fix wfmash v0.12.6 parameters and other bugs

.github/workflows/ci.yml

@@ -50,7 +50,7 @@ jobs:
     strategy:
       matrix:
         parameters:
-          - '--vcf_spec "gi|568815561:#,gi|568815567:#"'
+          - '--vcf_spec "gi|568815561:5,gi|568815567:25"'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -164,7 +164,7 @@ jobs:
         parameters:
           - "--communities"
           - "--communities --wfmash_chunks 2"
-          - '--communities --vcf_spec "gi|568815561:#,gi|568815567:#"'
+          - '--communities --vcf_spec "gi|568815561:5,gi|568815567:25"'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3

conf/hla.config

@@ -15,7 +15,7 @@ process {
     }
 
     withName:'SMOOTHXG' {
-        cpus = 4
+        cpus = 8
         memory = 8.GB
 //        container = "ghcr.io/pangenome/pggb:20230331171956507fc0"
     }

conf/modules.config

@@ -102,7 +102,7 @@ process {
     withName: WFMASH_MAP_ALIGN {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -114,6 +114,7 @@ process {
                 "${wfmash_sparse_map_cmd}",
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -126,7 +127,7 @@ process {
     withName: WFMASH_MAP {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -139,6 +140,7 @@ process {
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-m",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -151,7 +153,7 @@ process {
     withName: WFMASH_MAP_COMMUNITY {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -164,6 +166,7 @@ process {
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-m",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -185,7 +188,7 @@ process {
     withName: WFMASH_ALIGN {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -198,6 +201,7 @@ process {
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "--invert-filtering",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [

modules/local/vg_deconstruct/main.nf

@@ -29,7 +29,7 @@ process VG_DECONSTRUCT {
         'https://depot.galaxyproject.org/singularity/pggb:0.5.3--hdfd78af_2':
         'quay.io/biocontainers/pggb:0.5.3--hdfd78af_2' }"
 */
-    container "ghcr.io/pangenome/pggb:20230819064109936a2c"
+    container "ghcr.io/pangenome/pggb:202402032147026ffe7f"
 
     input:
     tuple val(meta), path(graph), val(vcf_spec)
@@ -47,16 +47,20 @@ process VG_DECONSTRUCT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     ref=\$(echo "$vcf_spec" | cut -f 1 -d:)
-    delim=\$(echo "$vcf_spec" | cut -f 2 -d:)
-    pop_length=\$(echo "$vcf_spec" | cut -f 3 -d:)
+    if [[ "$vcf_spec" == *":"* ]]; then
+        pop_length=\$(echo "$vcf_spec" | cut -f 2 -d:)
+    else
+        pop_length=""
+    fi
 
     if [[ -z \$pop_length ]]; then
         pop_length=0
     fi
 
     vcf="${graph}".\$(echo \$ref | tr '/|' '_').vcf
-    vg deconstruct -P \$ref -H \$delim -e -a -t "${task.cpus}" "${graph}" > \$vcf
+    vg deconstruct -P \$ref -H "#" -e -a -t "${task.cpus}" "${graph}" > \$vcf
     bcftools stats \$vcf > \$vcf.stats
+
     if [[ \$pop_length -gt 0 ]]; then
         vcf_decomposed=${graph}.final.\$(echo \$ref | tr '/|' '_').decomposed.vcf
         vcf_decomposed_tmp=\$vcf_decomposed.tmp.vcf
@@ -65,7 +69,7 @@ process VG_DECONSTRUCT {
         #TODO: to remove when vcfwave will be bug-free
         # The TYPE info sometimes is wrong/missing
         # There are variants without the ALT allele
-        bcftools sort \$vcf_decomposed_tmp | bcftools annotate -x INFO/TYPE \$vcf_decomposed_tmp  | awk '\$5 != "."' > \$vcf_decomposed
+        bcftools sort \$vcf_decomposed_tmp | bcftools annotate -x INFO/TYPE | awk '\$5 != "."' > \$vcf_decomposed
         rm \$vcf_decomposed_tmp \$vcf.gz
         bcftools stats \$vcf_decomposed > \$vcf_decomposed.stats
     fi

nextflow.config

@@ -27,6 +27,7 @@ params {
     wfmash_only                 = false
     wfmash_temp_dir             = null
     wfmash_hg_filter_ani_diff   = 30
+    wfmash_n_mappings           = 1
 
     // Seqwish options
     seqwish_paf = null

nextflow_schema.json

@@ -119,6 +119,11 @@
                     "type": "integer",
                     "default": 30,
                     "description": "Filter out mappings unlikely to be this Average Nucleotide Identity (ANI) less than the best mapping."
+                },
+                "wfmash_n_mappings": {
+                    "type": "integer",
+                    "default": 1,
+                    "description": "Number of mappings for each segment."
                 }
             }
         },

workflows/pangenome.nf

@@ -132,7 +132,7 @@ workflow PANGENOME {
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     if (!params.communities) {
         if (!params.wfmash_only) {
-            ch_multiqc_files = ch_multiqc_files.mix(PGGB.out.qc.map{return it[1..8]})
+            ch_multiqc_files = ch_multiqc_files.mix(PGGB.out.qc.map{return it[1..9]})
         }
     } else {
         ch_multiqc_files = ch_multiqc_files.mix(ODGI_QC.out.qc.map{return it[1..8]})