Parametrize hap1/hap2 within meta for scaffolding

sanger-tol · Aug 16, 2024 · fc3c7f9 · fc3c7f9
1 parent b0a9671
commit fc3c7f9
Show file tree

Hide file tree

Showing 4 changed files with 45 additions and 136 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -657,204 +657,104 @@ process {
 
     // Scaffolding hap1/hap2
     if (params.hifiasm_hic_on) {
-    // hap1 scaffolding
 
-    withName: '.*HIC_MAPPING_HAP1:SAMTOOLS_MARKDUP_HIC_MAPPING' {
+    withName: '.*HIC_MAPPING_HAP.*:SAMTOOLS_MARKDUP_HIC_MAPPING' {
         ext.prefix  = { "${meta.id}_mkdup" }
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1" },
+            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_HAP1:BAMTOBED_SORT' {
+    withName: '.*HIC_MAPPING_HAP.*:BAMTOBED_SORT' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1" },
+            path: { "${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_HAP1:CONVERT_STATS:SAMTOOLS_STATS' {
+    withName: '.*HIC_MAPPING_HAP.*:CONVERT_STATS:SAMTOOLS_STATS' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1" },
+            path: { "${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_HAP1:CONVERT_STATS:SAMTOOLS_FLAGSTAT' {
+    withName: '.*HIC_MAPPING_HAP.*:CONVERT_STATS:SAMTOOLS_FLAGSTAT' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1" },
+            path: { "${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_HAP1:CONVERT_STATS:SAMTOOLS_IDXSTATS' {
+    withName: '.*HIC_MAPPING_HAP.*:CONVERT_STATS:SAMTOOLS_IDXSTATS' {
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1" },
+            path: { "${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_HAP1:YAHS' {
-        ext.prefix = 'hap1'
+    withName: '.*SCAFFOLDING_HAP.*:YAHS' {
+        ext.prefix = { "${meta.hap_id}" }
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1/yahs/out.break.yahs" },
+            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_HAP1:COOLER_CLOAD' {
+    withName: '.*SCAFFOLDING_HAP.*: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}.${params.hifiasmhic}/scaffolding_hap1/yahs/out.break.yahs" },
+            path: { "${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_HAP1:PRETEXTSNAPSHOT' {
+    withName: '.*SCAFFOLDING_HAP.*:PRETEXTSNAPSHOT' {
         // Make one plot containing all sequences
         ext.args = '--sequences \"=full\"'
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1/yahs/out.break.yahs" },
+            path: { "${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_HAP1:JUICER_TOOLS_PRE' {
+    withName: '.*SCAFFOLDING_HAP.*: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}.${params.hifiasmhic}/scaffolding_hap1/yahs/out.break.yahs" },
+            path: { "${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_HAP1:JUICER_PRE' {
+    withName: '.*SCAFFOLDING_HAP.*:JUICER_PRE' {
         ext.args2 = "LC_ALL=C sort -k2,2d -k6,6d -S50G | awk '\$3>=0 && \$7>=0'"
         publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap1/yahs/out.break.yahs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-
-    // End of hap1 scaffolding
-
-    // hap2 scaffolding
-
-    withName: '.*HIC_MAPPING_HAP2:SAMTOOLS_MARKDUP_HIC_MAPPING' {
-        ext.prefix  = { "${meta.id}_mkdup" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*HIC_MAPPING_HAP2:BAMTOBED_SORT' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-
-    withName: '.*HIC_MAPPING_HAP2:CONVERT_STATS:SAMTOOLS_STATS' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*HIC_MAPPING_HAP2:CONVERT_STATS:SAMTOOLS_FLAGSTAT' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2" },
+            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: '.*HIC_MAPPING_HAP2:CONVERT_STATS:SAMTOOLS_IDXSTATS' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
-    withName: '.*SCAFFOLDING_HAP2:YAHS' {
-        ext.prefix = 'hap2'
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2/yahs/out.break.yahs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-
-    }
-
-    withName: '.*SCAFFOLDING_HAP2:COOLER_CLOAD' {
-        // Positions in the input file are zero-based;
-        // chrom1 field number (one-based) is 2;
-        // pos1 field number (one-based) is 3;
-        // chrom2 field number (one-based) is 6;
-        // pos2 field number (one-based) is 7
-        ext.args = 'pairs -0 -c1 2 -p1 3 -c2 6 -p2 7'
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2/yahs/out.break.yahs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*SCAFFOLDING_HAP2:PRETEXTSNAPSHOT' {
-        // Make one plot containing all sequences
-        ext.args = '--sequences \"=full\"'
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2/yahs/out.break.yahs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*SCAFFOLDING_HAP2:JUICER_TOOLS_PRE' {
-        ext.juicer_tools_jar = 'juicer_tools.1.9.9_jcuda.0.8.jar'
-        ext.juicer_jvm_params = '-Xms1g -Xmx6g'
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}.${params.hifiasmhic}/scaffolding_hap2/yahs/out.break.yahs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*SCAFFOLDING_HAP2: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_hap2/yahs/out.break.yahs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    }
-    // End of hap2 scaffolding
+    // End of hap1/hap2 scaffolding
 
     withName: '.*GENOME_STATISTICS_SCAFFOLDS_HAPS:GFASTATS_PRI' {
         ext.prefix = { "${meta.id}_scaffolds_final" }
@@ -911,7 +811,6 @@ process {
     // End of Scaffolding hap1/hap2
     // End of Set up of the scaffolding  pipeline
 
-
     //Set up of assembly stats subworkflow
     withName: 'BUSCO' {
         ext.args = "--mode genome"

diff --git a/subworkflows/local/hic_mapping.nf b/subworkflows/local/hic_mapping.nf
@@ -26,6 +26,7 @@ workflow HIC_MAPPING {
     reference_tuple     // Channel [ val(meta), path(file) ]
     hic_reads_path      // Channel [ val(meta), path(directory) ]
     hic_aligner_ch      // Channel [ val(meta), val(hic_aligner)]
+    hap_id              // Value hap_id
 
     main:
     ch_versions = Channel.empty()
@@ -67,7 +68,8 @@ workflow HIC_MAPPING {
             bwamem2       : it[0].aligner == "bwamem2"
         }
         .set{ch_aligner}
-
+
+
     //
     // SUBWORKFLOW: mapping hic reads using minimap2
     //
@@ -78,7 +80,7 @@ workflow HIC_MAPPING {
     ch_versions         = ch_versions.mix( HIC_MINIMAP2.out.versions )
     mappedbams           = HIC_MINIMAP2.out.mappedbams
 
-        //
+    //
     // SUBWORKFLOW: mapping hic reads using bwamem2
     //
     HIC_BWAMEM2 (
@@ -88,6 +90,9 @@ workflow HIC_MAPPING {
     ch_versions         = ch_versions.mix( HIC_BWAMEM2.out.versions )
     mappedbams           = mappedbams.mix(HIC_BWAMEM2.out.mappedbams)
 
+    mappedbams.map{meta, bams -> [[id: meta.id, hap_id:hap_id], bams]}
+              .set { mappedbams }
+
     //
     // LOGIC: GENERATE INDEX OF REFERENCE
     //

diff --git a/subworkflows/local/scaffolding.nf b/subworkflows/local/scaffolding.nf
@@ -16,6 +16,7 @@ workflow SCAFFOLDING {
     bed_in   // tuple(meta, bed)
     fasta_in // tuple(meta, fasta)
     cool_bin  // val: cooler cload parameter 
+    hap_id    // val: hap1/hap2/empty
 
     main:
     ch_versions = Channel.empty()
@@ -37,9 +38,14 @@ workflow SCAFFOLDING {
                     .set{ scaf_ref_fai }
 
     //
+    // LOGIC: MIX IN THE HAPLOTYPE ID TO CONTROL THE OUTPUT SUFFIX 
+    //
+    bed_in.map{ meta, bed -> [[id:meta.id, hap_id:hap_id],bed] }
+        .set{ bed_in_hap }
+    //
     // MODULE: PERFORM SCAAFFOLDING WITH YAHS
     //
-    YAHS( bed_in, scaf_ref, scaf_ref_fai )
+    YAHS( bed_in_hap , scaf_ref, scaf_ref_fai )
     ch_versions = ch_versions.mix(YAHS.out.versions)
 
     //
@@ -59,7 +65,7 @@ workflow SCAFFOLDING {
     YAHS.out.binary.join(YAHS.out.scaffolds_agp)
                     .combine(scaf_ref)
                     .combine(scaf_ref_fai)
-                    .map{meta, binary, agp, fa, fai -> [meta, binary, agp, fai]}
+                    .map{meta, binary, agp, fa, fai -> [[id:meta.id, hap_id:hap_id], binary, agp, fai]}
                     .set{ch_merge}
 
     //
@@ -71,7 +77,7 @@ workflow SCAFFOLDING {
     //
     // LOGIC: BIN CONTACT PAIRS
     //
-    JUICER_PRE.out.pairs.join(bed_in)
+    JUICER_PRE.out.pairs.join(bed_in_hap)
                         .combine(Channel.of(cool_bin))
                         .set{ch_juicer}
 

diff --git a/workflows/genomeassembly.nf b/workflows/genomeassembly.nf
@@ -340,13 +340,13 @@ workflow GENOMEASSEMBLY {
     //
     // SUBWORKFLOW: MAP HIC DATA TO THE PRIMARY ASSEMBLY
     //
-    HIC_MAPPING ( primary_contigs_ch,crams_ch,hic_aligner_ch )
+    HIC_MAPPING ( primary_contigs_ch,crams_ch,hic_aligner_ch, "")
     ch_versions = ch_versions.mix(HIC_MAPPING.out.versions)
 
     //
     // SUBWORKFLOW: SCAFFOLD THE PRIMARY ASSEMBLY
     //
-    SCAFFOLDING( HIC_MAPPING.out.bed, primary_contigs_ch, cool_bin )
+    SCAFFOLDING( HIC_MAPPING.out.bed, primary_contigs_ch, cool_bin, "")
     ch_versions = ch_versions.mix(SCAFFOLDING.out.versions)
 
     //
@@ -367,37 +367,36 @@ workflow GENOMEASSEMBLY {
                        unset_busco_alts
     )
 
-
     if ( hifiasm_hic_on ) {
         //
         // SUBWORKFLOW: MAP HIC DATA TO THE HAP1 CONTIGS
         //
-        HIC_MAPPING_HAP1 ( RAW_ASSEMBLY.out.hap1_hic_contigs, crams_ch, hic_aligner_ch )
+        HIC_MAPPING_HAP1 ( RAW_ASSEMBLY.out.hap1_hic_contigs, crams_ch, hic_aligner_ch, 'hap1' )
         ch_versions = ch_versions.mix(HIC_MAPPING_HAP1.out.versions)
 
         //
         // SUBWORKFLOW: SCAFFOLD HAP1
         //
-        SCAFFOLDING_HAP1( HIC_MAPPING_HAP1.out.bed, RAW_ASSEMBLY.out.hap1_hic_contigs, cool_bin )
+        SCAFFOLDING_HAP1( HIC_MAPPING_HAP1.out.bed, RAW_ASSEMBLY.out.hap1_hic_contigs, cool_bin, 'hap1' )
         ch_versions = ch_versions.mix(SCAFFOLDING_HAP1.out.versions)
 
         //
         // SUBWORKFLOW: MAP HIC DATA TO THE HAP2 CONTIGS
         //
-        HIC_MAPPING_HAP2 ( RAW_ASSEMBLY.out.hap2_hic_contigs, crams_ch, hic_aligner_ch )
+        HIC_MAPPING_HAP2 ( RAW_ASSEMBLY.out.hap2_hic_contigs, crams_ch, hic_aligner_ch, 'hap2' )
         ch_versions = ch_versions.mix(HIC_MAPPING_HAP2.out.versions)
 
         //
         // SUBWORKFLOW: SCAFFOLD HAP2
         //
-        SCAFFOLDING_HAP2( HIC_MAPPING_HAP2.out.bed, RAW_ASSEMBLY.out.hap2_hic_contigs, cool_bin )
+        SCAFFOLDING_HAP2( HIC_MAPPING_HAP2.out.bed, RAW_ASSEMBLY.out.hap2_hic_contigs, cool_bin, 'hap2' )
         ch_versions = ch_versions.mix(SCAFFOLDING_HAP2.out.versions)
 
         //
         // LOGIC: CREATE A CHANNEL FOR THE FULL HAP1/HAP2 ASSEMBLY
         //
         SCAFFOLDING_HAP1.out.fasta.combine(SCAFFOLDING_HAP2.out.fasta)
-                    .map{meta_s, fasta_s, meta_h, fasta_h -> [ meta_h, fasta_s, fasta_h ]}
+                    .map{meta_s, fasta_s, meta_h, fasta_h -> [ [id:meta_h.id], fasta_s, fasta_h ]}
                     .set{ stats_haps_input_ch }
 
         //