Switch to using bcftools-score

uclahs-cds · Jul 10, 2024 · 9f9605f · 9f9605f
1 parent 3ffc997
commit 9f9605f
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Showing 4 changed files with 5 additions and 13 deletions.
diff --git a/config/default.config b/config/default.config
@@ -15,14 +15,14 @@ params {
     docker_container_registry = "ghcr.io/uclahs-cds"
 
     // Docker images
-    bcftools_version   = '1.20'
+    bcftools_version   = 'branch-nwiltsie-bootstrap'     // FIXME
     bedtools_version   = '2.31.0'
     gatk_version       = '4.2.4.1'
     pipeval_version    = '5.0.0-rc.3'
     samtools_version   = '1.20'
     stablelift_version = 'branch-nwiltsie-bootstrap'    // FIXME
 
-    docker_image_bcftools = "${-> params.docker_container_registry}/bcftools:${params.bcftools_version}"
+    docker_image_bcftools = "${-> params.docker_container_registry}/bcftools-score:${params.bcftools_version}"
     docker_image_bedtools = "${-> params.docker_container_registry}/bedtools:${params.bedtools_version}"
     docker_image_gatk = "broadinstitute/gatk:${params.gatk_version}"
     docker_image_pipeval = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"

diff --git a/input/liftover.so b/input/liftover.so
diff --git a/main.nf b/main.nf
@@ -119,16 +119,11 @@ workflow {
         validated_vcf_with_index.map { [it.sample_id, it.vcf, it.index] },
         input_ch_src_sequence,
         input_ch_dest_sequence,
-        Channel.value(params.chain_file),
-        // FIXME This is not the correct approach
-        Channel.value("${projectDir}/input/liftover.so")
+        Channel.value(params.chain_file)
     )
 
-    funcotator_input = raw_liftover.out.liftover_vcf_with_index
-
     run_funcotator(
-        // raw_liftover.out.liftover_vcf_with_index,
-        funcotator_input,
+        raw_liftover.out.liftover_vcf_with_index,
         input_ch_dest_sequence,
         Channel.value(params.funcotator_data.data_source)
     )

diff --git a/module/liftover.nf b/module/liftover.nf
@@ -34,20 +34,17 @@ process raw_liftover {
         tuple val(src_fasta_id), path(src_fasta_ref), path(src_fasta_fai), path(src_fasta_dict)
         tuple val(dest_fasta_id), path(dest_fasta_ref), path(dest_fasta_fai), path(dest_fasta_dict)
         path (chain_file)
-        // FIXME This is not the correct approach
-        path liftover_plugin, stageAs: 'bcf_plugins/liftover.so'
 
     output:
         tuple val(sample_id), path('liftover.vcf.gz'), path('liftover.vcf.gz.tbi'), emit: liftover_vcf_with_index
 
     script:
         // FIXME Use a more standard path
-        intermediate_path = "${params.output_dir_base}/${params.bcftools_version}/intermediate/${task.process}"
+        intermediate_path = "${params.output_dir_base}/bcftools-${params.bcftools_version}/intermediate/${task.process}"
 
         slug = "LiftOver-${sample_id}-${src_fasta_id}-to-${dest_fasta_id}"
 
         """
-        export BCFTOOLS_PLUGINS="\$(pwd)/bcf_plugins"
         bcftools +liftover \
             --output-type u \
             "${vcf}" \