From e0b5c50b1b6a8d280ffa7643323d0955108f6cc7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Mar 2021 10:07:16 +0100
Subject: [PATCH] gatk4: change output to avoid using file_id var as it can be
a dict
---
src/nf_modules/gatk4/main.nf | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 44049069..737c1ea4 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -18,7 +18,7 @@ process variant_calling {
gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
-R ${fasta} \
-I ${bam} \
- -O ${file_id}.vcf
+ -O ${bam.simpleName}.vcf
"""
}
@@ -39,7 +39,7 @@ gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
-select-type SNP \
- -O ${file_id}_snp.vcf
+ -O ${vcf.simpleName}_snp.vcf
"""
}
@@ -60,7 +60,7 @@ gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
-select-type INDEL \
- -O ${file_id}_indel.vcf
+ -O ${vcf.simpleName}_indel.vcf
"""
}
@@ -84,7 +84,7 @@ gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-V ${vcf} \
--filter-expression "${high_confidence_snp_filter}" \
--filter-name "basic_snp_filter" \
- -O ${file_id}_filtered_snp.vcf
+ -O ${vcf.simpleName}_filtered_snp.vcf
"""
}
@@ -108,7 +108,7 @@ gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-V ${vcf} \
--filter-expression "${high_confidence_indel_filter}" \
--filter-name "basic_indel_filter" \
- -O ${file_id}_filtered_indel.vcf
+ -O ${vcf.simpleName}_filtered_indel.vcf
"""
}
@@ -155,7 +155,7 @@ gatk --java-options "-Xmx${xmx_memory}G" ApplyBQSR \
-R ${fasta} \
-I ${bam} \
--bqsr-recal-file recal_data_table \
- -O ${file_id}_recal.bam
+ -O ${bam.simpleName}_recal.bam
"""
}
@@ -176,7 +176,7 @@ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
-R ${fasta} \
-I ${bam} \
-ERC GVCF \
- -O ${file_id}.gvcf
+ -O ${bam.simpleName}.gvcf
"""
}
@@ -196,7 +196,7 @@ process gvcf_genotyping {
gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
-R ${fasta} \
-V ${gvcf} \
- -O ${file_id}_joint.vcf.gz
+ -O ${bam.simpleName}_joint.vcf.gz
"""
}
@@ -217,7 +217,7 @@ gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
-R ${fasta} \
-V ${vcf} \
-select-type SNP \
- -O ${file_id}_joint_snp.vcf
+ -O ${vcf.simpleName}_joint_snp.vcf
"""
}
@@ -259,7 +259,7 @@ process personalized_genome {
gatk --java-options "-Xmx${xmx_memory}G" FastaAlternateReferenceMaker\
-R ${reference} \
-V ${vcf} \
- -O ${file_id[0]}_genome.fasta
+ -O ${vcf.simpleName}_genome.fasta
"""
}
--
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