Readcov

assets/github_testing/TreeValTinyTest.yaml

@@ -7,8 +7,8 @@ assembly:
   project_id: DTOL
 reference_file: /home/runner/work/treeval/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa
 assem_reads:
-  longread_type: hifi
-  longread_data: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/pacbio/
+  read_type: hifi
+  read_data: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/pacbio/
   hic_data: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/hic-arima/
   supplementary_data: path
 kmer_profile:

assets/local_testing/nxOscDF5033.yaml

@@ -7,8 +7,8 @@ assembly:
   project_id: DTOL
 reference_file: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
 assem_reads:
-  longread_type: hifi
-  longread_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/
+  read_type: hifi
+  read_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/
   hic_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/
   supplementary_data: path
 kmer_profile:

conf/base.config

@@ -110,9 +110,9 @@ process {
     }
 
     // Standard parameters, covers most insecta
-    withName: '.*:.*:LONGREAD_COVERAGE:(MINIMAP2_ALIGN|MINIMAP2_ALIGN_SPLIT)' {
-        cpus    = { check_max( 16       * 1, 'cpus'                 ) }
-        memory  = { check_max( 100.GB   * task.attempt, 'memory'    ) }
+    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'      ) }
     }
 

conf/modules.config

@@ -68,7 +68,6 @@ process {
         ext.prefix      = { "${meta.id}.sorted" }
     }
 
-
     //
     // SUBWORKFLOW: SELFCOMP
     //
@@ -179,56 +178,51 @@ process {
 
 
     //
-    // SUBWORKFLOW: LONGREAD
+    // SUBWORKFLOW: READ_COVERAGE
     //
-    withName: ".*:.*:LONGREAD_COVERAGE:MINIMAP2_ALIGN" {
-            ext.args    = "--MD -t 8"
-            ext.prefix  = { "${meta.id}_alignment_${reference.getName().tokenize(".")[0]}" }
-    }
-
-    withName: ".*:.*:LONGREAD_COVERAGE:MINIMAP2_ALIGN_SPLIT" {
-            ext.args    = { "-t 20 --split-prefix ${meta.split_prefix}" }
-            ext.prefix  = { "${meta.id}_alignment_${reference.getName().tokenize(".")[0]}" }
+    withName: MINIMAP2_ALIGN {
+            ext.args = {'-ax '+ (meta.readtype.equals("hifi") ? "map-hifi" : meta.readtype.equals("clr") ? "map-pb" : meta.readtype.equals("ont") ? "map-ont" : meta.readtype.equals("illumina") ? "sr" : "") + ' --cs=short' + (reference.size() > 2.5e9 ? (" -I" + Math.ceil(reference.size()/1000000000)+"G") : "") }
+            ext.prefix  = { "${meta.id}_alignment_${reference.getName().tokenize('.')[0]}" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:SAMTOOLS_MERGE" {
+    withName: ".*:.*:READ_COVERAGE:SAMTOOLS_MERGE" {
         ext.prefix      = { "${meta.id}_merge" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:SAMTOOLS_SORT" {
+    withName: ".*:.*:READ_COVERAGE:SAMTOOLS_SORT" {
         ext.prefix      = { "${meta.id}_sorted" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:SAMTOOLS_VIEW" {
+    withName: ".*:.*:READ_COVERAGE:SAMTOOLS_VIEW_FILTER_PRIMARY" {
         ext.args        = "-b -hF 256"
         ext.prefix      = { "${meta.id}_view" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:BEDTOOLS_GENOMECOV" {
+    withName: ".*:.*:READ_COVERAGE:BEDTOOLS_GENOMECOV" {
         ext.args        = "-bga -split"
         ext.prefix      = { "${meta.id}_genome2cov" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:BEDTOOLS_MERGE_MAX" {
+    withName: ".*:.*:READ_COVERAGE:BEDTOOLS_MERGE_MAX" {
         ext.args        = "-d 50"
         ext.prefix      = { "maxdepth" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:BEDTOOLS_MERGE_MIN" {
+    withName: ".*:.*:READ_COVERAGE:BEDTOOLS_MERGE_MIN" {
         ext.args        = "-d 50"
         ext.prefix      = { "zerodepth" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:GNU_SORT" {
+    withName: ".*:.*:READ_COVERAGE:GNU_SORT" {
         ext.args        = { "-k1,1 -k2,2n -S${task.memory.mega - 100}M -T ." }
         ext.prefix      = { "${meta.id}_sorted" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:BED2BW_NORMAL" {
+    withName: ".*:.*:READ_COVERAGE:BED2BW_NORMAL" {
         ext.prefix      = { "${meta.id}_coverage_normal" }
     }
 
-    withName: ".*:.*:LONGREAD_COVERAGE:BED2BW_LOG" {
+    withName: ".*:.*:READ_COVERAGE:BED2BW_LOG" {
         ext.prefix      = { "${meta.id}_coverage_log" }
     }
 

modules.json

@@ -94,7 +94,8 @@
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
                     "minimap2/index": {
                         "branch": "master",
@@ -136,6 +137,11 @@
                         "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
                         "installed_by": ["modules"]
                     },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/markdup": {
                         "branch": "master",
                         "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",