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This is hopelessly out of date.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¶
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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.
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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¶
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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