fix sample name

nf-core · Jun 27, 2024 · c9b2298 · c9b2298
1 parent d7be511
commit c9b2298
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Showing 5 changed files with 34 additions and 3 deletions.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -50,7 +50,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+          pip install nf-core
 
       - name: Run nf-core lint
         env:

diff --git a/conf/modules.config b/conf/modules.config
@@ -97,6 +97,15 @@ process {
             mode: params.publish_dir_mode
         ]
     }
+    withName: BCFTOOLS_VIEW_SUBSET {
+        ext.prefix = { vcf.baseName }
+        ext.args  = {"--output-type z --samples 'QUERY'" }
+        publishDir = [
+            path: {"${params.outdir}/${meta.id}/test"},
+            pattern: "*{.test}",
+            mode: params.publish_dir_mode
+        ]
+    }
     withName: SURVIVOR_STATS {
         ext.prefix = {"${meta.id}.${meta.vartype}"}
         publishDir = [
@@ -149,7 +158,6 @@ process {
     }
     withName: "RTGTOOLS_VCFEVAL" {
         ext.prefix = {"${meta.id}.${params.sample}.${meta.vartype}"}
-        ext.args   = {params.preprocess.contains("prepy") ? "--sample 'truthHG002,QUERY'" : ""  }
         //ext.args   = {"--ref-overlap --all-record --output-mode ga4gh"}
         ext.when   = { params.method.split(',').contains('rtgtools') }
         publishDir = [

diff --git a/subworkflows/local/small_germline_benchmark.nf b/subworkflows/local/small_germline_benchmark.nf
@@ -7,6 +7,7 @@ params.options = [:]
 include { RTGTOOLS_FORMAT  } from '../../modules/nf-core/rtgtools/format/main'           addParams( options: params.options )
 include { RTGTOOLS_VCFEVAL } from '../../modules/nf-core/rtgtools/vcfeval/main'          addParams( options: params.options )
 include { HAPPY_HAPPY      } from '../../modules/nf-core/happy/happy/main'               addParams( options: params.options )
+include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_SUBSET } from '../../modules/nf-core/bcftools/view/main' addParams( options: params.options )
 
 workflow SMALL_GERMLINE_BENCHMARK {
     take:
@@ -33,11 +34,27 @@ workflow SMALL_GERMLINE_BENCHMARK {
             versions = versions.mix(RTGTOOLS_FORMAT.out.versions)
             sdf = RTGTOOLS_FORMAT.out.sdf
         }
+        test_ch = input_ch.map { it -> tuple(it[0], it[1], [2]) }
+        if (params.preprocess.contains("prepy")){
+            //
+            // MODULE: BCFTOOLS_VIEW
+            //
+            BCFTOOLS_VIEW_SUBSET(
+                input_ch.map { it -> tuple(it[0], it[1], it[2]) },
+                [],[],[]
+            )
+            versions = versions.mix(BCFTOOLS_VIEW_SUBSET.out.versions)
+
+            BCFTOOLS_VIEW_SUBSET.out.vcf.map{it -> tuple(it[0], it[1], [])}.set{test_ch}
+        }
+
+        truth_ch = input_ch.map { it -> tuple(it[0], it[3], it[4], it[5], []) }
+
         //
         // MODULE: RTGTOOLS_VCFEVAL
         //
         RTGTOOLS_VCFEVAL(
-            input_ch.map { it -> tuple(it[0], it[1], it[2], it[3], it[4], it[5], []) },
+            test_ch.join(truth_ch),
             sdf
         )
         versions = versions.mix(RTGTOOLS_VCFEVAL.out.versions)

diff --git a/subworkflows/local/sv_germline_benchmark.nf b/subworkflows/local/sv_germline_benchmark.nf
@@ -36,6 +36,7 @@ workflow SV_GERMLINE_BENCHMARK {
                 fasta,
                 fai
             )
+            versions = versions.mix(TRUVARI_PHAB.out.versions)
         }
         //
         // MODULE: TRUVARI_BENCH
@@ -112,9 +113,12 @@ workflow SV_GERMLINE_BENCHMARK {
         TABIX_BGZIP_QUERY(
             input_ch.map{it -> tuple(it[0], it[1])}
         )
+        versions = versions.mix(TABIX_BGZIP_QUERY.out.versions)
+
         TABIX_BGZIP_TRUTH(
             input_ch.map{it -> tuple(it[0], it[3])}
         )
+        versions = versions.mix(TABIX_BGZIP_TRUTH.out.versions)
         bed = input_ch.map{it -> tuple(it[0], it[5])}
 
         //

diff --git a/subworkflows/local/vcf_variant_deduplication.nf b/subworkflows/local/vcf_variant_deduplication.nf
@@ -31,10 +31,12 @@ workflow VCF_VARIANT_DEDUPLICATION {
     BCFTOOLS_SORT(
         BCFTOOLS_DEDUP.out.vcf
     )
+    versions = versions.mix(BCFTOOLS_SORT.out.versions)
 
     TABIX_TABIX(
         BCFTOOLS_SORT.out.vcf
     )
+    versions = versions.mix(TABIX_TABIX.out.versions)
 
     BCFTOOLS_SORT.out.vcf.join(TABIX_TABIX.out.tbi, by:0)
                         .set{ch_vcf}