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anand-imcmanand-imcm
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added annotate flag to avoid the transfer of VEP_CACHE 
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4 files changed

+24
-11
lines changed

4 files changed

+24
-11
lines changed

‎workflows/main.wdl‎

Lines changed: 13 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -45,17 +45,21 @@ workflow main {
4545
call svcall.CallStructuralVariants {
4646
input: raw_hifi_to_reference_alignment_bam = AlignHifiReads.raw_hifi_to_reference_alignment_bam, raw_hifi_to_reference_alignment_index = AlignHifiReads.raw_hifi_to_reference_alignment_index, genome_reference = genome_ref, file_label = prefix, docker = container_src
4747
}
48-
49-
call annotateSV.AnnotateSVs {
50-
input: vcf = CallStructuralVariants.raw_hifi_to_reference_alignment_structural_PASS_norm_variants, vep_cache = vep_cache, genome_reference = genome_ref, file_label = prefix, vep_docker = vep_docker
48+
49+
if (CallStructuralVariants.ann){
50+
call annotateSV.AnnotateSVs {
51+
input: vcf = CallStructuralVariants.raw_hifi_to_reference_alignment_structural_PASS_norm_variants, vep_cache = vep_cache, genome_reference = genome_ref, file_label = prefix, vep_docker = vep_docker
52+
}
5153
}
5254
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call phase.PhaseVariants {
5456
input: vcf = CallVariants.raw_hifi_to_reference_alignment_PASS_norm_variants, bam = AlignHifiReads.raw_hifi_to_reference_alignment_bam, bam_index = AlignHifiReads.raw_hifi_to_reference_alignment_index, genome_reference = genome_ref, file_label = prefix, docker = container_src
5557
}
5658
57-
call annotate.AnnotateVariants {
58-
input: vcf = PhaseVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_variants, vep_cache = vep_cache, genome_reference = genome_ref, file_label = prefix, vep_docker = vep_docker
59+
if (PhaseVariants.ann){
60+
call annotate.AnnotateVariants {
61+
input: vcf = PhaseVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_variants, vep_cache = vep_cache, genome_reference = genome_ref, file_label = prefix, vep_docker = vep_docker
62+
}
5963
}
6064
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call report.Summary {
@@ -72,8 +76,8 @@ workflow main {
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File raw_hifi_to_reference_alignment_structural_variants_vcf = CallStructuralVariants.raw_hifi_to_reference_alignment_structural_variants
7377
File raw_hifi_to_reference_alignment_structural_PASS_variants_vcf = CallStructuralVariants.raw_hifi_to_reference_alignment_structural_PASS_variants
7478
File raw_hifi_to_reference_alignment_structural_PASS_norm_variants_vcf = CallStructuralVariants.raw_hifi_to_reference_alignment_structural_PASS_norm_variants
75-
File raw_hifi_to_reference_alignment_structural_PASS_norm_annotated_variants = AnnotateSVs.raw_hifi_to_reference_alignment_structural_PASS_norm_annotated_variants
76-
File raw_hifi_to_reference_alignment_structural_PASS_norm_variants_vep_stats = AnnotateSVs.raw_hifi_to_reference_alignment_structural_PASS_norm_variants_vep_stats
79+
File? raw_hifi_to_reference_alignment_structural_PASS_norm_annotated_variants = AnnotateSVs.raw_hifi_to_reference_alignment_structural_PASS_norm_annotated_variants
80+
File? raw_hifi_to_reference_alignment_structural_PASS_norm_variants_vep_stats = AnnotateSVs.raw_hifi_to_reference_alignment_structural_PASS_norm_variants_vep_stats
7781

7882
File raw_hifi_to_reference_alignment_all_variants_vcf = CallVariants.raw_hifi_to_reference_alignment_all_variants_vcf
7983
File raw_hifi_to_reference_alignment_all_variants_stats = CallVariants.raw_hifi_to_reference_alignment_all_variants_stats
@@ -83,8 +87,8 @@ workflow main {
8387
File raw_hifi_to_reference_alignment_PASS_norm_phased_variants = PhaseVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_variants
8488
File raw_hifi_to_reference_alignment_PASS_norm_phased_stats = PhaseVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_stats
8589

86-
File raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_variants_vcf = AnnotateVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_variants
87-
File raw_hifi_to_reference_alignment_PASS_norm_phased_variants_vep_stats = AnnotateVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_variants_vep_stats
90+
File? raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_variants_vcf = AnnotateVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_annotated_variants
91+
File? raw_hifi_to_reference_alignment_PASS_norm_phased_variants_vep_stats = AnnotateVariants.raw_hifi_to_reference_alignment_PASS_norm_phased_variants_vep_stats
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8993
File raw_hifi_to_reference_alignment_PASS_norm_phased_variants_summary = Summary.raw_hifi_to_reference_alignment_PASS_norm_phased_variants_summary
9094
File raw_hifi_to_reference_alignment_PASS_norm_phased_VEP_annotation = Summary.raw_hifi_to_reference_alignment_PASS_norm_phased_VEP_annotation

‎workflows/tasks/call_structural_variants.wdl‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -37,12 +37,18 @@ task CallStructuralVariants {
3737
bcftools view -f PASS ~{file_label}_raw_hifi_to_reference_alignment_structural_variants.vcf -Ov -o ~{file_label}_raw_hifi_to_reference_alignment_structural_PASS_variants.vcf
3838
# bcftools norm and split bialleleic sites
3939
bcftools norm ~{file_label}_raw_hifi_to_reference_alignment_structural_PASS_variants.vcf -f genome_reference.fasta -m -any -Ov -o ~{file_label}_raw_hifi_to_reference_alignment_structural_PASS_norm_variants.vcf
40+
if [ $(cat ~{file_label}_raw_hifi_to_reference_alignment_structural_PASS_norm_variants.vcf| grep -v "#" | wc -l) -eq 0 ]; then
41+
echo "false" > annotate.txt
42+
else
43+
echo "true" > annotate.txt
44+
fi
4045
>>>
4146

4247
output {
4348
File raw_hifi_to_reference_alignment_structural_variants = file_label + "_raw_hifi_to_reference_alignment_structural_variants.vcf"
4449
File raw_hifi_to_reference_alignment_structural_PASS_variants = file_label + "_raw_hifi_to_reference_alignment_structural_PASS_variants.vcf"
4550
File raw_hifi_to_reference_alignment_structural_PASS_norm_variants = file_label + "_raw_hifi_to_reference_alignment_structural_PASS_norm_variants.vcf"
51+
Boolean ann = read_boolean("annotate.txt")
4652
}
4753

4854
runtime {

‎workflows/tasks/generate_summary.wdl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@ version 1.0
33
task Summary {
44

55
input {
6-
File vcf
7-
File vcfSV
6+
File? vcf
7+
File? vcfSV
88
File bed
99
File region_to_plot
1010
File depth

‎workflows/tasks/phase_variants.wdl‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@ task PhaseVariants {
2727
# Check if the output of samtools view command has any lines
2828
if [ $(zcat ~{vcf}| grep -v "#" | wc -l) -eq 0 ]; then
2929
touch ~{file_label}_raw_hifi_to_reference_alignment_PASS_norm_phased_variants.vcf ~{file_label}_raw_hifi_to_reference_alignment_PASS_norm_phased_stats.txt
30+
echo "false" > annotate.txt
3031
else
3132
# phasing
3233
whatshap phase \
@@ -40,12 +41,14 @@ task PhaseVariants {
4041
whatshap stats \
4142
~{file_label}_raw_hifi_to_reference_alignment_PASS_norm_phased_variants.vcf \
4243
--tsv=~{file_label}_raw_hifi_to_reference_alignment_PASS_norm_phased_stats.txt
44+
echo "true" > annotate.txt
4345
fi
4446
>>>
4547

4648
output {
4749
File raw_hifi_to_reference_alignment_PASS_norm_phased_variants = file_label + "_raw_hifi_to_reference_alignment_PASS_norm_phased_variants.vcf"
4850
File raw_hifi_to_reference_alignment_PASS_norm_phased_stats = file_label + "_raw_hifi_to_reference_alignment_PASS_norm_phased_stats.txt"
51+
Boolean ann = read_boolean("annotate.txt")
4952
}
5053

5154
runtime {

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