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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,15 +1,15 @@ | ||
| | Microsalt tags | Mandatory | HK tags | Used by | | ||
| |---------------------------------------|-----------|------------------------------|----------------| | ||
| | sampleinfo, analysis | True | config | storage, audit | | ||
| | microsalt-qc, result_aggregation | True | qc-report, visualization | deliver | | ||
| | result_aggregation, microsalt-type | False | typing-report, visualization | deliver | | ||
| | microsalt-json, result_aggregation | False | typing-report, qc-metrics | storage | | ||
| | analysis, runtime-settings | True | microsalt-config | storage, audit | | ||
| | assembly | False | assembly | storage | | ||
| | trimmed-forward-reads, concatination | False | fastq, forward-strand | storage | | ||
| | concatination, trimmed-reverse-reads | False | fastq, reverse-strand | storage | | ||
| | concatination, trimmed-unpaired-reads | False | fastq, unpaired-reads | storage | | ||
| | analysis, logfile | False | microsalt-log | audit | | ||
| | assembly, quast-results | False | qc-metrics, assembly | audit | | ||
| | alignment, reference-alignment-sorted | False | bam | storage | | ||
| | insertsize_calc, picard-insertsize | False | qc-metrics, picard | audit | | ||
| | Microsalt tags | Mandatory | HK tags | Used by | | ||
| |---------------------------------------|-------------|------------------------------|----------------| | ||
| | sampleinfo, analysis | True | config | storage, audit | | ||
| | microsalt-qc, result_aggregation | True | qc-report, visualization | deliver | | ||
| | microsalt-type, result_aggregation | False | typing-report, visualization | deliver | | ||
| | result_aggregation, microsalt-json | False | typing-report, qc-metrics | storage | | ||
| | analysis, runtime-settings | True | microsalt-config | storage, audit | | ||
| | assembly | False | assembly | storage | | ||
| | concatination, trimmed-forward-reads | False | fastq, forward-strand | storage | | ||
| | concatination, trimmed-reverse-reads | False | fastq, reverse-strand | storage | | ||
| | concatination, trimmed-unpaired-reads | False | fastq, unpaired-reads | storage | | ||
| | logfile, analysis | False | microsalt-log | audit | | ||
| | quast-results, assembly | False | qc-metrics, assembly | audit | | ||
| | alignment, reference-alignment-sorted | False | bam | storage | | ||
| | insertsize_calc, picard-insertsize | False | qc-metrics, picard | audit | |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,51 +1,51 @@ | ||
| | Mip-dna tags | Mandatory | HK tags | Used by | | ||
| |-------------------------------------|-----------|----------------------------------|--------------| | ||
| | chanjo_sexcheck | False | chanjo, sex-check | scout | | ||
| | sites, chromograph_upd | False | chromograph, upd, sites | scout | | ||
| | regions, chromograph_upd | False | chromograph, upd, regions | scout | | ||
| | tcov, chromograph_cov | False | chromograph, tcov | scout | | ||
| | autozyg, chromograph_rhoviz | False | chromograph, autozyg | scout | | ||
| | fracsnp, chromograph_rhoviz | False | chromograph, fracsnp | scout | | ||
| | clinical, endvariantannotationblock | True | vcf-snv-clinical | scout | | ||
| | research, endvariantannotationblock | True | vcf-snv-research | scout | | ||
| | sv_str, expansionhunter | False | vcf-str | scout | | ||
| | str_variants, expansionhunter | False | expansionhunter, vcf-str | scout | | ||
| | str_alignment, expansionhunter | False | expansionhunter, bam | scout | | ||
| | variant_catalog, expansionhunter | False | expansionhunter, variant-catalog | scout | | ||
| | glnexus_merge | False | deepvariant, snv, vcf | storage | | ||
| | markduplicates | False | cram | scout | | ||
| | gatk_combinevariantcallsets | True | snv-gbcf, snv-bcf | genotype | | ||
| | gens_generatedata, baf | False | gens, fracsnp, bed | scout | | ||
| | gens_generatedata, cov | False | gens, coverage, bed | scout | | ||
| | me_merge_vcfs | False | retroseq, vcf | audit | | ||
| | clinical, me_filter | False | mobile-elements, clinical, vcf | scout | | ||
| | research, me_filter | False | mobile-elements, research, vcf | scout | | ||
| | mip_analyse, config | True | mip-analyse, config | cg, audit | | ||
| | mip_analyse, config_analysis | True | mip-config | cg, audit | | ||
| | mip_analyse, log | True | mip-log | audit | | ||
| | pedigree, mip_analyse | True | pedigree-yaml | audit | | ||
| | pedigree_fam, mip_analyse | True | pedigree | scout | | ||
| | mip_analyse, references_info | True | mip-analyse, reference-info | audit | | ||
| | sample_info, mip_analyse | True | sample-info | cg, audit | | ||
| | html, multiqc_ar | True | multiqc-html | scout | | ||
| | json, multiqc_ar | True | multiqc-json | storage | | ||
| | mitodel | False | mitodel | scout | | ||
| | peddy_ar, ped_check | True | peddy, ped-check | audit, scout | | ||
| | peddy_ar, peddy | True | peddy, ped | audit, scout | | ||
| | peddy_ar, sex_check | True | peddy, sex-check | audit, scout | | ||
| | qccollect_ar, deliverable | True | qc-metrics, deliverable | audit | | ||
| | qccollect_ar, audit | True | qc-metrics, audit | audit | | ||
| | rhocall_viz | False | rhocall-viz | scout | | ||
| | sambamba_depth, coverage | True | coverage, sambamba-depth | chanjo | | ||
| | samtools_subsample_mt | False | bam-mt | scout | | ||
| | smncopynumbercaller | False | smn-calling | scout | | ||
| | star_caller | False | cyrius | scout | | ||
| | sv_combinevariantcallsets | True | sv-bcf | audit | | ||
| | sv_reformat, clinical | False | vcf-sv-clinical | scout | | ||
| | sv_reformat, research | False | vcf-sv-research | scout | | ||
| | telomerecat_ar | False | telomere-calling | scout | | ||
| | tiddit_coverage | False | tiddit-coverage, bigwig | scout | | ||
| | regions, upd_ar | False | upd, regions | scout | | ||
| | sites, upd_ar | False | upd, sites | scout | | ||
| | version_collect_ar | True | exe-ver | audit | | ||
| | vcf2cytosure_ar | False | vcf2cytosure | scout | | ||
| | Mip-dna tags | Mandatory | HK tags | Used by | | ||
| |-------------------------------------|-------------|----------------------------------|--------------| | ||
| | chanjo_sexcheck | False | chanjo, sex-check | scout | | ||
| | sites, chromograph_upd | False | chromograph, upd, sites | scout | | ||
| | chromograph_upd, regions | False | chromograph, upd, regions | scout | | ||
| | tcov, chromograph_cov | False | chromograph, tcov | scout | | ||
| | chromograph_rhoviz, autozyg | False | chromograph, autozyg | scout | | ||
| | chromograph_rhoviz, fracsnp | False | chromograph, fracsnp | scout | | ||
| | endvariantannotationblock, clinical | True | vcf-snv-clinical | scout | | ||
| | endvariantannotationblock, research | True | vcf-snv-research | scout | | ||
| | expansionhunter, sv_str | False | vcf-str | scout | | ||
| | expansionhunter, str_variants | False | expansionhunter, vcf-str | scout | | ||
| | str_alignment, expansionhunter | False | expansionhunter, bam | scout | | ||
| | expansionhunter, variant_catalog | False | expansionhunter, variant-catalog | scout | | ||
| | glnexus_merge | False | deepvariant, snv, vcf | storage | | ||
| | markduplicates | False | cram | scout | | ||
| | gatk_combinevariantcallsets | True | snv-gbcf, snv-bcf | genotype | | ||
| | gens_generatedata, baf | False | gens, fracsnp, bed | scout | | ||
| | cov, gens_generatedata | False | gens, coverage, bed | scout | | ||
| | me_merge_vcfs | False | retroseq, vcf | audit | | ||
| | clinical, me_filter | False | mobile-elements, clinical, vcf | scout | | ||
| | me_filter, research | False | mobile-elements, research, vcf | scout | | ||
| | mip_analyse, config | True | mip-analyse, config | cg, audit | | ||
| | mip_analyse, config_analysis | True | mip-config | cg, audit | | ||
| | mip_analyse, log | True | mip-log | audit | | ||
| | mip_analyse, pedigree | True | pedigree-yaml | audit | | ||
| | mip_analyse, pedigree_fam | True | pedigree | scout | | ||
| | mip_analyse, references_info | True | mip-analyse, reference-info | audit | | ||
| | mip_analyse, sample_info | True | sample-info | cg, audit | | ||
| | html, multiqc_ar | True | multiqc-html | scout | | ||
| | json, multiqc_ar | True | multiqc-json | storage | | ||
| | mitodel | False | mitodel | scout | | ||
| | ped_check, peddy_ar | True | peddy, ped-check | audit, scout | | ||
| | peddy_ar, peddy | True | peddy, ped | audit, scout | | ||
| | sex_check, peddy_ar | True | peddy, sex-check | audit, scout | | ||
| | qccollect_ar, deliverable | True | qc-metrics, deliverable | audit | | ||
| | audit, qccollect_ar | True | qc-metrics, audit | audit | | ||
| | rhocall_viz | False | rhocall-viz | scout | | ||
| | sambamba_depth, coverage | True | coverage, sambamba-depth | chanjo | | ||
| | samtools_subsample_mt | False | bam-mt | scout | | ||
| | smncopynumbercaller | False | smn-calling | scout | | ||
| | star_caller | False | cyrius | scout | | ||
| | sv_combinevariantcallsets | True | sv-bcf | audit | | ||
| | clinical, sv_reformat | False | vcf-sv-clinical | scout | | ||
| | sv_reformat, research | False | vcf-sv-research | scout | | ||
| | telomerecat_ar | False | telomere-calling | scout | | ||
| | tiddit_coverage | False | tiddit-coverage, bigwig | scout | | ||
| | upd_ar, regions | False | upd, regions | scout | | ||
| | sites, upd_ar | False | upd, sites | scout | | ||
| | version_collect_ar | True | exe-ver | audit | | ||
| | vcf2cytosure_ar | False | vcf2cytosure | scout | |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,30 @@ | ||
| | Mip-rna tags | Mandatory | HK tags | Used by | | ||
| |--------------------------------|-----------|-----------------------------|-----------| | ||
| | mip_analyse, config | True | mip-analyse, config | cg, audit | | ||
| | mip_analyse, config_analysis | True | mip-config | cg, audit | | ||
| | mip_analyse, log | True | mip-log | audit | | ||
| | mip_analyse, pedigree | True | pedigree-yaml | audit | | ||
| | mip_analyse, references_info | True | mip-analyse, reference-info | audit | | ||
| | mip_analyse, sample_info | True | sample-info | cg, audit | | ||
| | mip_analyse, pedigree_fam | True | pedigree | storage | | ||
| | html, multiqc_ar | True | multiqc-html | audit | | ||
| | json, multiqc_ar | True | multiqc-json | storage | | ||
| | deliverable, qccollect_ar | True | qc-metrics, deliverable | audit | | ||
| | qccollect_ar, audit | True | qc-metrics, audit | audit | | ||
| | version_collect_ar | True | exe-ver | audit | | ||
| | salmon_quant | True | salmon-quant | storage | | ||
| | blobfish | False | deseq2 | storage | | ||
| | star_fusion | False | fusion, star-fusion | storage | | ||
| | arriba_ar | False | fusion, arriba | storage | | ||
| | megafusion_ar | False | fusion, vcf | storage | | ||
| | svdb_merge_fusion | False | fusion, vcf | storage | | ||
| | research, merge_fusion_reports | False | fusion, research, pdf | scout | | ||
| | clinical, merge_fusion_reports | False | fusion, pdf, clinical | scout | | ||
| | coverage, build_sj_tracks | True | coverage, bigwig | scout | | ||
| | junction, build_sj_tracks | True | junction, bed | scout | | ||
| | markduplicates | True | cram | scout | | ||
| | stringtie_ar | False | stringtie, assembly | storage | | ||
| | gffcompare_ar | False | gffcompare | storage | | ||
| | gatk_asereadcounter | True | asereadcounter | storage | | ||
| | research, vcfparser_ar | True | vcf-snv-research | storage | | ||
| | vcfparser_ar, clinical | True | vcf-snv-clinical | storage | | ||
| | Mip-rna tags | Mandatory | HK tags | Used by | | ||
| |--------------------------------|-------------|-----------------------------|-----------| | ||
| | config, mip_analyse | True | mip-analyse, config | cg, audit | | ||
| | config_analysis, mip_analyse | True | mip-config | cg, audit | | ||
| | log, mip_analyse | True | mip-log | audit | | ||
| | pedigree, mip_analyse | True | pedigree-yaml | audit | | ||
| | references_info, mip_analyse | True | mip-analyse, reference-info | audit | | ||
| | sample_info, mip_analyse | True | sample-info | cg, audit | | ||
| | pedigree_fam, mip_analyse | True | pedigree | storage | | ||
| | multiqc_ar, html | True | multiqc-html | audit | | ||
| | multiqc_ar, json | True | multiqc-json | storage | | ||
| | qccollect_ar, deliverable | True | qc-metrics, deliverable | audit | | ||
| | qccollect_ar, audit | True | qc-metrics, audit | audit | | ||
| | version_collect_ar | True | exe-ver | audit | | ||
| | salmon_quant | True | salmon-quant | storage | | ||
| | blobfish | False | deseq2 | storage | | ||
| | star_fusion | False | fusion, star-fusion | storage | | ||
| | arriba_ar | False | fusion, arriba | storage | | ||
| | megafusion_ar | False | fusion, vcf | storage | | ||
| | svdb_merge_fusion | False | fusion, vcf | storage | | ||
| | research, merge_fusion_reports | False | fusion, research, pdf | scout | | ||
| | clinical, merge_fusion_reports | False | fusion, pdf, clinical | scout | | ||
| | coverage, build_sj_tracks | True | coverage, bigwig | scout | | ||
| | junction, build_sj_tracks | True | junction, bed | scout | | ||
| | markduplicates | True | cram | scout | | ||
| | stringtie_ar | False | stringtie, assembly | storage | | ||
| | gffcompare_ar | False | gffcompare | storage | | ||
| | gatk_asereadcounter | True | asereadcounter | storage | | ||
| | research, vcfparser_ar | True | vcf-snv-research | storage | | ||
| | clinical, vcfparser_ar | True | vcf-snv-clinical | storage | |
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