Merge pull request #258 from sanger-tol/read_cov_resource

larger genome alignment should go to basement for now
sanger-tol · Feb 16, 2024 · 8da7da6 · 8da7da6
2 parents 44ff877 + 024216d
commit 8da7da6
Show file tree

Hide file tree

Showing 6 changed files with 4 additions and 16 deletions.
diff --git 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)
@@ -128,15 +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'    ) }
     }
 
     withName: '.*:.*:READ_COVERAGE:SAMTOOLS_SORT' {

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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: