Replace baseName with simpleName.

For compatibilty with .vcf.gz files.
UMCUGenetics · May 23, 2022 · d9c3db1 · d9c3db1
1 parent 2193145
commit d9c3db1
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Showing 5 changed files with 30 additions and 42 deletions.
diff --git a/GATK/4.2.1.0/GenotypeGvcfs.nf b/GATK/4.2.1.0/GenotypeGvcfs.nf
@@ -11,8 +11,8 @@ process GenotypeGVCFs {
     output:
         tuple(
             analysis_id,
-            path("${analysis_id}_${interval_file.baseName}${ext_vcf}"),
-            path("${analysis_id}_${interval_file.baseName}${ext_vcf}${ext_vcf_index}"),
+            path("${analysis_id}_${interval_file.simpleName}${ext_vcf}"),
+            path("${analysis_id}_${interval_file.simpleName}${ext_vcf}${ext_vcf_index}"),
             emit:vcf_file
         )
 
@@ -24,14 +24,14 @@ process GenotypeGVCFs {
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" GenotypeGVCFs \
         --reference ${params.genome} \
         --variant $input_files \
-        --output ${analysis_id}_${interval_file.baseName}${ext_vcf} \
+        --output ${analysis_id}_${interval_file.simpleName}${ext_vcf} \
         --intervals ${interval_file} \
         ${params.optional}
         """
 }
 
 process GenotypeGVCF {
-    tag {"GATK GenotypeGVCF ${sample_id} - ${interval_file.baseName}"}
+    tag {"GATK GenotypeGVCF ${sample_id} - ${interval_file.simpleName}"}
     label 'GATK_4_2_1_0'
     label 'GATK_4_2_1_0_GenotypeGVCF'
     container = 'broadinstitute/gatk:4.2.1.0'
@@ -43,8 +43,8 @@ process GenotypeGVCF {
     output:
         tuple(
             val(sample_id),
-            path("${sample_id}_${interval_file.baseName}${ext_vcf}"),
-            path("${sample_id}_${interval_file.baseName}${ext_vcf}${ext_vcf_index}"),
+            path("${sample_id}_${interval_file.simpleName}${ext_vcf}"),
+            path("${sample_id}_${interval_file.simpleName}${ext_vcf}${ext_vcf_index}"),
             emit: vcf_file
         )
 
@@ -56,7 +56,7 @@ process GenotypeGVCF {
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" GenotypeGVCFs \
         --reference ${params.genome} \
         --variant $input_files \
-        --output ${sample_id}_${interval_file.baseName}${ext_vcf} \
+        --output ${sample_id}_${interval_file.simpleName}${ext_vcf} \
         --intervals ${interval_file} \
         ${params.optional}
         """

diff --git a/GATK/4.2.1.0/HaplotypeCaller.nf b/GATK/4.2.1.0/HaplotypeCaller.nf
@@ -11,24 +11,21 @@ process HaplotypeCaller {
     output:
         tuple(
             val(analysis_id),
-            path("${analysis_id}.${interval_file.baseName}${ext_vcf}"),
-            path("${analysis_id}.${interval_file.baseName}${ext_vcf}${ext_vcf_index}"),
+            path("${analysis_id}.${interval_file.simpleName}${ext_vcf}"),
+            path("${analysis_id}.${interval_file.simpleName}${ext_vcf}${ext_vcf_index}"),
             emit: vcf_file
         )
 
     script:
         def input_files = bam_files.collect{"$it"}.join(" --input ")
-        ext_vcf = ".vcf"
-        ext_vcf_index = ".idx"
-        if( params.compress )
-            ext_vcf = ".vcf.gz"
-            ext_vcf_index = ".tbi"
+        ext_vcf = params.compress ? ".vcf.gz" : ".vcf"
+        ext_vcf_index = params.compress ? ".tbi" : ".idx"
         """
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" HaplotypeCaller \
         --reference ${params.genome} \
         --input ${input_files} \
         --intervals ${interval_file} \
-        --output ${analysis_id}.${interval_file.baseName}${ext_vcf} \
+        --output ${analysis_id}.${interval_file.simpleName}${ext_vcf} \
         ${params.optional}
         """
 }
@@ -47,24 +44,21 @@ process HaplotypeCallerGVCF {
     output:
         tuple(
             val(sample_id),
-            path("${sample_id}_${interval_file.baseName}${ext_gvcf}"),
-            path("${sample_id}_${interval_file.baseName}${ext_gvcf}${ext_gvcf_index}"),
+            path("${sample_id}_${interval_file.simpleName}${ext_gvcf}"),
+            path("${sample_id}_${interval_file.simpleName}${ext_gvcf}${ext_gvcf_index}"),
             path(interval_file),
             emit: vcf_file
         )
 
     script:
-        ext_gvcf = ".g.vcf"
-        ext_gvcf_index = ".idx"
-        if( params.compress )
-            ext_gvcf = ".g.vcf.gz"
-            ext_gvcf_index = ".tbi"
+        ext_gvcf = params.compress ? ".g.vcf.gz" : ".g.vcf"
+        ext_gvcf_index = params.compress ? ".tbi" : ".idx"
         """
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" HaplotypeCaller \
         --reference ${params.genome} \
         --input ${bam_file} \
         --intervals ${interval_file} \
-        --output ${sample_id}_${interval_file.baseName}${ext_gvcf} \
+        --output ${sample_id}_${interval_file.simpleName}${ext_gvcf} \
         --emit-ref-confidence ${params.emit_ref_confidence} \
         ${params.optional}
         """

diff --git a/GATK/4.2.1.0/MergeVcfs.nf b/GATK/4.2.1.0/MergeVcfs.nf
@@ -13,11 +13,8 @@ process MergeVcfs {
 
     script:
         def input_files = vcf_files.collect{"$it"}.join(" --INPUT ")
-        ext_vcf = ".vcf"
-        ext_vcf_index = ".idx"
-        if( params.compress )
-            ext_vcf = ".vcf.gz"
-            ext_vcf_index = ".tbi"
+        ext_vcf = params.compress ? ".vcf.gz" : ".vcf"
+        ext_vcf_index = params.compress ? ".tbi" : ".idx"
         """
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" MergeVcfs --INPUT ${input_files} --OUTPUT ${output_name}${ext_vcf}
         """
@@ -39,11 +36,8 @@ process MergeGvcfs {
 
     script:
         def input_files = vcf_files.collect{"$it"}.join(" --INPUT ")
-        ext_gvcf = ".g.vcf"
-        ext_gvcf_index = ".idx"
-        if( params.compress )
-            ext_gvcf = ".g.vcf.gz"
-            ext_gvcf_index = ".tbi"
+        ext_gvcf = params.compress ? ".g.vcf.gz" : ".g.vcf"
+        ext_gvcf_index = params.compress ? ".tbi" : ".idx"
         """
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" MergeVcfs --INPUT ${input_files} --OUTPUT ${output_name}${ext_gvcf}
         """

diff --git a/GATK/4.2.1.0/SelectVariants.nf b/GATK/4.2.1.0/SelectVariants.nf
@@ -11,8 +11,8 @@ process SelectVariantsSample {
     output:
         tuple(
             sample_id,
-            path("${sample_id}_${vcf_file.baseName}${ext_vcf}"),
-            path("${sample_id}_${vcf_file.baseName}${ext_vcf}${ext_vcf_index}"),
+            path("${sample_id}_${vcf_file.simpleName}${ext_vcf}"),
+            path("${sample_id}_${vcf_file.simpleName}${ext_vcf}${ext_vcf_index}"),
             emit: vcf_file
         )
 
@@ -23,7 +23,7 @@ process SelectVariantsSample {
         gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants \
         --reference ${params.genome} \
         --variant ${vcf_file} \
-        --output ${sample_id}_${vcf_file.baseName}${ext_vcf} \
+        --output ${sample_id}_${vcf_file.simpleName}${ext_vcf} \
         --sample-name ${sample_id} \
         ${params.optional}
         """

diff --git a/GATK/4.2.1.0/VariantFiltration.nf b/GATK/4.2.1.0/VariantFiltration.nf
@@ -9,18 +9,18 @@ process VariantFiltrationSnpIndel {
         tuple(analysis_id, path(vcf_file), path(vcf_idx_file))
 
     output:
-        tuple(analysis_id, path("${vcf_file.baseName}.filter${ext_vcf}"), path("${vcf_file.baseName}.filter${ext_vcf}${ext_vcf_index}"), emit: vcf_file)
+        tuple(analysis_id, path("${vcf_file.simpleName}.filter${ext_vcf}"), path("${vcf_file.simpleName}.filter${ext_vcf}${ext_vcf_index}"), emit: vcf_file)
 
     script:
         ext_vcf = params.compress || vcf_file.getExtension() == ".gz" ? ".vcf.gz" : ".vcf"
         ext_vcf_index = params.compress || vcf_file.getExtension() == ".gz" ? ".tbi" : ".idx"
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants --reference ${params.genome} --variant $vcf_file --output ${vcf_file.baseName}.snp${ext_vcf} --select-type-to-exclude INDEL
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants --reference ${params.genome} --variant $vcf_file --output ${vcf_file.baseName}.indel${ext_vcf} --select-type-to-include INDEL
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants --reference ${params.genome} --variant $vcf_file --output ${vcf_file.simpleName}.snp${ext_vcf} --select-type-to-exclude INDEL
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants --reference ${params.genome} --variant $vcf_file --output ${vcf_file.simpleName}.indel${ext_vcf} --select-type-to-include INDEL
 
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration --reference ${params.genome} --variant ${vcf_file.baseName}.snp${ext_vcf} --output ${vcf_file.baseName}.snp_filter${ext_vcf} ${params.snp_filter} ${params.snp_cluster}
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration --reference ${params.genome} --variant ${vcf_file.baseName}.indel${ext_vcf} --output ${vcf_file.baseName}.indel_filter${ext_vcf} ${params.indel_filter}
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration --reference ${params.genome} --variant ${vcf_file.simpleName}.snp${ext_vcf} --output ${vcf_file.simpleName}.snp_filter${ext_vcf} ${params.snp_filter} ${params.snp_cluster}
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration --reference ${params.genome} --variant ${vcf_file.simpleName}.indel${ext_vcf} --output ${vcf_file.simpleName}.indel_filter${ext_vcf} ${params.indel_filter}
 
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" MergeVcfs --INPUT ${vcf_file.baseName}.snp_filter${ext_vcf} --INPUT ${vcf_file.baseName}.indel_filter${ext_vcf} --OUTPUT ${vcf_file.baseName}.filter${ext_vcf}
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" MergeVcfs --INPUT ${vcf_file.simpleName}.snp_filter${ext_vcf} --INPUT ${vcf_file.simpleName}.indel_filter${ext_vcf} --OUTPUT ${vcf_file.simpleName}.filter${ext_vcf}
         """
 }