Trio

.github/workflows/linting.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+        run: npm install -g editorconfig-checker@3.0.2
 
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile\|drawio')

assets/test.yaml

@@ -11,6 +11,11 @@ dataset:
   HiC:
     reads:
       - reads: https://tolit.cog.sanger.ac.uk/test-data/Undibacterium_unclassified/genomic_data/baUndUnlc1/hic-arima2/41741_2%237.sub.cram
+  trio:
+    matreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz
+    patreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz
 hic_motif: GATC,GANTC,CTNAG,TTAA
 hic_aligner: bwamem2
 busco:

assets/test_gfLaeSulp1.yaml

@@ -3,9 +3,15 @@ dataset:
   pacbio:
     reads:
       - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/pacbio/fasta/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz
-    HiC:
-      reads:
-        - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/hic-arima2/40063_3#5.cram
+  HiC:
+    reads:
+      - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/hic-arima2/40063_3#5.cram
+  trio:
+    matreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz
+    patreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz
+
 hic_motif: GATC,GANTC,CTNAG,TTAA
 hic_aligner: minimap2
 busco:

assets/test_gsMetZobe1.yaml

@@ -11,6 +11,11 @@ dataset:
   HiC:
     reads:
       - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/hic-arima2/35528_4#7.cram
+  trio:
+    matreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz
+    patreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz
 hic_motif: GATC,GANTC,CTNAG,TTAA
 hic_aligner: minimap2
 busco:

assets/test_iyVesGerm1.yaml

@@ -8,6 +8,11 @@ dataset:
   HiC:
     reads:
       - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/hic-arima2/34957_3#2.cram
+  trio:
+    matreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz
+    patreads:
+      - https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz
 hic_motif: GATC,GANTC,CTNAG,TTAA
 hic_aligner: minimap2
 busco:

conf/modules.config

@@ -756,6 +756,107 @@ process {
 
     // End of hap1/hap2 scaffolding
 
+    // start of PAT/MAT scaffolding
+    if (params.hifiasm_trio_on) {
+
+    withName: '.*HIC_MAPPING_HAP.*:SAMTOOLS_MARKDUP_HIC_MAPPING' {
+        ext.prefix  = { "${meta.id}_mkdup" }
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*HIC_MAPPING_HAP.*:BAMTOBED_SORT' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+
+    withName: '.*HIC_MAPPING_.*AT.*:CONVERT_STATS:SAMTOOLS_STATS' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*HIC_MAPPING_.*AT.*:CONVERT_STATS:SAMTOOLS_FLAGSTAT' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*HIC_MAPPING_.*AT.*:CONVERT_STATS:SAMTOOLS_IDXSTATS' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*SCAFFOLDING_.*AT.*:YAHS' {
+        ext.prefix = { "${meta.hap_id}" }
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}/yahs/out.break.yahs" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+
+    }
+
+    withName: '.*SCAFFOLDING_.*AT.*:COOLER_CLOAD' {
+        // Positions in the input file are zero-based;
+        // chrom1 field number (one-based) is 2;
+        // pos1 field number (one-based) is 3;
+        // chrom2 field number (one-based) is 6;
+        // pos2 field number (one-based) is 7
+        ext.args = 'pairs -0 -c1 2 -p1 3 -c2 6 -p2 7'
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}/yahs/out.break.yahs" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*SCAFFOLDING_.*AT.*:PRETEXTSNAPSHOT' {
+        // Make one plot containing all sequences
+        ext.args = '--sequences \"=full\"'
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}/yahs/out.break.yahs" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*SCAFFOLDING_.*AT.*:JUICER_TOOLS_PRE' {
+        ext.juicer_tools_jar = 'juicer_tools.1.9.9_jcuda.0.8.jar'
+        ext.juicer_jvm_params = '-Xms1g -Xmx6g'
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}/yahs/out.break.yahs" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*SCAFFOLDING_.*AT.*:JUICER_PRE' {
+        ext.args2 = "LC_ALL=C sort -k2,2d -k6,6d -S50G | awk '\$3>=0 && \$7>=0'"
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_${meta.hap_id}/yahs/out.break.yahs" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    }
+
+    //end of trio scaffolding
+
     withName: '.*GENOME_STATISTICS_SCAFFOLDS_HAPS:GFASTATS_PRI' {
         ext.prefix = { "${meta.id}_scaffolds_final" }
         publishDir = [
@@ -808,6 +909,14 @@ process {
         ]
     }
 
+    withName: YAK_COUNT_MAT {
+        ext.prefix      = { "${meta.id}_yak_mat" }
+    }
+
+    withName: YAK_COUNT_PAT {
+        ext.prefix      = { "${meta.id}_yak_pat" }
+    }
+
     // End of Scaffolding hap1/hap2
     // End of Set up of the scaffolding  pipeline
 

modules.json

@@ -116,7 +116,7 @@
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "95f7516731f960e86bff900b9f1d80a8904bffd8",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
@@ -249,6 +249,11 @@
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
+                    },
+                    "yak/count": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"]
                     }
                 }
             }