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updated VCF output file renaming in kSNP3 task #207

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merged 3 commits into from
Oct 26, 2023
Merged

updated VCF output file renaming in kSNP3 task #207

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577af7d
updated VCF output file renaming in kSNP3 task; also added 1 new File…
kapsakcj Oct 4, 2023
b104401
ksnp3 task:changed VCF file names to be predictable; split 2 ksnp3 op…
kapsakcj Oct 5, 2023
0b0b89e
added new string output to ksnp3 workflow "ksnp3_vcf_ref_samplename"
kapsakcj Oct 5, 2023
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19 changes: 14 additions & 5 deletions tasks/phylogenetic_inference/task_ksnp3.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,8 @@ task ksnp3 {
-in ksnp3_input.tsv \
-outdir ksnp3 \
-k ~{kmer_size} \
-core -vcf \
-core \
-vcf \
~{'-SNPs_all ' + previous_ksnp3_snps} \
~{ksnp3_args}

Expand All @@ -71,7 +72,13 @@ task ksnp3 {
echo "The core SNP matrix could not be produced" | tee SKIP_SNP_DIST # otherwise, skip
fi

mv -v ksnp3/VCF.*.vcf ksnp3/~{cluster_name}_core.vcf
# capture sample name of genome used as reference
ls ksnp3/*.vcf | cut -d '.' -f 2 | tee KSNP3_VCF_REF_SAMPLENAME.txt

# rename the 2 vcf files by appending ~{cluster_name} and removing the ref genome name to make final filenames predictable
mv -v ksnp3/VCF.*.vcf ksnp3/~{cluster_name}_VCF.reference_genome.vcf
mv -v ksnp3/VCF.SNPsNotinRef.* ksnp3/~{cluster_name}_VCF_.SNPsNotinRef.tsv

mv -v ksnp3/SNPs_all_matrix.fasta ksnp3/~{cluster_name}_pan_SNPs_matrix.fasta
mv -v ksnp3/tree.parsimony.tre ksnp3/~{cluster_name}_pan_parsimony.nwk

Expand All @@ -84,9 +91,11 @@ task ksnp3 {

>>>
output {
File ksnp3_core_matrix = "ksnp3/${cluster_name}_core_SNPs_matrix.fasta"
File ksnp3_core_tree = "ksnp3/${cluster_name}_core.nwk"
File ksnp3_core_vcf = "ksnp3/${cluster_name}_core.vcf"
File ksnp3_core_matrix = "ksnp3/~{cluster_name}_core_SNPs_matrix.fasta"
File ksnp3_core_tree = "ksnp3/~{cluster_name}_core.nwk"
File ksnp3_vcf_ref_genome = "ksnp3/~{cluster_name}_VCF.reference_genome.vcf"
File ksnp3_vcf_snps_not_in_ref = "ksnp3/~{cluster_name}_VCF_.SNPsNotinRef.tsv"
String ksnp3_vcf_ref_samplename = read_string("KSNP3_VCF_REF_SAMPLENAME.txt")
File ksnp3_pan_matrix = "ksnp3/~{cluster_name}_pan_SNPs_matrix.fasta"
File ksnp3_pan_parsimony_tree = "ksnp3/~{cluster_name}_pan_parsimony.nwk"
File? ksnp3_ml_tree = "ksnp3/~{cluster_name}_ML.nwk"
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4 changes: 3 additions & 1 deletion workflows/phylogenetics/wf_ksnp3.wdl
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Expand Up @@ -67,7 +67,9 @@ workflow ksnp3_workflow {
String ksnp3_docker = ksnp3_task.ksnp3_docker_image
# ksnp3_outputs
String ksnp3_snp_dists_version = pan_snp_dists.snp_dists_version
File ksnp3_core_vcf = ksnp3_task.ksnp3_core_vcf
File ksnp3_vcf_ref_genome = ksnp3_task.ksnp3_vcf_ref_genome
File ksnp3_vcf_snps_not_in_ref = ksnp3_task.ksnp3_vcf_snps_not_in_ref
String ksnp3_vcf_ref_samplename = ksnp3_task.ksnp3_vcf_ref_samplename
String ksnp3_core_snp_matrix_status = ksnp3_task.skip_core_snp_dists
File ksnp3_snps = ksnp3_task.ksnp3_snps_all
# ordered matrixes and reordered trees
Expand Down