Modkit

conf/test.config

@@ -57,4 +57,5 @@ params {
     vep_species        = "caenorhabditis_elegans"
     skip_wakhan        = true
     skip_ascat         = true
+    skip_modkit        = true
 }

modules.json

@@ -105,7 +105,8 @@
                     "modkit/pileup": {
                         "branch": "master",
                         "git_sha": "3d81317a30d1016b533982d6b84df07713ae520a",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/modkit/pileup/modkit-pileup.diff"
                     },
                     "mosdepth": {
                         "branch": "master",

modules/local/clair3/main.nf

@@ -42,7 +42,7 @@ process CLAIR3 {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}.phased_merge_output.vcf.gz
     touch ${prefix}.phased_merge_output.vcf.gz.tbi

modules/local/longphase/modcall/main.nf

@@ -16,7 +16,7 @@ process LONGPHASE_MODCALL {
     output:
     tuple val(meta), path("*.vcf")       , emit: mod_vcf
     tuple val(meta), path("*.log")       , emit: log , optional: true
-    path "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('longphase'), eval("longphase --version | head -n 1 | sed 's/Version: //'"), topic: versions, emit: versions_longphase
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,11 +38,6 @@ process LONGPHASE_MODCALL {
     if [ -f "${prefix}.out" ]; then
         mv ${prefix}.out ${prefix}.log
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        longphase: \$(longphase --version | head -n 1 | sed 's/Version: //')
-    END_VERSIONS
     """
 
     stub:
@@ -52,10 +47,5 @@ process LONGPHASE_MODCALL {
     """
     touch ${prefix}.vcf
     ${log}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        longphase: \$(longphase --version | head -n 1 | sed 's/Version: //')
-    END_VERSIONS
     """
 }

modules/local/wakhan/main.nf

@@ -26,8 +26,8 @@ process WAKHAN {
     tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf")                    , emit: vcf_files
     tuple val(meta), path("*_heatmap_ploidy_purity.html")                       , emit: heatmap_html
     tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf")                   , emit: heatmap_pdf
-    tuple val(meta), path("*_optimized_peak.html")                              , emit: optimized_peak_html
     tuple val(meta), path("coverage_data/*.csv")                                , emit: coverage_csv
+    tuple val(meta), path("coverage_data/*.png")                                , emit: coverage_png
     tuple val(meta), path("coverage_plots/*.html")                              , emit: coverage_plots_html
     tuple val(meta), path("coverage_plots/*.pdf")                               , emit: coverage_plots_pdf
     tuple val(meta), path("phasing_output/*.html")                              , emit: phasing_html
@@ -50,6 +50,7 @@ process WAKHAN {
 
     """
     wakhan \\
+        all \\
         --target-bam ${tumor_input} \\
         --breakpoints ${breakpoints} \\
         --reference ${reference} \\

nextflow.config

@@ -51,6 +51,7 @@ params {
     skip_m6a                    = false
     skip_vep                    = false
     skip_modcall                = false
+    skip_modkit                 = false
     use_gpu                     = false
     skip_whatshapstats          = false
 

subworkflows/local/deepsomatic.nf

@@ -6,7 +6,7 @@ workflow DEEPSOMATIC {
     take:
     ch_input     // [meta, normal_bam, normal_bai, tumor_bam, tumor_bai]
     //              normal_bam/bai may be [] for tumor-only mode
-    ch_intervals // [[:], []]  -- empty intervals (genome-wide calling)
+    _ch_intervals // [[:], []]  -- empty intervals (genome-wide calling)
     ch_fasta     // [[:], fasta]
     ch_fai       // [[:], fai]
     ch_gzi       // [[:], gzi]  -- bgzipped FASTA index (empty if FASTA is not bgzipped)

subworkflows/local/paired/paired_smallvar_germline.nf

@@ -14,9 +14,7 @@ workflow PAIRED_SMALLVAR_GERMLINE {
     clair3_models // [meta(id=model_name), model_dir]  -- downloaded Clair3 model directories
 
     main:
-    ch_versions = channel.empty()
     germline_vcf = channel.empty()
-    germline_tbi = channel.empty()
 
     // COMBINE NORMAL BAMS WITH DOWNLOADED CLAIR3 MODELS
     // Clair3 requires the model directory path; models are keyed by model name (meta.id)

subworkflows/local/paired/paired_smallvar_somatic.nf

@@ -15,9 +15,7 @@ workflow PAIRED_SMALLVAR_SOMATIC {
     fai               // [[:], fai]
 
     main:
-    ch_versions = channel.empty()
     somatic_vcf = channel.empty()
-    somatic_tbi = channel.empty()
 
     // CLAIRS: somatic SNV/indel calling from T/N paired BAMs
     if(params.somatic_var_keep.contains('clair')) {

subworkflows/local/phasing_haplotyping.nf

@@ -141,13 +141,13 @@ workflow PHASING_HAPLOTYPING {
     // Merge germline and somatic VCFs into a single file for somatic phasing
     // Longphase requires all variant sites in one VCF to produce a consistent phase block
     germline_vcf
-            .join(somatic_vcf)
-            .map { meta, germline_vcf, germline_tbi, somatic_vcf, somatic_tbi ->
-                    def vcfs = [somatic_vcf, germline_vcf]  // somatic first (higher priority in phasing)
-                    def tbis = [somatic_tbi, germline_tbi]
-                    return [ meta, vcfs, tbis]
-            }
-            .set{germline_somatic_vcfs}
+        .join(somatic_vcf)
+        .map { meta, germ_vcf, germ_tbi, som_vcf, som_tbi ->
+                def vcfs = [som_vcf, germ_vcf]  // somatic first (higher priority in phasing)
+                def tbis = [som_tbi, germ_tbi]
+                return [ meta, vcfs, tbis]
+        }
+        .set{germline_somatic_vcfs}
     // germline_somatic_vcfs (pre-concat): [meta, [somatic_vcf, germline_vcf], [somatic_tbi, germline_tbi]]
 
     //
@@ -157,7 +157,7 @@ workflow PHASING_HAPLOTYPING {
     //
         BCFTOOLS_CONCAT(germline_somatic_vcfs)
         BCFTOOLS_CONCAT.out.vcf
-                .set{concat_out}
+            .set{concat_out}
     // concat_out: [meta, vcf]  -- concatenated (unsorted) somatic+germline VCF
 
     //

subworkflows/local/small_variant_consensus.nf

@@ -13,7 +13,7 @@ workflow SMALL_VARIANT_CONSENSUS {
     mixed_vcfs       // [meta(+caller field), vcf, tbi]  -- one item per caller per sample
     //                    meta.caller is one of: 'clair3', 'clairs-to', 'clairs', 'deepvariant', 'deepsomatic'
     fasta            // [[:], fasta]
-    fai              // [[:], fai]
+    _fai             // [[:], fai]
     prioritize_caller // str: which caller's calls take priority ('deepvariant'/'deepsomatic' or 'clair')
     combine_method   // str: 'consensus' (intersection only) or 'all' (intersection + private calls from priority caller)
 
@@ -82,8 +82,8 @@ workflow SMALL_VARIANT_CONSENSUS {
     deepvariant_ch = annotated_vcfs_branched.deepvariant
 
     // Strip 'caller' field from meta before joining so both channels share the same key
-    clair_ch.
-        map {meta, vcfs, tbi ->
+    clair_ch
+        .map {meta, vcfs, tbi ->
             def new_meta = meta.subMap('id',
                             'paired_data',
                             'type',

subworkflows/local/tumor_only/tumoronly_smallvar.nf

@@ -20,11 +20,8 @@ workflow TUMORONLY_SMALLVAR {
 
     main:
 
-    ch_versions = channel.empty()
     somatic_vcf = channel.empty()
     germline_vcf = channel.empty()
-    somatic_tbi = channel.empty()
-    germline_tbi = channel.empty()
 
     // CLAIRS-TO: somatic AND germline variant calling from tumor-only BAM
     // ClairS-TO uses a panel-of-normals / population allele database to separate somatic from germline

tests/default.nf.test.snap

@@ -61,6 +61,12 @@
                 "LONGPHASE_HAPLOTAG": {
                     "longphase": "2.0.1"
                 },
+                "LONGPHASE_MODCALL_GERMLINE": {
+                    "longphase": "2.0.1"
+                },
+                "LONGPHASE_MODCALL_SOMATIC": {
+                    "longphase": "2.0.1"
+                },
                 "LONGPHASE_PHASE_GERMLINE": {
                     "longphase": "2.0.1"
                 },
@@ -76,6 +82,12 @@
                 "MOSDEPTH": {
                     "mosdepth": "0.3.11"
                 },
+                "NANOPLOT_POST": {
+                    "nanoplot": "1.46.1"
+                },
+                "NANOPLOT_PRE": {
+                    "nanoplot": "1.46.1"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
@@ -604,6 +616,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-27T17:04:12.049740619"
+        "timestamp": "2026-04-01T14:22:53.450440867"
     }
 }