nf-cmgg / structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

Introduction

nf-cmgg/structural is a bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads. The pipeline handles the calling of the variants and postprocessing (filtering, annotating...)

Please have a look at the documentation on how to run the pipeline

structural's Issues

MSG: ERROR: Cache directory vep/homo_sapiens not found

Description of the bug

For some reason it can't find the vep cache. I had something similar a while back and then used a custom config to fix this. I'm testing it helps now as well, if so we better fix this before the release.
Keep you posted.

Command used and terminal output

## command
nextflow \
	-log ${OUTDIR}/.nextflow.log \
	run nf-cmgg/structural \
	-r dev \
	-work-dir ${WORKDIR} \
	--input ${samplesheet} \
	--outdir ${OUTDIR} \
	-profile vsc_ugent,$SLURM_CLUSTERS \
	--genomes_base ${genomes_base} \
	-resume \
	-latest \
	-c /kyukon/data/gent/vo/000/gvo00082/research/ICT/VAL/vcfanno_custom.config \
	--callers manta,delly,smoove,qdnaseq,wisecondorx,expansionhunter \
	--output_callers \
	--igenomes_ignore true \
	--annotate \
	--vep_version 110.0 \
	--vep_cache_version 110 \
	--annotsv_annotations "${genomes_base}/Hsapiens/GRCh38.p14/variation/AnnotSV/AnnotSV-3.3.4.tar.gz" 

## terminal
Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Smartmatch is experimental at /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472.
  
  -------------------- EXCEPTION --------------------
  MSG: ERROR: Cache directory vep/homo_sapiens not found
  
  STACK Bio::EnsEMBL::VEP::CacheDir::dir /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:305
  STACK Bio::EnsEMBL::VEP::CacheDir::init /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:219
  STACK Bio::EnsEMBL::VEP::CacheDir::new /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
  STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:116
  STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:92
  STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170
  STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:128
  STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/share/ensembl-vep-110.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:200
  STACK toplevel /usr/local/bin/vep:46
  Date (localtime)    = Sun Mar 31 03:31:07 2024
  Ensembl API version = 110
  ---------------------------------------------------

Relevant files

nextflow_vepError.log

System information

HPC Doduo cluster

Handling duplicate rows in samplesheet with warnings

Warnings for duplicate sample sheet rows

When the samplesheet contains duplicate rows, it now says:

Samplesheet errors:
	The samplesheet contains duplicate rows for entry 5 and entry 17 ([sample:sample1, cram:s3://cmgg-results/WGS/cram/.../sample1/sample1.cram, crai:s3://cmgg-results/WGS/cram/.../sample1/sample1cram.crai])

Maybe it would be better if you issue a warning and proceed with the pipeline, ignoring any duplicated instances.

Just a thought
Mattias

Only save the last dev docs

Description of feature

Only the last dev documentation should be built as dev version. This documentation should also never be set as the latest

include gnomADv4 SV annotation

gnomAD v4 SV fields for annotation

I went over the gnomAD v4 SV header and selected a few fields that seem relevant for the annotation step. Here is an overview, we can discuss during the meeting next week.

1. All info fields can be selected for the whole dataset, or for subsets (from gnomADv3), using these prefixes:

• controls_and_biobanks_ only samples collected specifically as controls for disease studies, or samples belonging to biobanks (e.g. BioMe, Genizon) or general population studies (e.g., 1000 Genomes, HGDP, PAGE)
• non_neuro_ only samples that were not collected as part of a neurologic or psychiatric case/control study, or samples collected as part of a neurologic or psychiatric case/control study but designated as controls

2. All info fields can be selected for the whole dataset, or for populations (from gnomADv3), using these prefixes:

• afr_ African/African American
• ami_ Amish
• amr_ Latino/Admixed American
• asj_ Ashkenazi Jewish
• eas_ East Asian
• fin_ Finnish
• nfe_ Non-Finnish European
• mid_ Middle Eastern
• sas_ South Asian
• oth_ Other (population not assigned)

for 1 and 2: I don't expect us to differentiate at this point, but I'm putting it out there for any future implementations.

3. For annotation :

• use for vcfanno determination of identity
  CHROM POS REF ALT
##ALT=<ID=CNV,Description="Copy Number Polymorphism"> Seems like CNVs will have to determined on positions?!

##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate">	 
##INFO=<ID=POS2,Number=1,Type=Integer,Description="Start position of the structural variant on CHR2">
##INFO=<ID=END2,Number=1,Type=Integer,Description="End position of the structural variant on CHR2">

• ID rename to gnomad4ID the ID of the variant according to gnomADv4

• FILTER
##FILTER=<ID=PASS,Description="All filters passed"> maybe only annotate with SVs after filtering?, could add an annotation field saying it is present in gnomad4 but doesn't pass filtering? I made a table for the different type of FILTER value

1199117 PASS
 278316 UNRESOLVED
 186815 LOWQUAL_WHAM_SR_DEL;OUTLIER_SAMPLE_ENRICHED
 131479 LOWQUAL_WHAM_SR_DEL
 109905 OUTLIER_SAMPLE_ENRICHED
  82853 HIGH_NCR
  79159 HIGH_NCR;UNRESOLVED
  70291 HIGH_NCR;LOWQUAL_WHAM_SR_DEL
   7280 IGH_MHC_OVERLAP;UNRESOLVED
   5424 IGH_MHC_OVERLAP
   1624 HIGH_NCR;IGH_MHC_OVERLAP;UNRESOLVED
    882 IGH_MHC_OVERLAP;LOWQUAL_WHAM_SR_DEL
    514 HIGH_NCR;IGH_MHC_OVERLAP
    493 HIGH_NCR;IGH_MHC_OVERLAP;LOWQUAL_WHAM_SR_DEL
    254 FAIL_MANUAL_REVIEW
     57 REFERENCE_ARTIFACT
     23 FAIL_MANUAL_REVIEW;HIGH_NCR

• INFO
  ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> rename to gnomad4AC
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency (biallelic sites only)."> rename to gnomad4AF
##INFO=<ID=MALE_AF,Number=A,Type=Float,Description="MALE allele frequency (biallelic sites only)."> rename to gnomad4AF_MALE
##INFO=<ID=FEMALE_AF,Number=A,Type=Float,Description="FEMALE allele frequency (biallelic sites only)."> rename to gnomad4AF_FEMALE
##INFO=<ID=FREQ_HET,Number=1,Type=Float,Description="Heterozygous genotype frequency (biallelic sites only)."> rename to gnomad4HETF
##INFO=<ID=FREQ_HOMALT,Number=1,Type=Float,Description="Homozygous alternate genotype frequency (biallelic sites only)."> rename to gnomad4HOMF
##INFO=<ID=CN_NONREF_FREQ,Number=1,Type=Float,Description="Frequency of samples with non-reference copy states (multiallelic CNVs only)."> rename to gnomad4CNF
##INFO=<ID=CPX_INTERVALS,Number=.,Type=String,Description="Genomic intervals constituting complex variant."> rename to gnomad4INT
##INFO=<ID=CPX_TYPE,Number=1,Type=String,Description="Class of complex variant."> rename to gnomad4TYPE (the type of variant it is according to gnomADv4), use the same types as here

##CPX_TYPE_INS_iDEL="Insertion with deletion at insertion site."
##CPX_TYPE_INVdel="Complex inversion with 3' flanking deletion."
##CPX_TYPE_INVdup="Complex inversion with 3' flanking duplication."
##CPX_TYPE_dDUP="Dispersed duplication."
##CPX_TYPE_dDUP_iDEL="Dispersed duplication with deletion at insertion site."
##CPX_TYPE_delINV="Complex inversion with 5' flanking deletion."
##CPX_TYPE_delINVdel="Complex inversion with 5' and 3' flanking deletions."			
##CPX_TYPE_delINVdup="Complex inversion with 5' flanking deletion and 3' flanking duplication."
##CPX_TYPE_dupINV="Complex inversion with 5' flanking duplication."
##CPX_TYPE_dupINVdel="Complex inversion with 5' flanking duplication and 3' flanking deletion."
##CPX_TYPE_dupINVdup="Complex inversion with 5' and 3' flanking duplications."
##CPX_TYPE_piDUP_FR="Palindromic inverted tandem duplication, forward-reverse orientation."
##CPX_TYPE_piDUP_RF="Palindromic inverted tandem duplication, reverse-forward orientation."	

The following seem interesting to me, but should maybe be evaluated first for relevance and performance:

##INFO=<ID=PREDICTED_BREAKEND_EXONIC,Number=.,Type=String,Description="Gene(s) for which the SV breakend is predicted to fall in an exon.">
##INFO=<ID=PREDICTED_COPY_GAIN,Number=.,Type=String,Description="Gene(s) on which the SV is predicted to have a copy-gain effect.">
##INFO=<ID=PREDICTED_DUP_PARTIAL,Number=.,Type=String,Description="Gene(s) which are partially overlapped by an SV's duplication, but the transcription start site is not duplicated.">
##INFO=<ID=PREDICTED_INTERGENIC,Number=0,Type=Flag,Description="SV does not overlap any protein-coding genes.">
##INFO=<ID=PREDICTED_INTRAGENIC_EXON_DUP,Number=.,Type=String,Description="Gene(s) on which the SV is predicted to result in intragenic exonic duplication without breaking any coding sequences.">
##INFO=<ID=PREDICTED_INTRONIC,Number=.,Type=String,Description="Gene(s) where the SV was found to lie entirely within an intron.">
##INFO=<ID=PREDICTED_INV_SPAN,Number=.,Type=String,Description="Gene(s) which are entirely spanned by an SV's inversion.">
##INFO=<ID=PREDICTED_LOF,Number=.,Type=String,Description="Gene(s) on which the SV is predicted to have a loss-of-function effect.">
##INFO=<ID=PREDICTED_MSV_EXON_OVERLAP,Number=.,Type=String,Description="Gene(s) on which the multiallelic SV would be predicted to have a LOF, INTRAGENIC_EXON_DUP, COPY_GAIN, DUP_PARTIAL, TSS_DUP, or PARTIAL_EXON_DUP annotation if the SV were biallelic.">
##INFO=<ID=PREDICTED_NEAREST_TSS,Number=.,Type=String,Description="Nearest transcription start site to an intergenic variant.">
##INFO=<ID=PREDICTED_PARTIAL_EXON_DUP,Number=.,Type=String,Description="Gene(s) where the duplication SV has one breakpoint in the coding sequence.">
##INFO=<ID=PREDICTED_PROMOTER,Number=.,Type=String,Description="Gene(s) for which the SV is predicted to overlap the promoter region.">
##INFO=<ID=PREDICTED_TSS_DUP,Number=.,Type=String,Description="Gene(s) for which the SV is predicted to duplicate the transcription start site.">
##INFO=<ID=PREDICTED_UTR,Number=.,Type=String,Description="Gene(s) for which the SV is predicted to disrupt a UTR.">
##INFO=<ID=SOURCE,Number=1,Type=String,Description="Source of inserted sequence.">
##INFO=<ID=STRANDS,Number=1,Type=String,Description="Breakpoint strandedness [++,+-,-+,--]">

To be continued...

Add MergeBatchSites subworkflow

GATK-SV: MergeBatchSites.wdl

Standardize variants for callers of the same type

Description of feature

Not all callers report all variants in the same way. This needs some standardization.

Some links for inspiration:

• SV: https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/OutputFilesMantaVCFInterpretation_fDG.htm
• CNV: https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/CNVVCFFile_fDG_dtSW.htm => This can be done with bedgovcf
• Repeat expansions: https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/RepeatGenotyping_fDG_dtSW.htm

Better header handling

Description of feature

The current way just dumps all possible header fields inside of the VCF header, but that's not the most efficient and correct way of handling this problem. I need to find some dynamic way to add the correct headers (especially for custom headers added with VCFANNO)

Make the workflow pluggable

Description of feature

Remove all mentions of params in the workflows and add them all as inputs to the workflows/subworkflows
Emit all sensible outputs from the main workflow too

Add expansionhunter for detection of repeats

Description of feature

Add Expansionhunter for detection of repeats

Add comprehensive filter steps

Description of feature

After Jasmine some filter steps should still be added.

1. A possibility to filter commonly occurring variants given through an input VCF
2. A way to hard filter based on fields (like you can do with bcftools filter)

--callers all param

Description of feature

It would be lovely if --callers had the all option, instead of having to make a comma separated list of all callers.

Add HPO terms to the samplesheet

Description of feature

It can be useful to add HPO terms to the samplesheet for each sample. This can be used by AnnotSV to get more useful information.

Fully support conda for all modules

Description of the bug

Conda isn't supported for all modules for now (especially qdnaseq is missing a conda declaration for now). This should be fixed to increase the usability of the pipeline

Command used and terminal output

No response

Relevant files

No response

System information

No response

Add VCF to JSON conversion

Description of feature

Add VCF to JSON conversion with certain filter to use for the visualization of the SVs

use this repo

@mvheetve, you can use this repo to host any nf related work for structural variants

tune SVcaller parameters

Add GenotypeBatch subworkflow

GATK-SV: GenotypeBatch.wdl

Fix EVIDENCE_QC

Modules: lots and lots of modules
Subworkflows: EVIDENCE_QC
GATK-SV: EvidenceQC.wdl

This subworkflow still needs a lot of work! Most of the problems originate from the broken MAKE_BINCOV_MATRIX subworkflow at the moment, so that one should be fixed before starting this one. (see issue)

make testprofile document

New caller: svaba

Description of feature

https://github.com/walaj/svaba

Add family support

Description of feature

Add some way to merge single-sample VCFs into multi-sample VCFs (possible with bcftools merge)

Fix `MAKE_BINCOV_MATRIX`

Modules: bincov-matrix
Subworkflows: make-bincov-matrix.nf
GATK-SV: MakeBinCovMatrix

Current problem is that one sample is used to create a common bin size and bin location file and the other samples don't match the location file from this one sample, causing the workflow to fail.

Finish GATHER_BATCH_EVIDENCE

Subworkflows: GATHER_BATCH_EVIDENCE
GATK-SV: GatherBatchEvidence.wdl

re-add gridss support

Description of feature

consensus sequence can maybe created using this: https://samtools.github.io/bcftools/bcftools.html#consensus

Add BED => VCF support for CNVs

Description of feature

Add some way to convert the CNV BED files to VCF format

Vcfanno annotate gene panel overlaps

Description of feature

see title

Add ClusterBatch subworkflow

GATK-SV: ClusterBatch

Add GenerateBatchMetrics subworkflow

GATK-SV: GenerateBatchMetrics.wdl

smoove.vcf.gz indexin

Description of the bug

When using --output_callers, the directory containing

- smoove.vcf.gz
- svync.smoove.vcf.gz.tbi 

smoove.vcf.gz should be indexed when created and svync.smoove.vcf.gz.tbi can go.

Command used and terminal output

No response

Relevant files

No response

System information

No response

Investigate the use of Viola-SV

Description of feature

https://github.com/dermasugita/Viola-SV

This Python API supports VCFs created with Delly, Lumpy (see if Smoove VCFs also work), Manta and Gridss. It can standardize and merge these VCFs and convert them to either breakpoint or breakend notation

AnnotSV issue

Description of the bug

Encountered an issue during annotation related to AnnotSV. From what I understand it is a known bug for 64bit machines and is caused by Tcl and the allocated memory block limit. The workarounds proposed here require version changes of certain dependancies. If this is at an operating system level, maybe we need to drag the HPC crew into this.

All data, including jobscript, input, nextflow.log, stderror and stdout can be found at $VSC_DATA_VO/research/ICT/VAL/VAL_batch1.
Work directory is $VSC_SCRATCH_VO/gvo00082/vsc43079/VAL_batch1/structural, let me know if you need access.

Regards
M

Command used and terminal output

Input:

nextflow \
	-log ${OUTDIR}/.nextflow.log \
	run CenterForMedicalGeneticsGhent/nf-cmgg-structural \
	-r proper-testing \
	-work-dir ${WORKDIR} \
	--input ${samplesheet} \
	--outdir ${OUTDIR} \
	-profile vsc_ugent,$SLURM_CLUSTERS \
	--genomes_base ${genomes_base} \
	-resume \
	-latest \
	-c /kyukon/data/gent/vo/000/gvo00082/research/ICT/VAL/vep_cache.config \
	--callers manta,delly,smoove,qdnaseq,wisecondorx,expansionhunter \
	--output_callers \
	--igenomes_ignore true \
	--annotate \
	--vep_version 110.0 \
	--vep_cache_version 110 \
	--annotsv_annotations "${genomes_base}/Hsapiens/GRCh38.p14/variation/AnnotSV/AnnotSV-3.3.4.tar.gz" \
	--vcfanno_resources "/kyukon/data/gent/vo/000/gvo00082/WGS/custom_files/[!dbVar]*"


Output: 


WARN: Killing running tasks (5)
Join mismatch for the following entries: 
- key=[id:D2125260, sample:D2125260, family:D2125260, sex:female, family_count:1, variant_type:sv] values= 
- key=[id:D2200653, sample:D2200653, family:D2200653, sex:female, family_count:1, variant_type:sv] values=


Join mismatch for the following entries: 
- key=[id:D2018788, sample:D2018788, family:D2018788, sex:male, family_count:1, variant_type:sv] values= 
- key=[id:D2117741, sample:D2117741, family:D2117741, sex:male, family_count:1, variant_type:sv] values=



executor >  slurm (22)
[b0/2776d4] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 1 of 1, cached: 1 ✔
[1a/e88d7f] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 1 of 1, cached: 1 ✔
[a0/7da88f] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 2 of 2, cached: 2 ✔
[09/845236] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 2 of 2, cached: 2 ✔
[50/84ba0a] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[f5/b00c08] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 1 of 1, cached: 1 ✔
[b3/7ecd9d] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 1 of 1, cached: 1 ✔
[2b/baa2ea] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 12 of 12, cached: 12
[78/5057a2] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 12 of 12, cached: 12
[b7/7c8cb0] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[06/301dc7] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[cb/a7abbd] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[a1/70aaff] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[56/b3429c] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 12 of 12, cached:...
[be/8b46d4] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 12 of 12, cached: 11
[17/206ee6] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 12 of 12, cached: 11
[ff/bef45a] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 12 of 12, cached: 11
[1a/cee952] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[f3/870a88] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 8 of 8, cached: 8 ✔
[4d/e7e8bd] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 6 of 6, cached: 6 ✔
[26/8f6e89] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[c3/46954f] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[f9/a09f10] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[fc/016b86] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[dc/98318e] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[cd/ee0417] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[2c/15e1e1] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[94/ae531c] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[3c/9c7b8f] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[ff/0bc745] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[f6/48b8b2] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[1b/28e2b4] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 26 of 26, cached:...
[87/8e941f] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 33 of 33, cached:...
[29/e3a9dc] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 23 of 23, cached: 23
[75/5924cd] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 25 of 25, cached: 24
[f0/68a580] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 25 of 25, cached: 24
[6f/2faf20] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 23 of 23, cached: 23
[cd/f82150] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 23 of 23, cached: 23
[93/4d3850] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[7a/d90382] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[64/8caadb] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[f7/81d6e7] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... [100%] 14 of 14, cached:...
[-        ] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... -
[-        ] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... -
[-        ] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... -
[-        ] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... -
[-        ] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... -
[-        ] process > CMGG_CMGGSTRUCTURAL:CMGGSTR... -
ERROR ~ Error executing process > 'CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV (D2117741)'

Caused by:
  Process `CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV (D2117741)` terminated with an error exit status (134)

Command executed:

  AnnotSV \
      -annotationsDir annotsv_annotations \
       \
       \
       \
       \
      -outputFile D2117741.annot.tsv \
      -SVinputFile D2117741.filter.vcf \
      -vcf 1 -SVminSize 20
  
  mv *_AnnotSV/* .
  
  cat <<-END_VERSIONS > versions.yml
  "CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV":
      annotsv: $(echo $(AnnotSV -help 2>&1 | head -n1 | sed 's/^AnnotSV //'))
  END_VERSIONS

Command exit status:
  134

Command output:
  AnnotSV 3.3.6
  
  Copyright (C) 2017-2023 GEOFFROY Veronique
  
  Please feel free to contact me for any suggestions or bug reports
  email: [email protected]
  
  Tcl/Tk version: 8.6
  
  Application name used:
  /usr/local
  
  
  ...downloading the configuration data (December 01 2023 - 14:55)
  	...configuration data by default
  	...configuration data from /usr/local/etc/AnnotSV/configfile
  	...configuration data given in arguments
  	...checking all these configuration data
  
  ...VCF to BED (December 01 2023 - 14:55)
  	...WARNING: 197997 sample IDs with missing alleles in the GT field (./. or .|.) have been reported in the "Samples_ID" output field

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  max size for a Tcl value (2147483647 bytes) exceeded
  .command.sh: line 10:    43 Aborted                 (core dumped) AnnotSV -annotationsDir annotsv_annotations -outputFile D2117741.annot.tsv -SVinputFile D2117741.filter.vcf -vcf 1 -SVminSize 20

Work dir:
  /kyukon/scratch/gent/vo/000/gvo00082/vsc43079/VAL_batch1/structural/work/cf/1b73bfe151eb7e49faf0911b9f9e71

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/kyukon/data/gent/vo/000/gvo00082/research/ICT/VAL/VAL_batch1/structural/.nextflow.log' file for details
[b8/887295] NOTE: Process `CMGG_CMGGSTRUCTURAL:CMGGSTRUCTURAL:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV (D2018788)` terminated with an error exit status (143) -- Execution is retried (3)

### Relevant files

See `$VSC_DATA_VO/research/ICT/VAL/VAL_batch1`

### System information

See jobscript

Fully add annotation

Description of feature

Run AnnotSV and Ensembl VEP in parallel. Use the Ensembl VEP VCF as input to VCFanno and use the AnnotSV TSV file as an annotation source

Update tests

Description of feature

Change the tests to a more unit test/modular approach where each part is tested for all possible inputs and outputs. Only run the whole pipeline in stub form to test the connection between all parts

Investigate VDS format for the creation of a false positive variants list

Description of feature

https://hail.is/docs/0.2/vds/index.html

Some bugs found the output of the pipeline

Description of the bug

1. wisecondorx reports SVLEN wrong I guess:

chr21	13900001	wisecondorx_344	N	<DEL>	.	PASS	CNV_RATIO=-0.0368;ZSCORE=-8.95856;SVTYPE=CNV;END=24100000;SVLEN=1;CALLERS=wisecondorx	GT:CN	.:0
chr21	24100001	wisecondorx_345	N	<DUP>	.	PASS	CNV_RATIO=0.1254;ZSCORE=23.8602;SVTYPE=CNV;END=25700000;SVLEN=1;CALLERS=wisecondorx	GT:CN	.:0

2. not sure if this is a bug or not but in qdnaseq tool thereis only result for chr18,chrX and chrY
3. SVLEN is missing in DELLY

Issues reported by @kubranarci, thank you!

Command used and terminal output

No response

Relevant files

No response

System information

No response

Add MakeCohortVCF subworkflow

GATK-SV: MakeCohortVCF.wdl

Investigate stranger for repeat expansion annotation

Description of feature

https://github.com/Clinical-Genomics/stranger

Add CNV support

Not high on the priority list right now. We should first focus on adding general SV calling

Fully document the pipeline

Description of feature

The pipeline should be fully documented when it's ready for its first release

Finish Scramble

Modules: Scramble
Subworkflows: RUN_SCRAMBLE
GATK-SV: Scramble.wdl

This workflow needs to be properly added and fixed => Main issue here is the lack of a proper dataset (but should be fixed with Mathias' data)

Add MEI support

Description of feature

This should be added after CNV analysis has been fully implemented

Fix `manta` errors

Description of the bug

When running manta on an HPC, the following error occurs:

[2023-04-26T17:36:31.661233Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Initiating pyFlow run
[2023-04-26T17:36:31.661876Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] pyFlowClientWorkflowClass: MantaWorkflow
[2023-04-26T17:36:31.661892Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2023-04-26T17:36:31.661903Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2023-04-26T17:36:31.661914Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] WorkingDir: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/000/gvo00082/vsc44804/work-structural/53/73332a2c679df04e2df65e4f53d647'
[2023-04-26T17:36:31.661925Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] ProcessCmdLine: 'manta/runWorkflow.py -m local -j 12'
[2023-04-26T17:36:31.661935Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] mode: local
[2023-04-26T17:36:31.661945Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] nCores: 12
[2023-04-26T17:36:31.661954Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] memMb: 94883
[2023-04-26T17:36:31.661964Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] dataDir: /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/000/gvo00082/vsc44804/work-structural/53/73332a2c679df04e2df65e4f53d647/manta/workspace/pyflow.data
[2023-04-26T17:36:31.661975Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2023-04-26T17:36:31.661985Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] isContinue: False
[2023-04-26T17:36:31.661995Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2023-04-26T17:36:31.662005Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2023-04-26T17:36:31.662530Z] [node3214.victini.os] [2649321_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2023-04-26T17:36:31.662721Z] [node3214.victini.os] [2649321_1] [MantaWorkflow] Initiating Manta workflow version: 1.6.0
[2023-04-26T17:36:31.663546Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getAlignmentStats_makeTmpDir' to master workflow
[2023-04-26T17:36:31.664448Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getAlignmentStats_makeTmpDir' from master workflow
[2023-04-26T17:36:31.664919Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_000' to master workflow
[2023-04-26T17:36:31.665661Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getAlignmentStats_mergeStats' to master workflow
[2023-04-26T17:36:31.666299Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getAlignmentStats_removeTmpDir' to master workflow
[2023-04-26T17:36:31.667368Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'summarizeStats' to master workflow
[2023-04-26T17:36:31.668151Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getChromDepth_makeTmpDir' to master workflow
[2023-04-26T17:36:31.668619Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_makeTmpDir' to master workflow
[2023-04-26T17:36:31.669868Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getChromDepth_makeTmpDir' from master workflow
[2023-04-26T17:36:31.671954Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_estimateChromDepth_022_chrX' to master workflow
[2023-04-26T17:36:31.675020Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_catChromDepth' to master workflow
[2023-04-26T17:36:31.675512Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getChromDepth_mergeChromDepth' to master workflow
[2023-04-26T17:36:31.675864Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'getChromDepth_removeTmpDir' to master workflow
[2023-04-26T17:36:31.677351Z] [node3214.victini.os] [2649321_1] [TaskRunner:getAlignmentStats_makeTmpDir] Task initiated on local node
[2023-04-26T17:36:31.679054Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'makeGraphTmpDir' to master workflow
[2023-04-26T17:36:31.680753Z] [node3214.victini.os] [2649321_1] [TaskRunner:getChromDepth_makeTmpDir] Task initiated on local node
[2023-04-26T17:36:31.684658Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_022_chrX-253744-255091_0000_to_chromId_022_chrX-276323-303356_0000' to master workflow
[2023-04-26T17:36:31.688432Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_022_chrX-276323-303356_0000_to_chromId_022_chrX-333934-386955_0000' to master workflow
[2023-04-26T17:36:31.690414Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_022_chrX-333934-386955_0000_to_chromId_022_chrX-333934-386955_0000' to master workflow
[2023-04-26T17:36:31.692362Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_022_chrX-333934-386955_0000_to_chromId_022_chrX-333934-386955_0000' to master workflow
[2023-04-26T17:36:31.858902Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2023-04-26T17:36:31.859196Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
[2023-04-26T17:36:31.860726Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
[2023-04-26T17:36:31.861748Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2023-04-26T17:36:31.870277Z] [node3214.victini.os] [2649321_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
[2023-04-26T17:36:31.873655Z] [node3214.victini.os] [2649321_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2023-04-26T17:36:32.027083Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
[2023-04-26T17:36:32.028787Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_022_chrX' from master workflow
[2023-04-26T17:36:32.040267Z] [node3214.victini.os] [2649321_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_022_chrX] Task initiated on local node
[2023-04-26T17:36:37.996402Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_000' launched from master workflow
[2023-04-26T17:36:37.998083Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getAlignmentStats_mergeStats' from master workflow
[2023-04-26T17:36:38.006407Z] [node3214.victini.os] [2649321_1] [TaskRunner:getAlignmentStats_mergeStats] Task initiated on local node
[2023-04-26T17:36:38.212908Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getAlignmentStats_mergeStats' launched from master workflow
[2023-04-26T17:36:38.214380Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'summarizeStats' from master workflow
[2023-04-26T17:36:38.215292Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getAlignmentStats_removeTmpDir' from master workflow
[2023-04-26T17:36:38.227261Z] [node3214.victini.os] [2649321_1] [TaskRunner:summarizeStats] Task initiated on local node
[2023-04-26T17:36:38.228651Z] [node3214.victini.os] [2649321_1] [TaskRunner:getAlignmentStats_removeTmpDir] Task initiated on local node
[2023-04-26T17:36:38.380700Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getAlignmentStats_removeTmpDir' launched from master workflow
[2023-04-26T17:36:38.397495Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'summarizeStats' launched from master workflow
[2023-04-26T17:36:42.069870Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getChromDepth_sample000_estimateChromDepth_022_chrX' launched from master workflow
[2023-04-26T17:36:42.070787Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
[2023-04-26T17:36:42.082634Z] [node3214.victini.os] [2649321_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
[2023-04-26T17:36:42.336180Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
[2023-04-26T17:36:42.337454Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
[2023-04-26T17:36:42.349626Z] [node3214.victini.os] [2649321_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
[2023-04-26T17:36:42.603686Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
[2023-04-26T17:36:42.604793Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
[2023-04-26T17:36:42.605613Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'makeGraphTmpDir' from master workflow
[2023-04-26T17:36:42.618055Z] [node3214.victini.os] [2649321_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
[2023-04-26T17:36:42.624799Z] [node3214.victini.os] [2649321_1] [TaskRunner:makeGraphTmpDir] Task initiated on local node
[2023-04-26T17:36:42.772107Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'makeGraphTmpDir' launched from master workflow
[2023-04-26T17:36:42.773262Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_022_chrX-253744-255091_0000_to_chromId_022_chrX-276323-303356_0000' from master workflow
[2023-04-26T17:36:42.774037Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_022_chrX-333934-386955_0000_to_chromId_022_chrX-333934-386955_0000' from master workflow
[2023-04-26T17:36:42.774802Z] [node3214.victini.os] [2649321_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_022_chrX-276323-303356_0000_to_chromId_022_chrX-333934-386955_0000' from master workflow
[2023-04-26T17:36:42.787991Z] [node3214.victini.os] [2649321_1] [TaskRunner:makeLocusGraph_chromId_022_chrX-276323-303356_0000_to_chromId_022_chrX-333934-386955_0000] Task initiated on local node
[2023-04-26T17:36:42.788838Z] [node3214.victini.os] [2649321_1] [TaskRunner:makeLocusGraph_chromId_022_chrX-333934-386955_0000_to_chromId_022_chrX-333934-386955_0000] Task initiated on local node
[2023-04-26T17:36:42.791145Z] [node3214.victini.os] [2649321_1] [TaskRunner:makeLocusGraph_chromId_022_chrX-253744-255091_0000_to_chromId_022_chrX-276323-303356_0000] Task initiated on local node
[2023-04-26T17:36:42.792098Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
[2023-04-26T17:36:43.207232Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_022_chrX-333934-386955_0000_to_chromId_022_chrX-333934-386955_0000' launched from master workflow
[2023-04-26T17:36:43.322213Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_022_chrX-276323-303356_0000_to_chromId_022_chrX-333934-386955_0000' launched from master workflow
[2023-04-26T17:36:43.386734Z] [node3214.victini.os] [2649321_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_022_chrX-253744-255091_0000_to_chromId_022_chrX-276323-303356_0000' launched from master workflow
[2023-04-26T17:36:48.387914Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR] Failed to complete master workflow, error code: 1
[2023-04-26T17:36:48.388127Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR] errorMessage:
[2023-04-26T17:36:48.388150Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR] Unhandled Exception in TaskRunner-Thread-masterWorkflow
[2023-04-26T17:36:48.388166Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR] Traceback (most recent call last):
[2023-04-26T17:36:48.388181Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 1069, in run
[2023-04-26T17:36:48.388203Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     (retval, retmsg) = self._run()
[2023-04-26T17:36:48.388217Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 1121, in _run
[2023-04-26T17:36:48.388231Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     self.workflow.workflow()
[2023-04-26T17:36:48.388245Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/mantaWorkflow.py", line 853, in workflow
[2023-04-26T17:36:48.388260Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     graphTasks = runLocusGraph(self,dependencies=graphTaskDependencies)
[2023-04-26T17:36:48.388276Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/mantaWorkflow.py", line 286, in runLocusGraph
[2023-04-26T17:36:48.388293Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     graphTasks.add(self.addTask(graphTask,graphCmd,dependencies=dirTask,memMb=self.params.estimateMemMb))
[2023-04-26T17:36:48.388309Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 3707, in addTask
[2023-04-26T17:36:48.388323Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     self._addTaskCore(self._getNamespace(), label, payload, dependencies)
[2023-04-26T17:36:48.388337Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 4087, in _addTaskCore
[2023-04-26T17:36:48.388351Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     self._tdag.addTask(namespace, label, payload, dependencies)
[2023-04-26T17:36:48.388367Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 537, in wrapped
[2023-04-26T17:36:48.388381Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     return f(self, *args, **kw)
[2023-04-26T17:36:48.388394Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 2546, in addTask
[2023-04-26T17:36:48.388409Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR]     raise Exception("Task: '%s' is already in TaskDAG" % (fullLabel))
[2023-04-26T17:36:48.388424Z] [node3214.victini.os] [2649321_1] [WorkflowRunner] [ERROR] Exception: Task: 'makeLocusGraph_chromId_022_chrX-333934-386955_0000_to_chromId_022_chrX-333934-386955_00

Command used and terminal output

No response

Relevant files

No response

System information

No response

Add FilterBatch subworkflow

GATK-SV: FilterBatch.wdl

Copy samplesheet in output directory

Description of feature

See title

Reheader the Whamg VCFs

Modules: Create a new module that does the reheadering (The Whamg module is an nf-core so it shouldn't be changed) => can possibly also be done using bcftools/reheader from nf-core, but not sure
Subworkflows: RUN_WHAMG
GATK-SV: Whamg.wdl

The VCFs called using Whamg need to be reheadered

Add validation

Description of feature

Add a way to perform validation in the pipeline instead of having to manually validate the output

Add VCF to BEDPE conversion

Description of feature

https://github.com/ctsa/svtools

Automatically check if the VEP cache contains a merged cache

Description of feature

This should avoid issues when using VEP merged caches