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Add proper testing + fix some issues found #208

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Add proper testing + fix some issues found

Add proper testing + fix some issues found #208

Run time

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Job Run time
Run nf-test with pipeline_sv-23.10.0
1m 44s
Run nf-test with pipeline_cnv-23.10.0
1m 45s
Run nf-test with pipeline_repeats-23.10.0
1m 29s
Run nf-test with pipeline_duplicates-23.10.0
1m 44s
Run nf-test with pipeline_families-23.10.0
1m 46s
Run nf-test with bam_cnv_calling-23.10.0
1m 45s
Run nf-test with bam_prepare_samtools-23.10.0
1m 21s
Run nf-test with bam_repeat_estimation_expansionhunter-23.10.0
1m 7s
Run nf-test with bam_sv_calling-23.10.0
1m 46s
Run nf-test with bam_variant_calling_delly-23.10.0
1m 4s
Run nf-test with bam_variant_calling_gridss-23.10.0
1m 44s
Run nf-test with bam_variant_calling_manta-23.10.0
1m 26s
Run nf-test with bam_variant_calling_qdnaseq-23.10.0
1m 44s
Run nf-test with bam_variant_calling_smoove-23.10.0
1m 22s
Run nf-test with bam_variant_calling_wisecondorx-23.10.0
1m 26s
Run nf-test with vcf_annotate_vep_annotsv_vcfanno-23.10.0
1m 44s
Run nf-test with vcf_concat_bcftools-23.10.0
1m 12s
Run nf-test with vcf_merge_callers_jasmine-23.10.0
1m 8s
Run nf-test with vcf_merge_family_jasmine-23.10.0
1m 42s
Run nf-test with pipeline_sv-latest-everything
1m 41s
Run nf-test with pipeline_cnv-latest-everything
1m 45s
Run nf-test with pipeline_repeats-latest-everything
1m 42s
Run nf-test with pipeline_duplicates-latest-everything
1m 43s
Run nf-test with pipeline_families-latest-everything
1m 41s
Run nf-test with bam_cnv_calling-latest-everything
1m 45s
Run nf-test with bam_prepare_samtools-latest-everything
1m 6s
Run nf-test with bam_repeat_estimation_expansionhunter-latest-everything
1m 11s
Run nf-test with bam_sv_calling-latest-everything
1m 44s
Run nf-test with bam_variant_calling_delly-latest-everything
56s
Run nf-test with bam_variant_calling_gridss-latest-everything
1m 44s
Run nf-test with bam_variant_calling_manta-latest-everything
1m 42s
Run nf-test with bam_variant_calling_qdnaseq-latest-everything
1m 43s
Run nf-test with bam_variant_calling_smoove-latest-everything
1m 24s
Run nf-test with bam_variant_calling_wisecondorx-latest-everything
1m 35s
Run nf-test with vcf_annotate_vep_annotsv_vcfanno-latest-everything
1m 42s
Run nf-test with vcf_concat_bcftools-latest-everything
1m 1s
Run nf-test with vcf_merge_callers_jasmine-latest-everything
1m 26s
Run nf-test with vcf_merge_family_jasmine-latest-everything
1m 42s
58m 12s