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Store intermediate MultiQC files for Balsamic #95

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merged 14 commits into from
Feb 21, 2024
Merged

Store intermediate MultiQC files for Balsamic #95

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8906030
Add intermediate MultiQC files
ivadym Feb 6, 2024
b87f450
Sort
ivadym Feb 6, 2024
d9466ea
Typo
ivadym Feb 6, 2024
1fc1e88
Merge branch 'main' of github.com:Clinical-Genomics/hermes into add-m…
ivadym Feb 7, 2024
895a1d4
Add used_by janus
ivadym Feb 7, 2024
da27dd4
TN-panel
ivadym Feb 16, 2024
f4fb420
T-panel
ivadym Feb 16, 2024
9414067
TN-wgs
ivadym Feb 16, 2024
7700b6b
T-wgs
ivadym Feb 16, 2024
a40d1ec
Add fastp files
ivadym Feb 16, 2024
f158815
update tags
ivadym Feb 16, 2024
5995987
Merge branch 'main' of github.com:Clinical-Genomics/hermes into add-m…
ivadym Feb 19, 2024
28af124
Extra deliverable tag
ivadym Feb 19, 2024
7993934
Update tags
ivadym Feb 19, 2024
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55 changes: 55 additions & 0 deletions cg_hermes/config/balsamic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,14 @@
"BALSAMIC_X.X.X_graph.pdf": ["balsamic-dag"],
"multiqc_report.html": ["html", "multiqc-html"],
"multiqc_data.json": ["json", "multiqc-json"],
"multiqc_picard_AlignmentSummaryMetrics.json": ["multiqc", "picard", "alignmentsummarymetrics"],
"multiqc_picard_dups.json": ["multiqc", "picard", "dups"],
"multiqc_picard_HsMetrics.json": ["multiqc", "picard", "hsmetrics"],
"multiqc_picard_insertSize.json": ["multiqc", "picard", "insertsize"],
"multiqc_picard_wgsmetrics.json": ["multiqc", "picard", "wgsmetrics"],
"multiqc_fastp.json": ["multiqc", "fastp"],
"multiqc_samtools_stats.json": ["multiqc", "samtools", "stats"],
"multiqc_somalier.json": ["multiqc", "somalier"],
# Custom QC
"metrics_deliverables.yaml": ["yaml", "qc-metrics-yaml"],
# Alignment files (PANEL & WGS)
Expand Down Expand Up @@ -237,6 +245,46 @@
"is_mandatory": True,
"used_by": ["audit"],
},
frozenset(RAW_TAGS["multiqc_picard_AlignmentSummaryMetrics.json"]): {
"tags": ["qc-metrics", "multiqc", "picard-alignment"],
"is_mandatory": True,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_picard_dups.json"]): {
"tags": ["qc-metrics", "multiqc", "picard-duplicates"],
"is_mandatory": True,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_picard_HsMetrics.json"]): {
"tags": ["qc-metrics", "multiqc", "picard-hs"],
"is_mandatory": True,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_picard_insertSize.json"]): {
"tags": ["qc-metrics", "multiqc", "picard-insert-size"],
"is_mandatory": True,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_picard_wgsmetrics.json"]): {
"tags": ["qc-metrics", "multiqc", "picard-wgs"],
"is_mandatory": False,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_fastp.json"]): {
"tags": ["qc-metrics", "multiqc", "fastp"],
"is_mandatory": True,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_samtools_stats.json"]): {
"tags": ["qc-metrics", "multiqc", "samtools-stats"],
"is_mandatory": True,
"used_by": ["storage", "janus"],
},
frozenset(RAW_TAGS["multiqc_somalier.json"]): {
"tags": ["qc-metrics", "multiqc", "somalier"],
"is_mandatory": False,
"used_by": ["storage", "janus"],
},
# Custom QC
frozenset(RAW_TAGS["metrics_deliverables.yaml"]): { # QC metrics
"tags": ["qc-metrics"],
Expand Down Expand Up @@ -559,6 +607,8 @@
}

TUMOR_ONLY_WGS_TAGS = {
# QC
frozenset(RAW_TAGS["multiqc_picard_wgsmetrics.json"]): {"is_mandatory": True},
# SNVs (WGS)
frozenset(RAW_TAGS["tnscope.vcf.gz"]): {"is_mandatory": True},
frozenset(RAW_TAGS["tnscope.vcf.gz.tbi"]): {"is_mandatory": True},
Expand All @@ -581,6 +631,9 @@
}

TUMOR_NORMAL_WGS_TAGS = {
# QC
frozenset(RAW_TAGS["multiqc_picard_wgsmetrics.json"]): {"is_mandatory": True},
frozenset(RAW_TAGS["multiqc_somalier.json"]): {"is_mandatory": True},
# Alignment files (PANEL & WGS)
frozenset(RAW_TAGS["normal.merged.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.merged.cram.crai"]): {"is_mandatory": True},
Expand Down Expand Up @@ -637,6 +690,8 @@
}

TUMOR_NORMAL_PANEL_TAGS = {
# QC
frozenset(RAW_TAGS["multiqc_somalier.json"]): {"is_mandatory": True},
# Alignment files (PANEL & WGS)
frozenset(RAW_TAGS["normal.merged.cram"]): {"is_mandatory": True},
frozenset(RAW_TAGS["normal.merged.cram.crai"]): {"is_mandatory": True},
Expand Down
149 changes: 74 additions & 75 deletions cg_hermes/config/tags.py
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119 changes: 64 additions & 55 deletions docs/all_tags.md
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158 changes: 83 additions & 75 deletions docs/balsamic_map.md
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2 changes: 2 additions & 0 deletions docs/fluffy_map.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,6 @@
|------------------------|-------------|-----------------|-----------|
| multiqc | True | multiqc-html | nipt |
| nipt_csv | True | metrics | nipt |
| nipt_first_pass_csv | False | first-pass | nipt |
| nipt_second_pass_csv | False | second-pass | nipt |
| wisecondor_aberrations | True | wisecondor, cnv | nipt |
30 changes: 15 additions & 15 deletions docs/microsalt_map.md
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@@ -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 |
102 changes: 51 additions & 51 deletions docs/mip-dna_map.md
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@@ -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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