Skip to content

Commit

Permalink
Merge branch 'main' into refactor-pipeline-to-workflow
Browse files Browse the repository at this point in the history
  • Loading branch information
@henrikstranneheim
henrikstranneheim authored Feb 8, 2024
2 parents 7514b25 + 1e2ba09 commit 3304d4f
Show file tree
Hide file tree
Showing 14 changed files with 204 additions and 177 deletions.
2 changes: 1 addition & 1 deletion .bumpversion.cfg
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 3.0.0
current_version = 3.0.1
commit = True
tag = True
tag_name = {new_version}
Expand Down
2 changes: 1 addition & 1 deletion cg_hermes/config/balsamic.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -241,7 +241,7 @@
frozenset(RAW_TAGS["metrics_deliverables.yaml"]): { # QC metrics
"tags": ["qc-metrics"],
"is_mandatory": True,
"used_by": ["audit", "cg", "vogue"],
"used_by": ["audit", "cg"],
},
}

Expand Down
2 changes: 1 addition & 1 deletion cg_hermes/config/microsalt.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
frozenset({"microsalt-json", "result_aggregation"}): {
"is_mandatory": False,
"tags": ["typing-report", "qc-metrics"],
"used_by": ["vogue"],
"used_by": ["storage"],
},
frozenset({"runtime-settings", "analysis"}): {
"is_mandatory": True,
Expand Down
2 changes: 1 addition & 1 deletion cg_hermes/config/mip_dna.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@
frozenset(["multiqc_ar", "json"]): {
"tags": ["multiqc-json"],
"is_mandatory": True,
"used_by": ["vogue"],
"used_by": ["storage"],
},
frozenset(["mitodel"]): {
"tags": ["mitodel"],
Expand Down
2 changes: 1 addition & 1 deletion cg_hermes/config/mip_rna.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
frozenset(["multiqc_ar", "json"]): {
"tags": ["multiqc-json"],
"is_mandatory": True,
"used_by": ["vogue"],
"used_by": ["storage"],
},
frozenset(["qccollect_ar", "deliverable"]): {
"tags": ["qc-metrics", "deliverable"],
Expand Down
4 changes: 2 additions & 2 deletions cg_hermes/config/mutant.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,12 +73,12 @@
frozenset({"metrics", "result_aggregation"}): {
"is_mandatory": False,
"tags": ["metrics"],
"used_by": ["vogue"],
"used_by": ["storage"],
},
frozenset({"multiqc-json", "report"}): {
"is_mandatory": True,
"tags": ["multiqc-json"],
"used_by": ["vogue"],
"used_by": ["storage"],
},
frozenset({"nextclade-summary", "report"}): {
"is_mandatory": True,
Expand Down
2 changes: 1 addition & 1 deletion cg_hermes/config/tags.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,7 @@
"nipt",
"scout",
"storage",
"vogue",
"janus",
}

COMMON_TAG_CATEGORIES = {
Expand Down
150 changes: 75 additions & 75 deletions docs/balsamic_map.md
View file

Large diffs are not rendered by default.

30 changes: 15 additions & 15 deletions docs/microsalt_map.md
View file
Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
| Microsalt tags | Mandatory | HK tags | Used by |
|---------------------------------------|-------------|------------------------------|----------------|
| analysis, sampleinfo | True | config | storage, audit |
| microsalt-qc, result_aggregation | True | qc-report, visualization | deliver |
| microsalt-type, result_aggregation | True | typing-report, visualization | deliver |
| microsalt-json, result_aggregation | False | typing-report, qc-metrics | vogue |
| runtime-settings, analysis | True | microsalt-config | storage, audit |
| assembly | True | 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 |
| analysis, logfile | True | microsalt-log | audit |
| assembly, quast-results | False | qc-metrics, assembly | audit |
| reference-alignment-sorted, alignment | True | 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 |
| 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 |
68 changes: 35 additions & 33 deletions docs/mip-dna_map.md
View file
Original file line number Diff line number Diff line change
@@ -1,49 +1,51 @@
| Mip-dna tags | Mandatory | HK tags | Used by |
| ----------------------------------- | --------- | -------------------------------- | ------------ |
|-------------------------------------|-----------|----------------------------------|--------------|
| chanjo_sexcheck | False | chanjo, sex-check | scout |
| chromograph_cov, tcov | False | chromograph, tcov | 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 |
| clinical, me_filter | False | clinical, mobile-elements, vcf | scout |
| clinical, sv_reformat | False | vcf-sv-clinical | scout |
| config, mip_analyse | True | mip-analyse, config | cg, audit |
| config_analysis, mip_analyse | True | mip-config | cg, audit |
| coverage, sambamba_depth | True | coverage, sambamba-depth | chanjo |
| expansionhunter, str_alignments | False | expansionhunter, bam | scout |
| expansionhunter, str_variants | False | expansionhunter, vcf-str | scout |
| expansionhunter, variant_catalog | False | expansionhunter, variant-catalog | scout |
| gatk_baserecalibration | False | cram | scout |
| gatk_combinevariantcallsets | True | snv-gbcf, snv-bcf | genotype |
| gens_generatedata, baf | False | gens, fracsnp | scout |
| gens_generatedata, cov | False | gens, coverage | 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 |
| html, multiqc_ar | True | multiqc-html | scout |
| json, multiqc_ar | True | multiqc-json | vogue |
| log, mip_analyse | True | mip-log | audit |
| 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 |
| mitodel | False | mitodel | scout |
| peddy, peddy_ar | True | peddy, ped | audit, scout |
| peddy_ar, ped_check | True | peddy, ped-check | audit, scout |
| 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 |
| qccollect_ar, audit | True | qc-metrics, audit | audit |
| 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 |
| references_info, mip_analyse | True | mip-analyse, reference-info | audit |
| regions, chromograph_upd | False | chromograph, upd, regions | scout |
| research, endvariantannotationblock | True | vcf-snv-research | scout |
| research, me_filter | False | research, mobile-elements, vcf | scout |
| research, sv_reformat | False | vcf-sv-research | scout |
| qccollect_ar, audit | True | qc-metrics, audit | audit |
| rhocall_viz | False | rhocall-viz | scout |
| sample_info, mip_analyse | True | sample-info | cg, audit |
| sambamba_depth, coverage | True | coverage, sambamba-depth | chanjo |
| samtools_subsample_mt | False | bam-mt | scout |
| sex_check, peddy_ar | True | peddy, sex-check | audit, scout |
| sites, chromograph_upd | False | chromograph, upd, sites | scout |
| sites, upd_ar | False | upd, sites | scout |
| smncopynumbercaller | False | smn-calling | scout |
| star_caller | False | cyrius | scout |
| sv_combinevariantcallsets | True | sv-bcf | audit |
| sv_str, expansionhunter | False | vcf-str | scout |
| 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 |
| upd_ar, regions | False | upd, regions | scout |
| vcf2cytosure_ar | False | vcf2cytosure | 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 |
59 changes: 30 additions & 29 deletions docs/mip-rna_map.md
View file
Original file line number Diff line number Diff line change
@@ -1,29 +1,30 @@
| Mip-rna tags | Mandatory | HK tags | Used by |
|-------------------------------------|-------------|-----------------------------|--------------|
| arriba_ar | True | fusion, arriba | storage |
| blobfish | False | deseq2 | storage |
| build_sj_tracks, coverage | True | bigwig, coverage | scout |
| build_sj_tracks, junction | True | bed, junction | scout |
| config, mip_analyse | True | mip-analyse, config | cg, audit |
| config_analysis, mip_analyse | True | mip-config | cg, audit |
| gatk_asereadcounter | True | asereadcounter | storage |
| html, multiqc_ar | True | multiqc-html | scout |
| json, multiqc_ar | True | multiqc-json | vogue |
| log, mip_analyse | True | mip-log | audit |
| markduplicates | True | cram | storage |
| megafusion_ar | True | fusion, vcf | storage |
| merege_fusion_reports, clinical | True | fusion, pdf, clinical | scout |
| merege_fusion_reports, research | True | fusion, pdf, research | scout |
| pedigree, mip_analyse | True | pedigree-yaml | audit |
| pedigree_fam, mip_analyse | True | pedigree | scout |
| qccollect_ar, deliverable | True | qc-metrics, deliverable | audit |
| qccollect_ar, audit | True | qc-metrics, audit | audit |
| references_info, mip_analyse | True | mip-analyse, reference-info | audit |
| salmon_quant | True | salmon-quant | storage |
| sample_info, mip_analyse | True | sample-info | cg, audit |
| star_fusion | True | fusion, star-fusion | storage |
| stringtie_ar | True | assembly, stringtie | storage |
| svdb_merge_fusion | True | fusion, vcf | storage |
| vcfparser_ar, clinical | True | vcf-snv-clinical | storage |
| vcfparser_ar, research | True | vcf-snv-research | storage |
| version_collect_ar | True | exe-ver | audit |
| 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 |
Loading

0 comments on commit 3304d4f

Please sign in to comment.