diff --git a/docs/all_tags.md b/docs/all_tags.md index 3f4bbad..f4f5158 100644 --- a/docs/all_tags.md +++ b/docs/all_tags.md @@ -12,82 +12,89 @@ | Tag name | Description | |------------------|-------------------------------------------------------| +| aspcf-plot | Plot of LogR and BAF values | | assembly | Assembly | | autozyg | Autozygous region | | bed | Bed file | | bed-index | Following index | | bigwig | Bigwig formated file | +| circular-plot | Circular plot | | clinical | Clinical subset | | config | Config file | | coverage | Output with coverage information | -| scatter-plot | Scatter plot | -| circular-plot | Circular plot | -| profile-plot | Copy number profile plot | -| raw-profile-plot | Copy number profile without rounding to whole numbers | -| aspcf-plot | Plot of LogR and BAF values | -| sunrise-plot | Sunrise plot | -| tumor-plot | Plot of LogR and BAF values for tumor sample | -| germline-plot | Plot of LogR and BAF values for normal sample | | filtered | Filtered data | +| first-pass | Data metrics first pass | | fracsnp | Fraction of reads with snp | | fusion | Fusion transcripts | | genes | Related to genes | +| germline-plot | Plot of LogR and BAF values for normal sample | | junction | Junction data | | metrics | Data metrics | -| first-pass | Data metrics first pass | -| second-pass | Data metrics second pass | +| profile-plot | Copy number profile plot | +| qc-cram | QC alignment file in CRAM format | +| qc-cram-index | QC index file for alignment file in CRAM format | +| raw-profile-plot | Copy number profile without rounding to whole numbers | | reference-info | Information about references used in analysis | | regions | Output for regions | | research | Research set | +| scatter-plot | Scatter plot | +| second-pass | Data metrics second pass | | segments | Output for segments | | sites | Output for sites | +| sunrise-plot | Sunrise plot | | tcov | Coverage output | | tiddit-coverage | Coverage output from tiddit | -| visualization | Visualizes data | +| tumor-plot | Plot of LogR and BAF values for tumor sample | | umi | Files related to UMI workflow | | umi-cram | UMI consensus filtered cram file | | umi-cram-index | Index for the UMI consensus filtered cram file | -| qc-cram | QC alignment file in CRAM format | -| qc-cram-index | QC index file for alignment file in CRAM format | | vcf-fusion | Converted RNA fusion file to SV VCF | +| visualization | Visualizes data | ## FAMILY TAGS | Tag name | Description | |------------|----------------------| -| pedigree | Pedigree information | | ped | Pedigree information | +| pedigree | Pedigree information | ## RAW DATA | Tag name | Description | |----------------|-------------------------------------| -| fastq | Files with raw data in fastq format | | fasta | Files with raw data in fasta format | +| fastq | Files with raw data in fastq format | | forward-strand | Reads from forward strand | | reverse-strand | Reads from reverse strand | -| unpaired-reads | Reads that could not be paired | | rna | Data generated from RNA samples | +| unpaired-reads | Reads that could not be paired | ## REPORTING TAGS -| Tag name | Description | -|-------------------|-------------------------------------------------| -| audit | Audit file | -| csv | Comma separated values | -| deliverable | Deliverables file | -| delivery-report | Delivery report with result for upload to Scout | -| multiqc-html | Multiqc report for the run in html format | -| multiqc-json | Multiqc report for the run in json format | -| pdf | Portable document format | -| qc-report | Results and QC | -| sambamba-depth | Coverage information from sambamba | -| summary | Overview file without detailed information | -| tsv | Tab separated values | -| vcf-report | Results and QC from variant calling | -| cnv-report | CNV variant calling report | -| software-versions | Versions of software used in analysis | -| gene-counts | STAR read counts output per gene | +| Tag name | Description | +|--------------------|--------------------------------------------------------| +| audit | Audit file | +| cnv-report | CNV variant calling report | +| csv | Comma separated values | +| deliverable | Deliverables file | +| delivery-report | Delivery report with result for upload to Scout | +| gene-counts | STAR read counts output per gene | +| multiqc | MultiQC related files | +| multiqc-html | MultiQC analysis report in HTML format | +| multiqc-json | MultiQC analysis report in JSON format | +| pdf | Portable document format | +| picard-alignment | High level metrics about the alignment of reads | +| picard-duplicates | Metrics calculated during marking duplicates | +| picard-hs | Metrics for the analysis of target-capture sequencing | +| picard-insert-size | Metrics about the insert size distribution | +| picard-wgs | Metrics for evaluating the performance of WGS analysis | +| qc-report | Results and QC | +| sambamba-depth | Coverage information from sambamba | +| samtools-stats | Comprehensive statistics from alignment file | +| software-versions | Versions of software used in analysis | +| summary | Overview file without detailed information | +| tsv | Tab separated values | +| vcf-report | Results and QC from variant calling | ## TOOL TAGS @@ -95,32 +102,35 @@ |-----------------------|------------------------------------------------------------------| | arriba | Fusion caller | | ascatngs | Tool to identify somatically acquired copy-number alterations | -| cnvpytor | Tool for CNV/CNA analysis from depth-of-coverage by mapped reads | | asereadcounter | Count reads mapping to heterozygous sites | | chanjo | Tool to keep track of coverage over specific regions | | chromograph | Tool to create PNG images from BED and WIG files from mikaell | | cnvkit | Tool to call copy number variations | +| cnvpytor | Tool for CNV/CNA analysis from depth-of-coverage by mapped reads | | cyrius | Tool to call the problematic CYP2D6 gene | | deepvariant | Variantcaller | | delly | Cancer structural variant prediction tool | | deseq2 | Differential expression analysis with DESeq2 | | dnascope | Call snv indels | +| expansionhunter | Call repeat expansions | +| fastp | Preprocessing tool for FastQ files | | fusioncatcher | Fusion caller | | fusioncatcher-summary | Fusion caller summary | | fusioninspector | Fusion inspection | -| expansionhunter | Call repeat expansions | | genotyper | SNV indel caller from sention | | gens | CNV visualization tool | | gffcompare | Compare gff files | | haplotype-caller | Call snv and indels | | manta | Tool to call structural variants | | mitodel | Tool to identify mitochondrial deletion signatures | +| nextclade | Viral genome clade assignment | | peddy | Tool to check pedigree and ancestral relations | | picard | Picard set of bioinformatic tools | | pizzly | Fusion caller | | retroseq | Mobile element caller | | salmon-quant | Transcript quantification | | sention | Sention algorithm | +| somalier | Tool for sample-swap and relatedness checks | | squid | Fusion caller | | star-fusion | Fusion caller | | stringtie | Transcript assembler | @@ -131,7 +141,6 @@ | upd | Uniparent disomy caller from bjhall | | vardict | Cancer variant caller | | wisecondor | NIPT caller | -| nextclade | Viral genome clade assignment | ## VALIDATION TAGS @@ -146,15 +155,16 @@ | Tag name | Description | |-------------------------------|-----------------------------------------------------| | cnv | Copy number variants | +| germline | Associated with germline variants | | mobile-elements | Mobile elements | | normal | Associated with normal sample | -| germline | Associated with germline variants | -| somatic | Associated with somatic variants | | rhocall-viz | Runs of homozygosity index | | smn-calling | Copy number calls for the SMN gene | | snv | Single nucleotide variants and short indels | | snv-bcf | Gvcf including all SNV variants | | snv-gbcf | Gvcf including all SNV variants | +| somatic | Associated with somatic variants | +| sv | Structural variants | | sv-bcf | Gvcf including all SV variants | | sv-vcf | Variant call formated file with structural variants | | sv-vcf-index | Following index | @@ -162,38 +172,37 @@ | tmb | Tumor mutational burden information | | tumor | Associated with tumor sample | | upd | Uniparental disomy variants | +| variants | File pertaining variant information in some way | | vcf | Variant call formated file | | vcf-index | Following index | | vcf-snv | SNV variant call formated file | -| vcf-snv-index | Following index | -| sv | Structural variants | -| vcf-sv | SV variant call formated file | -| vcf-sv-index | Following index | -| vcf-snv-filtered | SNV variants filtered by BALSAMIC | -| vcf-snv-filtered-index | Following index | | vcf-snv-clinical | SNV variants from clinical panels | | vcf-snv-clinical-index | Following index | +| vcf-snv-filtered | SNV variants filtered by BALSAMIC | +| vcf-snv-filtered-index | Following index | +| vcf-snv-germline-normal | SNV germline normal variants | +| vcf-snv-germline-normal-index | Following index | +| vcf-snv-germline-tumor | SNV germline tumor variants | +| vcf-snv-germline-tumor-index | Following index | +| vcf-snv-index | Following index | | vcf-snv-research | SNV variants from whole genome | | vcf-snv-research-index | Following index | | vcf-str | Short tandem repeat variants | | vcf-str-index | Following index | +| vcf-sv | SV variant call formated file | | vcf-sv-clinical | SV variants from clinical panels | | vcf-sv-clinical-index | Following index | +| vcf-sv-germline-normal | SV germline normal variants | +| vcf-sv-germline-normal-index | Following index | +| vcf-sv-germline-tumor | SV germline tumor variants | +| vcf-sv-germline-tumor-index | Following index | +| vcf-sv-index | Following index | | vcf-sv-research | SV variants from whole genome | | vcf-sv-research-index | Following index | | vcf-umi-snv | Raw SNV UMI variant formatted file | +| vcf-umi-snv-clinical | SNV UMI variants from clinical panels | +| vcf-umi-snv-clinical-index | Following index | | vcf-umi-snv-index | Following index | | vcf-umi-snv-research | SNV UMI variant formatted file | | vcf-umi-snv-research-index | Following index | -| vcf-umi-snv-clinical | SNV UMI variants from clinical panels | -| vcf-umi-snv-clinical-index | Following index | -| vcf-snv-germline-tumor | SNV germline tumor variants | -| vcf-snv-germline-tumor-index | Following index | -| vcf-snv-germline-normal | SNV germline normal variants | -| vcf-snv-germline-normal-index | Following index | -| vcf-sv-germline-tumor | SV germline tumor variants | -| vcf-sv-germline-tumor-index | Following index | -| vcf-sv-germline-normal | SV germline normal variants | -| vcf-sv-germline-normal-index | Following index | | vcf2cytosure | Conversion from vcf format to cytosure format | -| variants | File pertaining variant information in some way | diff --git a/docs/balsamic_map.md b/docs/balsamic_map.md index 3a1800b..8718d12 100644 --- a/docs/balsamic_map.md +++ b/docs/balsamic_map.md @@ -1,75 +1,83 @@ -| 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 | +| 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 | +| alignmentsummarymetrics, picard, multiqc | True | qc-metrics, multiqc, picard-alignment | storage, janus | +| picard, multiqc, dups | True | qc-metrics, multiqc, picard-duplicates | storage, janus | +| picard, multiqc, hsmetrics | True | qc-metrics, multiqc, picard-hs | storage, janus | +| picard, multiqc, insertsize | True | qc-metrics, multiqc, picard-insert-size | storage, janus | +| wgsmetrics, picard, multiqc | False | qc-metrics, multiqc, picard-wgs | storage, janus | +| multiqc, fastp | True | qc-metrics, multiqc, fastp | storage, janus | +| samtools, stats, multiqc | True | qc-metrics, multiqc, samtools-stats | storage, janus | +| multiqc, somalier | False | qc-metrics, multiqc, somalier | storage, janus | +| yaml, qc-metrics-yaml | True | qc-metrics | audit, cg | +| cram, tumor-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 | +| snv, germline-vcf-tumor, dnascope, vcf-tumor | True | germline, vcf-snv-germline-tumor | deliver | +| snv, dnascope, germline-vcf-tumor-index, vcf-tumor | True | germline, vcf-snv-germline-tumor-index | deliver | +| snv, vcf-normal, dnascope, germline-vcf-normal | False | germline, vcf-snv-germline-normal | deliver | +| snv, vcf-normal, dnascope, germline-vcf-normal-index | 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, vcf-tumor, manta-germline | True | germline, vcf-sv-germline-tumor | deliver | +| sv, germline-vcf-tumor-index, vcf-tumor, manta-germline | True | germline, vcf-sv-germline-tumor-index | deliver | +| sv, vcf-normal, manta-germline, germline-vcf-normal | False | germline, vcf-sv-germline-normal | deliver | +| sv, vcf-normal, germline-vcf-normal-index, manta-germline | False | germline, vcf-sv-germline-normal-index | deliver | +| vcf-svdb, research-vcf-svdb | True | svdb, vcf-sv | deliver | +| research-vcf-svdb-index, vcf-svdb | True | svdb, vcf-sv-index | deliver | +| research-vcf-pass-svdb, vcf-pass-svdb | True | svdb, vcf-sv-research | deliver | +| vcf-pass-svdb, research-vcf-pass-svdb-index | True | svdb, vcf-sv-research-index | deliver | +| vcf-pass-svdb, clinical-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 | +| research-vcf-pass-tnscope, snv, vcf-pass-tnscope | False | tnscope, vcf-snv-research | deliver | +| snv, research-vcf-pass-tnscope-index, vcf-pass-tnscope | False | tnscope, vcf-snv-research-index | deliver | +| snv, clinical-vcf-pass-tnscope, vcf-pass-tnscope | False | tnscope, vcf-snv-clinical | deliver, scout | +| snv, clinical-vcf-pass-tnscope-index, vcf-pass-tnscope | False | tnscope, vcf-snv-clinical-index | deliver, scout | +| ascat-copynumber, clinical-ascat-copynumber | False | ascatngs, metrics | deliver | +| clinical-rd-delly, 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 | +| cov, cnv-gens-bed, gens-bed | False | gens, coverage, bed | scout | +| cov, cnv-gens-bed-index, gens-bed | False | gens, coverage, bed-index | scout | +| baf, cnv-gens-bed, gens-bed | False | gens, fracsnp, bed | scout | +| baf, cnv-gens-bed-index, gens-bed | False | gens, fracsnp, bed-index | scout | +| research-vcf-vardict, vcf-vardict | False | vardict, vcf-snv | deliver | +| research-vcf-vardict-index, vcf-vardict | False | vardict, vcf-snv-index | deliver | +| snv, research-vcf-pass-vardict, vcf-pass-vardict | False | vardict, vcf-snv-research | deliver | +| snv, research-vcf-pass-vardict-index, vcf-pass-vardict | False | vardict, vcf-snv-research-index | deliver | +| snv, clinical-vcf-pass-vardict, vcf-pass-vardict | False | vardict, vcf-snv-clinical | deliver, scout | +| snv, clinical-vcf-pass-vardict-index, vcf-pass-vardict | False | vardict, vcf-snv-clinical-index | deliver, scout | +| cns, cnv-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 | +| clinical-circular-cnvpytor, circular-cnvpytor | False | circular-plot, cnvpytor, visualization | storage | +| scatter-cnvpytor, clinical-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 | +| clinical-plot-tumor, 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 | +| research-tmb, snv, vardict, tmb | False | research, vardict, tmb | storage | +| research-tmb, snv, tmb, tnscope | 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 | +| 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 | +| snv, research-vcf-pass-tnscope-umi, vcf-pass-tnscope-umi | True | tnscope-umi, vcf-umi-snv-research | deliver | +| snv, research-vcf-pass-tnscope-umi-index, vcf-pass-tnscope-umi | True | tnscope-umi, vcf-umi-snv-research-index | deliver | +| snv, vcf-pass-tnscope-umi, clinical-vcf-pass-tnscope-umi | True | tnscope-umi, vcf-umi-snv-clinical | deliver, scout | +| snv, clinical-vcf-pass-tnscope-umi-index, vcf-pass-tnscope-umi | True | tnscope-umi, vcf-umi-snv-clinical-index | deliver, scout | +| research-tmb, snv, tnscope-umi, tmb | True | research, tnscope-umi, tmb | storage | diff --git a/docs/fluffy_map.md b/docs/fluffy_map.md index 944febf..1eb0c96 100644 --- a/docs/fluffy_map.md +++ b/docs/fluffy_map.md @@ -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 | diff --git a/docs/microsalt_map.md b/docs/microsalt_map.md index 58f798d..d0db7b0 100644 --- a/docs/microsalt_map.md +++ b/docs/microsalt_map.md @@ -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 | diff --git a/docs/mip-dna_map.md b/docs/mip-dna_map.md index 00e7944..b4e06e9 100644 --- a/docs/mip-dna_map.md +++ b/docs/mip-dna_map.md @@ -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 | diff --git a/docs/mip-rna_map.md b/docs/mip-rna_map.md index 1201bc7..62b6a27 100644 --- a/docs/mip-rna_map.md +++ b/docs/mip-rna_map.md @@ -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 | diff --git a/docs/mutant_map.md b/docs/mutant_map.md index 85fc9ff..1cbd229 100644 --- a/docs/mutant_map.md +++ b/docs/mutant_map.md @@ -1,27 +1,27 @@ -| Mutant tags | Mandatory | HK tags | Used by | -|---------------------------------------|-----------|----------------------------------------------------------------|------------------| -| sampleinfo, runinfo | True | config | 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 | -| 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 | -| 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 | -| 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 | -| 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 | -| typing, SARS-CoV-2-type | False | artic-type, csv | audit | +| Mutant tags | Mandatory | HK tags | Used by | +|---------------------------------------|-------------|----------------------------------------------------------------|------------------| +| sampleinfo, runinfo | True | config | storage, audit | +| instrument-properties, report | 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 | +| concatination, reverse-reads | False | fastq, reverse-strand | storage | +| report, SARS-CoV-2-info | False | fohm-delivery, komplettering, visualization | deliver | +| result_aggregation, SARS-CoV-2-qc | False | fohm-delivery, pangolin-typing, csv, visualization | audit | +| report, pangolin-typing | False | fohm-delivery, pangolin-typing, visualization, csv | audit | +| report, pangolin-typing-fohm | 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 | +| result_aggregation, metrics | False | metrics | storage | +| report, multiqc-json | True | multiqc-json | storage | +| report, nextclade-summary | True | ks-delivery, typing-summary, nextclade | deliver | +| report, ks-results | True | ks-delivery, ks-results, typing-report, visualization, csv | deliver | +| report, ks-aux-results | True | ks-delivery, ks-aux-results, typing-report, visualization, csv | deliver | +| consensus, analysis | True | ks-delivery, fastq, consensus | deliver, storage | +| consensus, consensus-sample | False | fohm-delivery, fasta, consensus-sample | deliver, storage | +| multiqc-html, report | True | ks-delivery, multiqc-html | deliver | +| report, SARS-CoV-2-sum | False | artic-sum, csv | audit | +| report, SARS-CoV-2-var | False | artic-var, csv | audit | +| typing, SARS-CoV-2-type | False | artic-type, csv | audit | diff --git a/docs/rnafusion_map.md b/docs/rnafusion_map.md index 0f65c9b..bed55c1 100644 --- a/docs/rnafusion_map.md +++ b/docs/rnafusion_map.md @@ -1,17 +1,17 @@ | Rnafusion tags | Mandatory | HK tags | Used by | |--------------------------------------|-------------|-------------------------------------------------------|----------------| | arriba | True | arriba, fusion | deliver | -| arriba-visualisation, arriba | False | arriba-visualisation, visualization, arriba, research | deliver, scout | +| arriba, arriba-visualisation | False | arriba-visualisation, visualization, arriba, research | deliver, scout | | fusioncatcher | True | fusioncatcher, fusion | deliver | | fusioncatcher-summary, fusioncatcher | True | fusioncatcher-summary | deliver | | star-fusion | True | star-fusion, fusion | deliver | | report, fusionreport | True | fusionreport, research | deliver, scout | -| fusioninspector, report | False | fusioninspector | deliver | -| fusioninspector-html, report | False | fusioninspector-html, research | deliver, scout | -| multiqc-html, report | True | multiqc-html, rna | deliver, scout | -| star-fusion, star-fusion-cram | True | cram | deliver, scout | +| report, fusioninspector | False | fusioninspector | deliver | +| report, fusioninspector-html | False | fusioninspector-html, research | deliver, scout | +| report, multiqc-html | True | multiqc-html, rna | deliver, scout | +| star-fusion-cram, star-fusion | True | cram | deliver, scout | | star-fusion-cram-index, star-fusion | True | cram-index | deliver, scout | -| star-align, star-align-gene-counts | True | gene-counts | deliver | +| star-align-gene-counts, star-align | True | gene-counts | deliver | | multiqc-json | True | multiqc-json | deliver | | qc-metrics | True | qc-metrics | cg | | vcf-fusion, vcf-collect | False | vcf-fusion | deliver, scout |