chopdgd bfx-tools-wdl issues

chopdgd / bfx-tools-wdl

WDL tasks for commonly used BFX tools

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Move output_filename variables to inputs

#126 Tayazseven closed 4 years ago
0
Manta CNV Calling for Mito pipeline

#125 Tayazseven closed 4 years ago
2
Resolves #104 - Added Slivar to the package

#124 genomics-geek closed 5 years ago
0
increased memory

#123 Tayazseven closed 5 years ago
0
install command's queue updated to all.q

#122 Tayazseven closed 5 years ago
0
created memory and cpu as optional param

#121 jayaramanp closed 5 years ago
0
removed float and cpu

#120 jayaramanp closed 5 years ago
0
New variant calling tools need WDL tasks

#119 mark-welsh opened 5 years ago
0
Resolves #113 - Adds tar command for compressing/archiving files & directory

#118 mark-welsh closed 5 years ago
0
Resolves #116 - Adds pipefail statement to CreateVirtualenv task

#117 mark-welsh closed 5 years ago
0
CreateVirtualenv task does not have pipefail setting!

#116 mark-welsh closed 5 years ago
1
Hotfix 112

#115 Tayazseven closed 5 years ago
0
output-file-name string moved to task-inputs

#114 Tayazseven closed 5 years ago
0
Missing a compression/zip tool for directories

#113 mark-welsh closed 5 years ago
0
Update File-name-outputs in snpeff-annotation subworkflow

#112 Tayazseven closed 5 years ago
0
HOTFIX - Move output_name strings to the task-inputs in Unix Tasks

#111 Tayazseven closed 5 years ago
0
Add GATK/Picard tasks for generating WGS qc metrics

#110 mark-welsh opened 5 years ago
1
Resolves #108 - Unload Python/2.7 module after pyenv is created

#109 mark-welsh closed 5 years ago
0
virtualenv creation includes packages in the python/2.7 respublica module

#108 mark-welsh closed 5 years ago
0
Resolves #106 - Adds tasks for tools used in RNASeq pipeline

#107 mark-welsh closed 5 years ago
1
add tasks for tools used by RNASeq pipeline

#106 mark-welsh closed 5 years ago
1
Add support for Picard AddOrReplaceReadGroups

#105 genomics-geek closed 5 years ago
1
Add support for slivar

#104 genomics-geek closed 5 years ago
0
will output file path of runWorkflow.py

#103 jayaramanp closed 5 years ago
0
output_filename must be file

#102 jayaramanp closed 5 years ago
0
instead of passing in string, pass in file

#101 jayaramanp closed 5 years ago
0
Feature pindel2vcf formito

#100 jayaramanp closed 4 years ago
2
pindel2vcf needs to be different task for mito

#99 jayaramanp closed 4 years ago
0
typo fix

#98 jayaramanp closed 5 years ago
0
updated gsnap command

#97 jayaramanp closed 5 years ago
0
Flipped type for reference_name and reference_dir

#96 jayaramanp closed 5 years ago
0
variable duplicated for input and output

#95 jayaramanp closed 5 years ago
0
variable changed

#94 jayaramanp closed 5 years ago
0
created reference as optional parameter

#93 jayaramanp closed 4 years ago
4
changed task name

#92 jayaramanp closed 5 years ago
0
Feature circular alignment subworkflow

#91 jayaramanp closed 4 years ago
1
circular alignment subworkflow needs gsnap and extract mapped reads

#90 jayaramanp closed 4 years ago
0
Feature 88 - Mito also has an additional task ExtractMappedReads

#89 jayaramanp closed 4 years ago
2
feature - mito alignment subworkflow needs extractMappedreads task in there

#88 jayaramanp closed 4 years ago
0
manta WDL files to run manta on shifted reference alignment for mito

#87 jayaramanp closed 4 years ago
1
Revert "target intervals changed with bait intervals"

#86 genomics-geek closed 5 years ago
0
target intervals changed with bait intervals

#85 Tayazseven closed 5 years ago
0
BamQC intervals for DepthofCoverage

#84 Tayazseven closed 5 years ago
0
Updated the Float parameter

#83 genomics-geek closed 5 years ago
0
BAMQUALITY CONTROL - Switch to Sorted bam file

#82 Tayazseven closed 5 years ago
0
variant calling intervals new variable

#81 Tayazseven closed 5 years ago
0
Feature bedtools intersect merge

#80 genomics-geek closed 5 years ago
0
Resolved #68 - Added VarScan tools for CNV Calling

#79 genomics-geek closed 5 years ago
0
Feature unix sort cut cat sed

#78 genomics-geek closed 5 years ago
0
modify the input vcf filename

#77 Tayazseven closed 5 years ago
0

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