ) }
time = { check_max( 20.h * task.attempt, 'time' ) }
time = { check_max( 1.h * (reference.size() < 1e9 ? 10 : reference.size() < 2.5e9 ? 30 : 300), 'time' ) }
//time = { check_max( 30.h * task.attempt, 'time' ) }
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Remove the unneeded time line

}

withName: '.*:.*:READ_COVERAGE:SAMTOOLS_SORT' {
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4 changes: 0 additions & 4 deletions conf/modules.config
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Expand Up @@ -96,10 +96,6 @@ process {
ext.prefix = { "${meta.id}.ancestral.sorted" }
}

withName: ".*:.*:.*:PEP_ALIGNMENTS:BEDTOOLS_SORT" {
ext.prefix = { "${meta.id}.prot.sorted" }
}

//
// BAMTOBED_SORT Block
//
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1 change: 0 additions & 1 deletion subworkflows/local/busco_annotation.nf
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Expand Up @@ -9,7 +9,6 @@
// MODULE IMPORT BLOCK
//
include { BUSCO } from '../../modules/nf-core/busco/main'
include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main'
include { UCSC_BEDTOBIGBED } from '../../modules/nf-core/ucsc/bedtobigbed/main'
include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/sort/main'
include { EXTRACT_BUSCOGENE } from '../../modules/local/extract_buscogene'
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5 changes: 0 additions & 5 deletions subworkflows/local/hic_mapping.nf
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Expand Up @@ -8,23 +8,18 @@
//
// MODULE IMPORT BLOCK
//
include { BWAMEM2_INDEX } from '../../modules/nf-core/bwamem2/index/main'
include { COOLER_CLOAD } from '../../modules/nf-core/cooler/cload/main'
include { COOLER_ZOOMIFY } from '../../modules/nf-core/cooler/zoomify/main'
include { PRETEXTMAP as PRETEXTMAP_STANDRD } from '../../modules/nf-core/pretextmap/main'
include { PRETEXTMAP as PRETEXTMAP_HIGHRES } from '../../modules/nf-core/pretextmap/main'
include { PRETEXTSNAPSHOT as SNAPSHOT_SRES } from '../../modules/nf-core/pretextsnapshot/main'
include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main'
include { GENERATE_CRAM_CSV } from '../../modules/local/generate_cram_csv'
include { CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT } from '../../modules/local/cram_filter_align_bwamem2_fixmate_sort'
include { CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT } from '../../modules/local/cram_filter_minimap2_filter5end_fixmate_sort'
include { JUICER_TOOLS_PRE } from '../../modules/local/juicer_tools_pre'
include { SUBSAMPLE_BAM } from '../../modules/local/subsample_bam.nf'
include { PRETEXT_INGESTION as PRETEXT_INGEST_SNDRD } from '../../subworkflows/local/pretext_ingestion'
include { PRETEXT_INGESTION as PRETEXT_INGEST_HIRES } from '../../subworkflows/local/pretext_ingestion'
include { HIC_BAMTOBED as HIC_BAMTOBED_COOLER } from '../../subworkflows/local/hic_bamtobed'
include { HIC_BAMTOBED as HIC_BAMTOBED_JUICER } from '../../subworkflows/local/hic_bamtobed'
include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/index/main'
include { HIC_MINIMAP2 } from '../../subworkflows/local/hic_minimap2'
include { HIC_BWAMEM2 } from '../../subworkflows/local/hic_bwamem2'

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1 change: 0 additions & 1 deletion subworkflows/local/nuc_alignments.nf
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Expand Up @@ -5,7 +5,6 @@
//
include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main'
include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main'
include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/sort/main'
include { BEDTOOLS_BAMTOBED } from '../../modules/nf-core/bedtools/bamtobed/main'
include { UCSC_BEDTOBIGBED } from '../../modules/nf-core/ucsc/bedtobigbed/main'
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2 changes: 0 additions & 2 deletions subworkflows/local/selfcomp.nf
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Expand Up @@ -7,7 +7,6 @@ import java.math.BigDecimal;
// MODULE IMPORT BLOCK
//
include { MUMMER } from '../../modules/nf-core/mummer/main'
include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main'
include { UCSC_BEDTOBIGBED } from '../../modules/nf-core/ucsc/bedtobigbed/main'
include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/sort/main'
include { SELFCOMP_SPLITFASTA } from '../../modules/local/selfcomp_splitfasta'
Expand All @@ -17,7 +16,6 @@ include { CHUNKFASTA } from '../../modules/local/chunkfasta'
include { CAT_CAT } from '../../modules/nf-core/cat/cat/main'
include { SELFCOMP_ALIGNMENTBLOCKS } from '../../modules/local/selfcomp_alignmentblocks'
include { CONCATBLOCKS } from '../../modules/local/concatblocks'
include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge/main'

workflow SELFCOMP {
take:
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