From 34d376acff057ec46d44497fc01193e1a722cdc4 Mon Sep 17 00:00:00 2001 From: Vadym Date: Wed, 7 Feb 2024 14:30:50 +0100 Subject: [PATCH 1/2] Remove Vogue tag, add Janus (#96) ### Added - janus as a valid tag for the used_by field ### Removed - vogue tag --- cg_hermes/config/balsamic.py | 2 +- cg_hermes/config/microsalt.py | 2 +- cg_hermes/config/mip_dna.py | 2 +- cg_hermes/config/mip_rna.py | 2 +- cg_hermes/config/mutant.py | 4 +- cg_hermes/config/tags.py | 2 +- docs/balsamic_map.md | 150 +++++++++++++++++----------------- docs/microsalt_map.md | 30 +++---- docs/mip-dna_map.md | 68 +++++++-------- docs/mip-rna_map.md | 59 ++++++------- docs/mutant_map.md | 30 +++---- tests/cli/test_export_tags.py | 24 ++++++ 12 files changed, 201 insertions(+), 174 deletions(-) diff --git a/cg_hermes/config/balsamic.py b/cg_hermes/config/balsamic.py index 99d9384d..2360a3f4 100644 --- a/cg_hermes/config/balsamic.py +++ b/cg_hermes/config/balsamic.py @@ -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"], }, } diff --git a/cg_hermes/config/microsalt.py b/cg_hermes/config/microsalt.py index 357aeac6..8fa6dd35 100644 --- a/cg_hermes/config/microsalt.py +++ b/cg_hermes/config/microsalt.py @@ -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, diff --git a/cg_hermes/config/mip_dna.py b/cg_hermes/config/mip_dna.py index 6c2ca8df..ca23e724 100644 --- a/cg_hermes/config/mip_dna.py +++ b/cg_hermes/config/mip_dna.py @@ -162,7 +162,7 @@ frozenset(["multiqc_ar", "json"]): { "tags": ["multiqc-json"], "is_mandatory": True, - "used_by": ["vogue"], + "used_by": ["storage"], }, frozenset(["mitodel"]): { "tags": ["mitodel"], diff --git a/cg_hermes/config/mip_rna.py b/cg_hermes/config/mip_rna.py index e5451251..d960e2d4 100644 --- a/cg_hermes/config/mip_rna.py +++ b/cg_hermes/config/mip_rna.py @@ -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"], diff --git a/cg_hermes/config/mutant.py b/cg_hermes/config/mutant.py index fad642fd..ff1b1c5f 100644 --- a/cg_hermes/config/mutant.py +++ b/cg_hermes/config/mutant.py @@ -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, diff --git a/cg_hermes/config/tags.py b/cg_hermes/config/tags.py index 68d93ebb..81a85056 100644 --- a/cg_hermes/config/tags.py +++ b/cg_hermes/config/tags.py @@ -260,7 +260,7 @@ "nipt", "scout", "storage", - "vogue", + "janus", } COMMON_TAG_CATEGORIES = { diff --git a/docs/balsamic_map.md b/docs/balsamic_map.md index f00d094e..3a1800b1 100644 --- a/docs/balsamic_map.md +++ b/docs/balsamic_map.md @@ -1,75 +1,75 @@ -| Balsamic tags | Mandatory | HK tags | Used by | -|----------------------------------------------------------------|-------------|-------------------------------------------|-----------------------| -| balsamic-config | True | balsamic-config | audit, cg | -| balsamic-report | True | balsamic-report | audit | -| balsamic-dag | True | balsamic-dag | audit | -| html, multiqc-html | True | multiqc-html | audit, deliver, scout | -| multiqc-json, json | True | multiqc-json | audit | -| yaml, qc-metrics-yaml | True | qc-metrics | audit, cg, vogue | -| tumor-cram, cram | True | tumor, cram | deliver, scout | -| cram, tumor-cram-index | True | tumor, cram-index | deliver, scout | -| cram, normal-cram | False | normal, cram | deliver, scout | -| cram, normal-cram-index | False | normal, cram-index | deliver, scout | -| vcf-tumor, germline-vcf-tumor, dnascope, snv | True | germline, vcf-snv-germline-tumor | deliver | -| vcf-tumor, germline-vcf-tumor-index, dnascope, snv | True | germline, vcf-snv-germline-tumor-index | deliver | -| vcf-normal, germline-vcf-normal, dnascope, snv | False | germline, vcf-snv-germline-normal | deliver | -| vcf-normal, snv, dnascope, germline-vcf-normal-index | False | germline, vcf-snv-germline-normal-index | deliver | -| genotype-vcf-dnascope, vcf-dnascope | False | dnascope, normal, vcf | cg, genotype | -| genotype-vcf-dnascope-index, vcf-dnascope | False | dnascope, normal, vcf-index | cg, genotype | -| vcf-tumor, manta-germline, sv, germline-vcf-tumor | True | germline, vcf-sv-germline-tumor | deliver | -| vcf-tumor, manta-germline, germline-vcf-tumor-index, sv | True | germline, vcf-sv-germline-tumor-index | deliver | -| vcf-normal, manta-germline, sv, germline-vcf-normal | False | germline, vcf-sv-germline-normal | deliver | -| vcf-normal, manta-germline, sv, germline-vcf-normal-index | False | germline, vcf-sv-germline-normal-index | deliver | -| research-vcf-svdb, vcf-svdb | True | svdb, vcf-sv | deliver | -| research-vcf-svdb-index, vcf-svdb | True | svdb, vcf-sv-index | deliver | -| vcf-pass-svdb, research-vcf-pass-svdb | True | svdb, vcf-sv-research | deliver | -| vcf-pass-svdb, research-vcf-pass-svdb-index | True | svdb, vcf-sv-research-index | deliver | -| clinical-vcf-pass-svdb, vcf-pass-svdb | True | svdb, vcf-sv-clinical | deliver, scout | -| clinical-vcf-pass-svdb-index, vcf-pass-svdb | True | svdb, vcf-sv-clinical-index | deliver, scout | -| vcf-tnscope, research-vcf-tnscope | False | tnscope, vcf-snv | deliver | -| vcf-tnscope, research-vcf-tnscope-index | False | tnscope, vcf-snv-index | deliver | -| vcf-pass-tnscope, research-vcf-pass-tnscope, snv | False | tnscope, vcf-snv-research | deliver | -| vcf-pass-tnscope, research-vcf-pass-tnscope-index, snv | False | tnscope, vcf-snv-research-index | deliver | -| vcf-pass-tnscope, snv, clinical-vcf-pass-tnscope | False | tnscope, vcf-snv-clinical | deliver, scout | -| vcf-pass-tnscope, clinical-vcf-pass-tnscope-index, snv | False | tnscope, vcf-snv-clinical-index | deliver, scout | -| clinical-ascat-copynumber, ascat-copynumber | False | ascatngs, metrics | deliver | -| rd-delly, clinical-rd-delly | True | delly, coverage | deliver | -| cnv-somatic-cgh-tumor, cgh-tumor | False | cnvkit, tumor, vcf2cytosure | deliver, scout | -| cgh-normal, cnv-somatic-cgh-normal | False | tiddit, normal, vcf2cytosure | deliver, scout | -| gens-bed, cov, cnv-gens-bed | False | gens, coverage, bed | scout | -| gens-bed, cov, cnv-gens-bed-index | False | gens, coverage, bed-index | scout | -| gens-bed, cnv-gens-bed, baf | False | gens, fracsnp, bed | scout | -| gens-bed, cnv-gens-bed-index, baf | False | gens, fracsnp, bed-index | scout | -| research-vcf-vardict, vcf-vardict | False | vardict, vcf-snv | deliver | -| vcf-vardict, research-vcf-vardict-index | False | vardict, vcf-snv-index | deliver | -| vcf-pass-vardict, research-vcf-pass-vardict, snv | False | vardict, vcf-snv-research | deliver | -| vcf-pass-vardict, research-vcf-pass-vardict-index, snv | False | vardict, vcf-snv-research-index | deliver | -| vcf-pass-vardict, clinical-vcf-pass-vardict, snv | False | vardict, vcf-snv-clinical | deliver, scout | -| vcf-pass-vardict, clinical-vcf-pass-vardict-index, snv | False | vardict, vcf-snv-clinical-index | deliver, scout | -| cns, cnv-cns | False | cnvkit, metrics, segments | deliver | -| cnv-cnr, cnr | False | cnvkit, regions | storage | -| cnv-gene-metrics, gene-metrics | False | cnvkit, metrics, genes | deliver | -| clinical-cnv-report-pdf, cnv-report-pdf | True | cnv-report | deliver, scout | -| circular-cnvpytor, clinical-circular-cnvpytor | False | circular-plot, cnvpytor, visualization | storage | -| scatter-cnvpytor, clinical-scatter-cnvpytor | False | scatter-plot, cnvpytor, visualization | storage | -| clinical-plot-ascat-profile, plot-ascat-profile | False | profile-plot, ascatngs, visualization | storage | -| clinical-plot-raw-profile, plot-raw-profile | False | raw-profile-plot, ascatngs, visualization | storage | -| clinical-plot-aspcf, plot-aspcf | False | aspcf-plot, ascatngs, visualization | storage | -| plot-tumor, clinical-plot-tumor | False | tumor-plot, ascatngs, visualization | storage | -| plot-germline, clinical-plot-germline | False | germline-plot, ascatngs, visualization | storage | -| clinical-plot-sunrise, plot-sunrise | False | sunrise-plot, ascatngs, visualization | storage | -| cov-tumor-tiddit, clinical-cov-tumor-tiddit | False | tiddit, tumor, coverage | deliver | -| cov-normal-tiddit, clinical-cov-normal-tiddit | False | tiddit, normal, coverage | deliver | -| tmb, vardict, research-tmb, snv | False | research, vardict, tmb | storage | -| tmb, tnscope, research-tmb, snv | False | research, tnscope, tmb | storage | -| cram, umi-tumor-cram | True | umi-cram, tumor | deliver, scout | -| cram, umi-tumor-cram-index | True | umi-cram-index, tumor | deliver, scout | -| cram, umi-normal-cram | False | umi-cram, normal | deliver, scout | -| cram, umi-normal-cram-index | False | umi-cram-index, normal | deliver, scout | -| vcf-tnscope-umi, research-vcf-tnscope-umi | True | tnscope-umi, vcf-umi-snv | deliver | -| vcf-tnscope-umi, research-vcf-tnscope-umi-index | True | tnscope-umi, vcf-umi-snv-index | deliver | -| research-vcf-pass-tnscope-umi, vcf-pass-tnscope-umi, snv | True | tnscope-umi, vcf-umi-snv-research | deliver | -| vcf-pass-tnscope-umi, research-vcf-pass-tnscope-umi-index, snv | True | tnscope-umi, vcf-umi-snv-research-index | deliver | -| vcf-pass-tnscope-umi, clinical-vcf-pass-tnscope-umi, snv | True | tnscope-umi, vcf-umi-snv-clinical | deliver, scout | -| vcf-pass-tnscope-umi, clinical-vcf-pass-tnscope-umi-index, snv | True | tnscope-umi, vcf-umi-snv-clinical-index | deliver, scout | -| tnscope-umi, tmb, research-tmb, snv | True | research, tnscope-umi, tmb | storage | +| Balsamic tags | Mandatory | HK tags | Used by | +|----------------------------------------------------------------|-----------|-------------------------------------------|-----------------------| +| balsamic-config | True | balsamic-config | audit, cg | +| balsamic-report | True | balsamic-report | audit | +| balsamic-dag | True | balsamic-dag | audit | +| html, multiqc-html | True | multiqc-html | audit, deliver, scout | +| json, multiqc-json | True | multiqc-json | audit | +| yaml, qc-metrics-yaml | True | qc-metrics | audit, cg | +| tumor-cram, cram | True | tumor, cram | deliver, scout | +| cram, tumor-cram-index | True | tumor, cram-index | deliver, scout | +| cram, normal-cram | False | normal, cram | deliver, scout | +| cram, normal-cram-index | False | normal, cram-index | deliver, scout | +| dnascope, germline-vcf-tumor, vcf-tumor, snv | True | germline, vcf-snv-germline-tumor | deliver | +| dnascope, germline-vcf-tumor-index, vcf-tumor, snv | True | germline, vcf-snv-germline-tumor-index | deliver | +| dnascope, germline-vcf-normal, vcf-normal, snv | False | germline, vcf-snv-germline-normal | deliver | +| dnascope, germline-vcf-normal-index, vcf-normal, snv | False | germline, vcf-snv-germline-normal-index | deliver | +| vcf-dnascope, genotype-vcf-dnascope | False | dnascope, normal, vcf | cg, genotype | +| vcf-dnascope, genotype-vcf-dnascope-index | False | dnascope, normal, vcf-index | cg, genotype | +| sv, germline-vcf-tumor, manta-germline, vcf-tumor | True | germline, vcf-sv-germline-tumor | deliver | +| manta-germline, sv, germline-vcf-tumor-index, vcf-tumor | True | germline, vcf-sv-germline-tumor-index | deliver | +| vcf-normal, germline-vcf-normal, sv, manta-germline | False | germline, vcf-sv-germline-normal | deliver | +| germline-vcf-normal-index, manta-germline, sv, vcf-normal | False | germline, vcf-sv-germline-normal-index | deliver | +| vcf-svdb, research-vcf-svdb | True | svdb, vcf-sv | deliver | +| vcf-svdb, research-vcf-svdb-index | True | svdb, vcf-sv-index | deliver | +| vcf-pass-svdb, research-vcf-pass-svdb | True | svdb, vcf-sv-research | deliver | +| research-vcf-pass-svdb-index, vcf-pass-svdb | True | svdb, vcf-sv-research-index | deliver | +| vcf-pass-svdb, clinical-vcf-pass-svdb | True | svdb, vcf-sv-clinical | deliver, scout | +| vcf-pass-svdb, clinical-vcf-pass-svdb-index | True | svdb, vcf-sv-clinical-index | deliver, scout | +| research-vcf-tnscope, vcf-tnscope | False | tnscope, vcf-snv | deliver | +| research-vcf-tnscope-index, vcf-tnscope | False | tnscope, vcf-snv-index | deliver | +| vcf-pass-tnscope, research-vcf-pass-tnscope, snv | False | tnscope, vcf-snv-research | deliver | +| research-vcf-pass-tnscope-index, vcf-pass-tnscope, snv | False | tnscope, vcf-snv-research-index | deliver | +| clinical-vcf-pass-tnscope, vcf-pass-tnscope, snv | False | tnscope, vcf-snv-clinical | deliver, scout | +| clinical-vcf-pass-tnscope-index, vcf-pass-tnscope, snv | False | tnscope, vcf-snv-clinical-index | deliver, scout | +| ascat-copynumber, clinical-ascat-copynumber | False | ascatngs, metrics | deliver | +| rd-delly, clinical-rd-delly | True | delly, coverage | deliver | +| cnv-somatic-cgh-tumor, cgh-tumor | False | cnvkit, tumor, vcf2cytosure | deliver, scout | +| cnv-somatic-cgh-normal, cgh-normal | False | tiddit, normal, vcf2cytosure | deliver, scout | +| cov, cnv-gens-bed, gens-bed | False | gens, coverage, bed | scout | +| cnv-gens-bed-index, cov, gens-bed | False | gens, coverage, bed-index | scout | +| baf, cnv-gens-bed, gens-bed | False | gens, fracsnp, bed | scout | +| cnv-gens-bed-index, baf, gens-bed | False | gens, fracsnp, bed-index | scout | +| research-vcf-vardict, vcf-vardict | False | vardict, vcf-snv | deliver | +| vcf-vardict, research-vcf-vardict-index | False | vardict, vcf-snv-index | deliver | +| vcf-pass-vardict, research-vcf-pass-vardict, snv | False | vardict, vcf-snv-research | deliver | +| vcf-pass-vardict, research-vcf-pass-vardict-index, snv | False | vardict, vcf-snv-research-index | deliver | +| vcf-pass-vardict, clinical-vcf-pass-vardict, snv | False | vardict, vcf-snv-clinical | deliver, scout | +| vcf-pass-vardict, clinical-vcf-pass-vardict-index, snv | False | vardict, vcf-snv-clinical-index | deliver, scout | +| cnv-cns, cns | False | cnvkit, metrics, segments | deliver | +| cnr, cnv-cnr | False | cnvkit, regions | storage | +| cnv-gene-metrics, gene-metrics | False | cnvkit, metrics, genes | deliver | +| clinical-cnv-report-pdf, cnv-report-pdf | True | cnv-report | deliver, scout | +| circular-cnvpytor, clinical-circular-cnvpytor | False | circular-plot, cnvpytor, visualization | storage | +| clinical-scatter-cnvpytor, scatter-cnvpytor | False | scatter-plot, cnvpytor, visualization | storage | +| plot-ascat-profile, clinical-plot-ascat-profile | False | profile-plot, ascatngs, visualization | storage | +| clinical-plot-raw-profile, plot-raw-profile | False | raw-profile-plot, ascatngs, visualization | storage | +| plot-aspcf, clinical-plot-aspcf | False | aspcf-plot, ascatngs, visualization | storage | +| plot-tumor, clinical-plot-tumor | False | tumor-plot, ascatngs, visualization | storage | +| plot-germline, clinical-plot-germline | False | germline-plot, ascatngs, visualization | storage | +| plot-sunrise, clinical-plot-sunrise | False | sunrise-plot, ascatngs, visualization | storage | +| cov-tumor-tiddit, clinical-cov-tumor-tiddit | False | tiddit, tumor, coverage | deliver | +| clinical-cov-normal-tiddit, cov-normal-tiddit | False | tiddit, normal, coverage | deliver | +| vardict, research-tmb, tmb, snv | False | research, vardict, tmb | storage | +| tmb, tnscope, research-tmb, snv | False | research, tnscope, tmb | storage | +| umi-tumor-cram, cram | True | umi-cram, tumor | deliver, scout | +| cram, umi-tumor-cram-index | True | umi-cram-index, tumor | deliver, scout | +| umi-normal-cram, cram | False | umi-cram, normal | deliver, scout | +| cram, umi-normal-cram-index | False | umi-cram-index, normal | deliver, scout | +| research-vcf-tnscope-umi, vcf-tnscope-umi | True | tnscope-umi, vcf-umi-snv | deliver | +| research-vcf-tnscope-umi-index, vcf-tnscope-umi | True | tnscope-umi, vcf-umi-snv-index | deliver | +| research-vcf-pass-tnscope-umi, vcf-pass-tnscope-umi, snv | True | tnscope-umi, vcf-umi-snv-research | deliver | +| research-vcf-pass-tnscope-umi-index, vcf-pass-tnscope-umi, snv | True | tnscope-umi, vcf-umi-snv-research-index | deliver | +| vcf-pass-tnscope-umi, clinical-vcf-pass-tnscope-umi, snv | True | tnscope-umi, vcf-umi-snv-clinical | deliver, scout | +| vcf-pass-tnscope-umi, clinical-vcf-pass-tnscope-umi-index, snv | True | tnscope-umi, vcf-umi-snv-clinical-index | deliver, scout | +| tmb, tnscope-umi, research-tmb, snv | True | research, tnscope-umi, tmb | storage | diff --git a/docs/microsalt_map.md b/docs/microsalt_map.md index 4c1e9925..58f798d3 100644 --- a/docs/microsalt_map.md +++ b/docs/microsalt_map.md @@ -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 | diff --git a/docs/mip-dna_map.md b/docs/mip-dna_map.md index 7365e6d4..00e7944d 100644 --- a/docs/mip-dna_map.md +++ b/docs/mip-dna_map.md @@ -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 | diff --git a/docs/mip-rna_map.md b/docs/mip-rna_map.md index d703b1ff..1201bc72 100644 --- a/docs/mip-rna_map.md +++ b/docs/mip-rna_map.md @@ -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 | diff --git a/docs/mutant_map.md b/docs/mutant_map.md index 9d4512a4..85fc9ff0 100644 --- a/docs/mutant_map.md +++ b/docs/mutant_map.md @@ -1,27 +1,27 @@ -| MUTANT tags | Mandatory | HK tags | Used by | +| Mutant tags | Mandatory | HK tags | Used by | |---------------------------------------|-----------|----------------------------------------------------------------|------------------| | sampleinfo, runinfo | True | config | storage, audit | -| instrument-properties, report | False | fohm-delivery, instrument-properties | storage, audit | +| report, instrument-properties | False | fohm-delivery, instrument-properties | storage, audit | | runtime-settings, runinfo | True | mutant-config | storage, audit | | software-versions, runinfo | True | software-versions | storage, audit | -| runinfo, logfile | True | mutant-log | audit | -| concatination, forward-reads | True | fastq, forward-strand | storage | +| logfile, runinfo | True | mutant-log | audit | +| forward-reads, concatination | True | fastq, forward-strand | storage | | concatination, reverse-reads | False | fastq, reverse-strand | storage | | SARS-CoV-2-info, report | False | fohm-delivery, komplettering, visualization | deliver | -| SARS-CoV-2-qc, result_aggregation | False | fohm-delivery, pangolin-typing, csv, visualization | audit | -| pangolin-typing, report | False | fohm-delivery, pangolin-typing, csv, visualization | audit | -| pangolin-typing-fohm, report | False | fohm-delivery, pangolin-typing-fohm, csv | deliver | -| alignment, reference-alignment-sorted | False | bam | storage | -| vcf-covid, genotyping | False | vcf, vcf-report, fohm-delivery | deliver | -| vcf-covid, variant-calling | False | tsv, vcf-report | deliver | -| metrics, result_aggregation | False | metrics | vogue | -| multiqc-json, report | True | multiqc-json | vogue | +| result_aggregation, SARS-CoV-2-qc | False | fohm-delivery, pangolin-typing, csv, visualization | audit | +| pangolin-typing, report | False | fohm-delivery, pangolin-typing, visualization, csv | audit | +| report, pangolin-typing-fohm | False | fohm-delivery, pangolin-typing-fohm, csv | deliver | +| reference-alignment-sorted, alignment | False | bam | storage | +| genotyping, vcf-covid | False | vcf, vcf-report, fohm-delivery | deliver | +| variant-calling, vcf-covid | False | tsv, vcf-report | deliver | +| result_aggregation, metrics | False | metrics | storage | +| multiqc-json, report | True | multiqc-json | storage | | nextclade-summary, report | True | ks-delivery, typing-summary, nextclade | deliver | -| ks-results, report | True | ks-delivery, ks-results, typing-report, visualization, csv | deliver | +| report, ks-results | True | ks-delivery, ks-results, typing-report, visualization, csv | deliver | | ks-aux-results, report | True | ks-delivery, ks-aux-results, typing-report, visualization, csv | deliver | | consensus, analysis | True | ks-delivery, fastq, consensus | deliver, storage | | consensus-sample, consensus | False | fohm-delivery, fasta, consensus-sample | deliver, storage | -| multiqc-html, report | True | ks-delivery, multiqc-html | deliver | +| report, multiqc-html | True | ks-delivery, multiqc-html | deliver | | SARS-CoV-2-sum, report | False | artic-sum, csv | audit | | SARS-CoV-2-var, report | False | artic-var, csv | audit | -| SARS-CoV-2-type, typing | False | artic-type, csv | audit | +| typing, SARS-CoV-2-type | False | artic-type, csv | audit | diff --git a/tests/cli/test_export_tags.py b/tests/cli/test_export_tags.py index 73358f3c..bf651a29 100644 --- a/tests/cli/test_export_tags.py +++ b/tests/cli/test_export_tags.py @@ -78,3 +78,27 @@ def test_export_rnafusion_tags(cli_runner: CliRunner): assert result.exit_code == 0 # THEN assert that the rnafusion tags was exported assert "Rnafusion tags" in result.output + + +def test_export_microsalt_tags(cli_runner: CliRunner): + # GIVEN a cli runner + + # WHEN running the export tags command for MicroSALT + result = cli_runner.invoke(app, ["--pipeline", "microsalt"]) + + # THEN assert that the command exits without problems + assert result.exit_code == 0 + # THEN assert that the MicroSALT tags was exported + assert "Microsalt tags" in result.output + + +def test_export_mutant_tags(cli_runner: CliRunner): + # GIVEN a cli runner + + # WHEN running the export tags command for Mutant + result = cli_runner.invoke(app, ["--pipeline", "mutant"]) + + # THEN assert that the command exits without problems + assert result.exit_code == 0 + # THEN assert that the MicroSALT tags was exported + assert "Mutant tags" in result.output From 1e2ba095412f610b58d6623d8799647997b56d22 Mon Sep 17 00:00:00 2001 From: Clinical Genomics Bot Date: Wed, 7 Feb 2024 13:31:15 +0000 Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=203.0.0=20=E2=86=92=203.0.1?= =?UTF-8?q?=20[skip=20ci]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 98c9c257..8cfe4dce 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 3.0.0 +current_version = 3.0.1 commit = True tag = True tag_name = {new_version} diff --git a/pyproject.toml b/pyproject.toml index cd743977..71b77f06 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "cg-hermes" -version = "3.0.0" +version = "3.0.1" description = "Convert information between pipelines and CG" authors = ["Måns Magnusson "]