.. _Workflows: Packaged Workflows ================== Workflows are to be found in the $SYQADA/workflows directory, subdivided into general topic. Each leaf directory usually contains a control directory, which contains task files, a templates directory holding the templates invoked by those task files, and one or more protocol files ordering the tasks into a workflow. Nota Bene: ========== This is hopelessly out of date. It has not been updated since protocols became first-class objects. When SyQADA tries to resolve the path to a taskfile or template file that it finds in a protocol file or a task file, it looks for the file first in the local directory. If it does not find it there, SyQADA appends the path to each element of the environment variable, SYQADAPATH, so that workflow files can located elsewhere in the file system than the current directory. By default, SYQADAPATH is set to $SYQADA. This allows the protocol file and the task files to specify task and template files directly from the installed workflows directory, which will usually work fine for well-established workflows. Sequence Data Workflows -------------------------- .. hlist:: :columns: 3 * alignment * local recalibration * preprocessing * singlevariants * jointvariants * somaticvariants * haplohseq Workflows:: workflows/seqdata/protocols/coverage-titration.protocol workflows/seqdata/protocols/exome-alignment.protocol workflows/seqdata/protocols/exome-somatic-processing.protocol workflows/seqdata/protocols/exome-variant-processing.protocol workflows/seqdata/alignment/control/ 01.bwa.task 02.bwa-sampe.task 03.clean-sam.task 04.sam-to-bam.task 05.sort-sam.task 06.QC1-bedtools-coverage.task 06.QC2-bam-statistics.task 06.merge-and-index.task 07.filter-exome.task workflows/seqdata/alignment/templates/ QC1-bedtools-coverage.template QC2-bam-statistics.template bwa-sampe.template bwa.template clean-sam.template filter-exome.template merge-and-index.template sam-to-bam.template workflows/seqdata/jointvariants/control/ 32.gatk-recall-dense-matrix.task J01.call-square-matrix.task J02.combine-samples.task workflows/seqdata/jointvariants/templates/ gatk-call-square-matrix.template gatk-recall-dense-matrix.template workflows/seqdata/preprocessing/control/ 00.bam-to-fastq.task workflows/seqdata/preprocessing/templates/ workflows/seqdata/recalibration/control/ 10.gatk-realign.task 11.merge-intervals.task 12.gatk-indelrealigner.task 13.mark-duplicates.task 14.gatk-baserecalibrator.task 15.sort-sam.task 16.QC-exon-coverage.task 16.merge-and-filter.task workflows/seqdata/recalibration/templates/ gatk-baserecalibrator.template gatk-indelrealigner.template gatk-realign.template mark-duplicates.template merge-and-filter.template merge-intervals.template workflows/seqdata/singlevariants/control/ 21.gatk-unified-genotyper.task 22.gatk-combine-vcfs.task 22.gatk-select-variants.task 24.bed-intersect-exome.task workflows/seqdata/singlevariants/templates/ bed-intersect-exome.template gatk-combine-variants.template gatk-select-variants.template gatk-unified-genotyper.template workflows/seqdata/somaticvariants/control/ 41.mutect.task 42.indelocator.task 43.gatk-combine-chromosomes.task 45.merge-vcfs.task mutect-indels.protocol mutect-snpsonly.protocol workflows/seqdata/somaticvariants/templates/ gatk-combine-variants.template indelocator.template merge-vcfs.template mutect.template varscan.template workflows/seqdata/utilities/control/ U01.titrate-sam.task workflows/seqdata/utilities/templates/ index-bam.template sort-sam.template titrate-sam.template SNP Chip Workflows ------------------- These workflows depend on a library of tools called hsuite, which transform files into and out of Scheet Lab "gs" format. .. hlist:: :columns: 2 * snp6 conversion * haploh :: workflows/snpdata/protocols/ affy-snp6-haploh.protocol affy-snp6-paired-haploh.protocol workflows/snpdata/affy-snp6-gs/control: 01.compute-bafs.task 02.affy-to-gs.task workflows/snpdata/affy-snp6-gs/templates: affy-to-gs.template compute-bafs.template workflows/snpdata/fastphase-haploh/control: 00-README-THIS-IS-UNPROVEN 10.gs-to-fastphase.task workflows/snpdata/fastphase-haploh/templates: workflows/snpdata/mach-haploh/control: 10.gs-to-machinput.task 11.run-mach.task 13.concatenate-mach-phased.task 15.haploh.task 21.paired-haploh.task workflows/snpdata/mach-haploh/templates: gs-to-machinput.template haploh.template paired-haploh.template run-mach.template Variant Workflows -------------------- .. hlist:: :columns: 3 * vtools * evsfilters * evsvariants :: workflows/variants/vtools/VTOOLS.config workflows/variants/vtools/protocols: germline-annotation.protocol mutect-annotation.protocol workflows/variants/vtools/control: 100.import-single-vcfs.task 101.import-mutect-vcfs.task 110.annotate-project.task 111.annotate-cancer-variants.task 120.case-control.task 131.build-annotated-csv.task 141.summarize-kegg-pathways.task 142.summarize-kegg-genes.task workflows/variants/vtools/templates: annotate-cancer-variants.template annotate-project.template build-annotated-csv.template import-mutect-vcfs.template import-single-vcfs.template summarize-kegg-pathways.template summarize-kegg-genes.template .. note:: These variant workflows were developed for Osteonecrosis and have not been fully integrated again. They depend on code that is in the syqada trunk under variant_analysis/main. The usage of that code is documented in the svn repository under repo/projects/stjude. :: workflows/variants/evsfilters/control: 31.syqada-filter.task workflows/variants/evsfilters/templates: syqada-filter.template workflows/variants/evsfilters/ 30-Optional-GATK-FilterEvs.sh 31-SyqadaFilter.sh workflows/seqdata/evsvariants/ GatkUnifiedGenotyperEvs.sh GLF-Multiples-HOWTO