Merge pull request #88 from IntGenomicsLab/clair3_model_fix

Clair3 model fix

Author: ljwharbers

subworkflows/local/prepare_reference_files.nf

@@ -19,6 +19,7 @@ workflow PREPARE_REFERENCE_FILES {
         ascat_loci_gc
         ascat_loci_rt
         basecall_meta
+        clair3_modelMap
 
     main:
         ch_versions = Channel.empty()
@@ -41,8 +42,9 @@ workflow PREPARE_REFERENCE_FILES {
 
         basecall_meta.map { meta, basecall_model_meta, kinetics_meta ->
             def meta_new = [id: basecall_model_meta]
+            def model = clair3_modelMap.get(meta.basecall_model.toString().trim())
             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 = "${download_prefix}/${basecall_model_meta}.tar.gz"
+            def url = "${download_prefix}/${model}.tar.gz"
             return [ meta_new, url ]
             }
             .unique()

subworkflows/local/tumor_normal_happhase.nf

@@ -44,6 +44,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
         .combine(downloaded_model_files,by:0)
         .map{ basecall_model, meta, bam, bai, meta2, model ->
             def platform = (meta.platform == "pb") ? "hifi" : "ont"
+            def clair3_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(meta.basecall_model.toString().trim()) : meta.clair3_model
             return [meta, bam, bai, model, platform]
         }
         .set{normal_bams}
@@ -92,7 +93,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
 
     normal_bams
         .join(CLAIR3.out.vcf)
-        .map { meta, bam, bai, clair3_model, user_model, platform, vcf ->
+        .map { meta, bam, bai, clair3_model, platform, vcf ->
             def svs = []
             def mods = []
             return [meta, bam, bai, vcf, svs, mods]
@@ -126,7 +127,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
 
     normal_bams
         .join(LONGPHASE_PHASE.out.vcf)
-        .map { meta, bam, bai, clair3_model, user_model, platform, vcf ->
+        .map { meta, bam, bai, clair3_model, platform, vcf ->
             def new_meta = meta + [type: "normal"]
             def snvs = []
             def mods = []

workflows/lr_somatic.nf

@@ -163,7 +163,8 @@ workflow LR_SOMATIC {
         params.ascat_loci_files,
         params.ascat_gc_files,
         params.ascat_rt_files,
-        basecall_meta
+        basecall_meta,
+        clair3_modelMap
     )
 
     ch_versions = ch_versions.mix(PREPARE_REFERENCE_FILES.out.versions)