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Add proper testing + fix some issues found #213

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Add proper testing + fix some issues found

Add proper testing + fix some issues found #213

Run time

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Job Run time
Run nf-test with pipeline_sv-23.10.0
5m 20s
Run nf-test with pipeline_cnv-23.10.0
6m 3s
Run nf-test with pipeline_repeats-23.10.0
7m 59s
Run nf-test with pipeline_duplicates-23.10.0
7m 58s
Run nf-test with pipeline_families-23.10.0
7m 59s
Run nf-test with bam_cnv_calling-23.10.0
5m 29s
Run nf-test with bam_prepare_samtools-23.10.0
3m 37s
Run nf-test with bam_repeat_estimation_expansionhunter-23.10.0
3m 13s
Run nf-test with bam_sv_calling-23.10.0
8m 1s
Run nf-test with bam_variant_calling_delly-23.10.0
2m 37s
Run nf-test with bam_variant_calling_gridss-23.10.0
4m 35s
Run nf-test with bam_variant_calling_manta-23.10.0
3m 25s
Run nf-test with bam_variant_calling_qdnaseq-23.10.0
3m 53s
Run nf-test with bam_variant_calling_smoove-23.10.0
2m 38s
Run nf-test with bam_variant_calling_wisecondorx-23.10.0
6m 28s
Run nf-test with vcf_annotate_vep_annotsv_vcfanno-23.10.0
3m 48s
Run nf-test with vcf_concat_bcftools-23.10.0
2m 59s
Run nf-test with vcf_merge_callers_jasmine-23.10.0
3m 0s
Run nf-test with vcf_merge_family_jasmine-23.10.0
4m 6s
Run nf-test with pipeline_sv-latest-everything
7m 59s
Run nf-test with pipeline_cnv-latest-everything
4m 54s
Run nf-test with pipeline_repeats-latest-everything
3m 53s
Run nf-test with pipeline_duplicates-latest-everything
7m 58s
Run nf-test with pipeline_families-latest-everything
7m 57s
Run nf-test with bam_cnv_calling-latest-everything
3m 47s
Run nf-test with bam_prepare_samtools-latest-everything
2m 39s
Run nf-test with bam_repeat_estimation_expansionhunter-latest-everything
7m 13s
Run nf-test with bam_sv_calling-latest-everything
5m 14s
Run nf-test with bam_variant_calling_delly-latest-everything
2m 58s
Run nf-test with bam_variant_calling_gridss-latest-everything
4m 15s
Run nf-test with bam_variant_calling_manta-latest-everything
3m 19s
Run nf-test with bam_variant_calling_qdnaseq-latest-everything
7m 30s
Run nf-test with bam_variant_calling_smoove-latest-everything
3m 54s
Run nf-test with bam_variant_calling_wisecondorx-latest-everything
2m 59s
Run nf-test with vcf_annotate_vep_annotsv_vcfanno-latest-everything
7m 58s
Run nf-test with vcf_concat_bcftools-latest-everything
5m 52s
Run nf-test with vcf_merge_callers_jasmine-latest-everything
6m 19s
Run nf-test with vcf_merge_family_jasmine-latest-everything
4m 11s
3h 13m 57s