Channel update

modules/local/cramino/main.nf

@@ -1,6 +1,6 @@
 process CRAMINO {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

nextflow.config

@@ -55,7 +55,7 @@ params {
     ascat_penalty               = 150
     ascat_purity                = null
     ascat_longread_bins         = 2000
-    ascat_pdf_plots             = "FALSE"
+    ascat_pdf_plots             = false
     ascat_allelecounter_flags   = "-f 0"
     ascat_chroms                = null // Only use if running on a subset of chromosomes (c(1:22, 'X', 'Y'))
 

nextflow_schema.json

@@ -166,6 +166,10 @@
                 "ascat_rt_files": {
                     "type": "string",
                     "description": "path to (zip) of RT files"
+                },
+                "ascat_pdf_plots": {
+                    "type": "boolean",
+                    "description": "Boolean for ASCAT production of pdf plots (entered as string)"
                 }
             }
         },

subworkflows/local/prepare_reference_files.nf

@@ -39,23 +39,25 @@ workflow PREPARE_REFERENCE_FILES {
             ch_prepared_fasta = [ [:], fasta ]
         }
 
+        // if clair3 model is specified, then download that
+        // otherwise use info in bam header and download that
 
         basecall_meta.map { meta, basecall_model_meta, kinetics_meta ->
-            def id_new = basecall_model_meta ?: meta.clair3_model
+            def id_new = basecall_model_meta ? clair3_modelMap.get(basecall_model_meta) : basecall_model_meta
             def meta_new = [id: id_new]
             def model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(basecall_model_meta) : meta.clair3_model
             def download_prefix = ( basecall_model_meta == 'hifi_revio' ? "https://www.bio8.cs.hku.hk/clair3/clair3_models/" : "https://cdn.oxfordnanoportal.com/software/analysis/models/clair3" )
             def url = "${download_prefix}/${model}.tar.gz"
             return [ meta_new, url ]
         }
         .unique()
-        .set{ model_urls }
+        .set{ clair3_model_urls }
 
         //
         // MODULE: Download model
         //
 
-        WGET ( model_urls )
+        WGET ( clair3_model_urls )
 
         ch_versions = ch_versions.mix(WGET.out.versions)
 
@@ -69,7 +71,7 @@ workflow PREPARE_REFERENCE_FILES {
 
         ch_versions = ch_versions.mix(UNTAR.out.versions)
 
-        UNTAR.out.untar.set { downloaded_model_files }
+        UNTAR.out.untar.set { downloaded_clair3_models }
 
         //
         // MODULE: Index the fasta
@@ -126,7 +128,7 @@ workflow PREPARE_REFERENCE_FILES {
         loci_files
         gc_file
         rt_file
-        downloaded_model_files
+        downloaded_clair3_models
 
         versions = ch_versions
 }

subworkflows/local/tumor_normal_happhase.nf

@@ -13,7 +13,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
     fai
     clair3_modelMap
     clairs_modelMap
-    downloaded_model_files
+    downloaded_clair3_models
 
     main:
 
@@ -33,34 +33,42 @@ workflow TUMOR_NORMAL_HAPPHASE {
     // Get normal bams and add platform/model info for Clair3 usage
     // remove type from so that information can be merged easier later
 
-    downloaded_model_files
+    downloaded_clair3_models
         .map{ meta, file ->
-            def basecall_model = meta.id
-            return [basecall_model, meta, file]
+            def clair3_model = meta.id
+            return [meta, clair3_model, file]
         }
-        .set{downloaded_model_files}
+        .set{downloaded_clair3_models}
 
-     mixed_bams.normal
+    mixed_bams.normal
         .map{ meta, bam, bai ->
-            def basecall_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? meta.basecall_model : meta.clair3_model
             def new_meta = [id: meta.id,
                             paired_data: meta.paired_data,
                             platform: meta.platform,
                             sex: meta.sex,
                             fiber: meta.fiber,
-                            basecall_model: basecall_model,
-                            clairS_model: meta.clairS_model]
-            return [ basecall_model, new_meta, bam, bai ]
+                            clair3_model: meta.clair3_model,
+                            clairS_model: meta.clairS_model,
+                            clairSTO_model: meta.clairSTO_model,
+                            kinetics: meta.kinetics]
+            return [ new_meta, meta.clair3_model, bam, bai ]
         }
         .set { normal_bams_model }
 
     normal_bams_model
-        .combine(downloaded_model_files,by:0)
-        .map{ basecall_model, meta, bam, bai, meta2, model ->
+        .combine(downloaded_clair3_models,by:1)
+        .map {clair3_model, meta_bam, bam, bai, meta_model, model ->
+            def platform = (meta_bam.platform == 'pb') ? 'hifi' : meta_bam.platform
+            return [meta_bam, bam, bai, model, platform]
+        }
+        .set{ normal_bams }
+
+    /*
+    .map{ basecall_model, meta, bam, bai, meta2, model ->
             def platform = (meta.platform == "pb") ? "hifi" : "ont"
             return [meta, bam, bai, model, platform]
         }
-        .set{ normal_bams }
+    */
 
     // normal_bams -> meta:         [id, paired_data, platform, sex, fiber, basecall_model]
     //                bam:          list of concatenated aligned bams
@@ -73,14 +81,15 @@ workflow TUMOR_NORMAL_HAPPHASE {
     // remove type from so that information can be merged easier later
     mixed_bams.tumor
         .map{ meta, bam, bai ->
-            def basecall_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? meta.basecall_model : meta.clair3_model
             def new_meta = [id: meta.id,
                             paired_data: meta.paired_data,
                             platform: meta.platform,
                             sex: meta.sex,
                             fiber: meta.fiber,
-                            basecall_model: basecall_model,
-                            clairS_model: meta.clairS_model]
+                            clair3_model: meta.clair3_model,
+                            clairS_model: meta.clairS_model,
+                            clairSTO_model: meta.clairSTO_model,
+                            kinetics: meta.kinetics]
             return[new_meta, bam, bai]
         }
         .set{ tumor_bams }
@@ -162,6 +171,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
 
     // Add phased vcf to tumour bams and type information
     // mix with the normal bams
+
     tumor_bams
         .join(LONGPHASE_PHASE.out.snv_vcf)
         .map { meta, bam, bai, vcf ->
@@ -211,13 +221,11 @@ workflow TUMOR_NORMAL_HAPPHASE {
     )
 
     ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
-
     // Add index to channel
     mixed_bams_vcf
         .join(mixed_hapbams)
         .join(SAMTOOLS_INDEX.out.bai)
         .set{ mixed_hapbams }
-
     // mixed_hapbams -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model]
     //                  bams: haplotagged aligned bams
     //                  bais: indexes for bam files
@@ -230,8 +238,10 @@ workflow TUMOR_NORMAL_HAPPHASE {
                             platform: meta.platform,
                             sex: meta.sex,
                             fiber: meta.fiber,
-                            basecall_model: meta.basecall_model,
-                            clairS_model: meta.clairS_model]
+                            clair3_model: meta.clair3_model,
+                            clairS_model: meta.clairS_model,
+                            clairSTO_model: meta.clairSTO_model,
+                            kinetics: meta.kinetics]
             return[new_meta, [[type: meta.type], hapbam], [[type: meta.type], hapbai]]
         }
         .groupTuple(size: 2)
@@ -245,7 +255,6 @@ workflow TUMOR_NORMAL_HAPPHASE {
         }
         .join(LONGPHASE_PHASE.out.snv_vcf)
         .set{tumor_normal_severus}
-
     // tumor_normal_severus -> meta:       [id, paired_data, platform, sex, fiber, basecall_model]
     //                         tumor_bam:  haplotagged aligned bam for tumor
     //                         tumor_bai:  indexes for tumor bam files
@@ -256,11 +265,9 @@ workflow TUMOR_NORMAL_HAPPHASE {
     // Get ClairS input channel
     tumor_normal_severus
         .map { meta, tumor_bam, tumor_bai, normal_bam, normal_bai, vcf ->
-            def model = (!meta.clairS_model || meta.clairS_model.toString().trim() in ['', '[]']) ? clairs_modelMap.get(meta.basecall_model.toString().trim()) : meta.clairS_model
-            return[meta , tumor_bam, tumor_bai, normal_bam, normal_bai, model]
+            return[meta , tumor_bam, tumor_bai, normal_bam, normal_bai, meta.clairS_model]
         }
         .set { clairs_input }
-
     //
     // MODULE: CLAIRS
     //

subworkflows/local/tumor_only_happhase.nf

@@ -25,8 +25,7 @@ workflow TUMOR_ONLY_HAPPHASE {
 
     tumor_bams
         .map{ meta, bam, bai ->
-            def clairSTO_model = (!meta.clairSTO_model || meta.clairSTO_model.toString().trim() in ['', '[]']) ? clairSTO_modelMap.get(meta.basecall_model.toString().trim()) : meta.clairSTO_model
-            return [meta, bam, bai, clairSTO_model]
+            return [meta, bam, bai, meta.clairSTO_model]
         }
         .set{ tumor_bams }
 
@@ -168,7 +167,10 @@ workflow TUMOR_ONLY_HAPPHASE {
                             platform: meta.platform,
                             sex: meta.sex,
                             fiber: meta.fiber,
-                            basecall_model: meta.basecall_model]
+                            clair3_model: meta.clair3_model,
+                            clairS_model: meta.clairS_model,
+                            clairSTO_model: meta.clairSTO_model,
+                            kinetics: meta.kinetics]
             return [new_meta, hap_bam, hap_bai, [], [], vcf]
             }
         .set{ tumor_only_severus }

tests/default.nf.test

@@ -19,6 +19,30 @@ nextflow_pipeline {
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
+                { //files exist
+                    assert file("$launchDir/output/sample1/variants/clair3/merge_output.vcf.gz").exists()
+                    assert file("$launchDir/output/sample1/variants/clair3/merge_output.vcf.gz.tbi").exists()
+                    assert file("$launchDir/output/sample1/variants/clairs/indel.vcf.gz").exists()
+                    assert file("$launchDir/output/sample1/variants/clairs/indel.vcf.gz.tbi").exists()
+                    assert file("$launchDir/output/sample1/variants/clairs/snvs.vcf.gz").exists()
+                    assert file("$launchDir/output/sample1/variants/clairs/snvs.vcf.gz.tbi").exists()
+                    assert file("$launchDir/output/sample1/variants/severus/somatic_SVs/severus_somatic.vcf.gz").exists()
+                    assert file("$launchDir/output/sample2/variants/clair3/merge_output.vcf.gz").exists()
+                    assert file("$launchDir/output/sample2/variants/clair3/merge_output.vcf.gz.tbi").exists()
+                    assert file("$launchDir/output/sample2/variants/clairs/indel.vcf.gz").exists()
+                    assert file("$launchDir/output/sample2/variants/clairs/indel.vcf.gz.tbi").exists()
+                    assert file("$launchDir/output/sample2/variants/clairs/snvs.vcf.gz").exists()
+                    assert file("$launchDir/output/sample2/variants/clairs/snvs.vcf.gz.tbi").exists()
+                    assert file("$launchDir/output/sample2/variants/severus/somatic_SVs/severus_somatic.vcf.gz").exists()
+                    assert file("$launchDir/output/sample1/bamfiles/sample1_normal.bam").exists()
+                    assert file("$launchDir/output/sample1/bamfiles/sample1_tumor.bam").exists()
+                    assert file("$launchDir/output/sample1/bamfiles/sample1_normal.bam.bai").exists()
+                    assert file("$launchDir/output/sample1/bamfiles/sample1_tumor.bam.bai").exists()
+                    assert file("$launchDir/output/sample3/variants/clairsto/indel.vcf.gz").exists()
+                    assert file("$launchDir/output/sample3/variants/clairsto/snv.vcf.gz").exists()
+                    assert file("$launchDir/output/sample3/variants/clairsto/somatic.vcf.gz").exists()
+                    assert file("$launchDir/output/sample3/variants/clairsto/germline.vcf.gz").exists()
+                },
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/lrsomatic_software_mqc_versions.yml"),

tests/default.nf.test.snap

@@ -309,10 +309,10 @@
                 "sample1.stats:md5,da6ea076dd90b4e35ab2e23b8e6ead25",
                 "breakpoints_double.csv:md5,57e4f0d5509db44179e7c5044c6bc259",
                 "read_qual.txt:md5,1ad9d1900f8dcb291c97adc65c9d341c",
-                "sample2_normal.bam:md5,7e6cdc6c51235a205548be160d798d38",
-                "sample2_normal.bam.bai:md5,7ad774be4cf80ae968f94d760bddf3c8",
-                "sample2_tumor.bam:md5,9938db44490835ec0e11069b4da37547",
-                "sample2_tumor.bam.bai:md5,202852a62fc5bf4cf1c196676068606a",
+                "sample2_normal.bam:md5,554b89692e84b9ddd0615649e2b15820",
+                "sample2_normal.bam.bai:md5,af193f1922d90b8741212d2bf690c418",
+                "sample2_tumor.bam:md5,26c4e52c12aa0e874fe52ae3b729beba",
+                "sample2_tumor.bam.bai:md5,e9e64e13328aa3621e7976f8e3f29a78",
                 "sample2.mosdepth.global.dist.txt:md5,6cdc97a81a603db702cb5a113b8bc62a",
                 "sample2.mosdepth.summary.txt:md5,864370930ec1d695d942f4960bcf8fc6",
                 "sample2.flagstat:md5,cce0bb7ca79e14d8369ccc714adf4be3",
@@ -323,7 +323,7 @@
                 "sample2.flagstat:md5,83e7d7d922941691d2b023f0bd9655aa",
                 "sample2.idxstats:md5,fe8a5d1263481ea7902d575b4d95f655",
                 "sample2.stats:md5,defe74842396209b6cff4b32994287c7",
-                "breakpoints_double.csv:md5,c5a59c9ea2486f7bb9d5e40fea8f916d",
+                "breakpoints_double.csv:md5,b71bba578c126b9217765d854b21028a",
                 "read_qual.txt:md5,27edf87814aec6fa18546c8606aae4ed",
                 "sample3_tumor.bam:md5,2308beb1b4be1f0e1d6c8e52bd4f9266",
                 "sample3_tumor.bam.bai:md5,840eb3ad5ed3216a97c6a58563d4dcb1",
@@ -337,9 +337,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-07T12:24:56.969201207"
+        "timestamp": "2026-01-09T17:08:56.493545818"
     }
 }