diff --git a/conf/base.config b/conf/base.config index 437b0852..9f4abdba 100755 --- a/conf/base.config +++ b/conf/base.config @@ -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) @@ -128,7 +128,7 @@ 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' ) } } @@ -136,7 +136,8 @@ process { 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' ) } } withName: '.*:.*:READ_COVERAGE:SAMTOOLS_SORT' { diff --git a/conf/modules.config b/conf/modules.config index 15ab6d01..7eee22ab 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -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 // diff --git a/subworkflows/local/busco_annotation.nf b/subworkflows/local/busco_annotation.nf index 230e3fa8..974738f6 100755 --- a/subworkflows/local/busco_annotation.nf +++ b/subworkflows/local/busco_annotation.nf @@ -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' diff --git a/subworkflows/local/hic_mapping.nf b/subworkflows/local/hic_mapping.nf index 42f3f712..02d23def 100755 --- a/subworkflows/local/hic_mapping.nf +++ b/subworkflows/local/hic_mapping.nf @@ -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' diff --git a/subworkflows/local/nuc_alignments.nf b/subworkflows/local/nuc_alignments.nf index 71f47a44..31ca7040 100755 --- a/subworkflows/local/nuc_alignments.nf +++ b/subworkflows/local/nuc_alignments.nf @@ -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' diff --git a/subworkflows/local/selfcomp.nf b/subworkflows/local/selfcomp.nf index cf69c42f..c99d59e8 100755 --- a/subworkflows/local/selfcomp.nf +++ b/subworkflows/local/selfcomp.nf @@ -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' @@ -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: