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kids-first
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kf-alignment-workflow
:microscope: Alignment workflow for Kids-First DRC
Apache License 2.0
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✨ set T flag for bwa
#94
dmiller15
closed
4 years ago
2
🔧 no escapes in arguments
#93
dmiller15
closed
4 years ago
0
📚 added input examples
#92
dmiller15
closed
4 years ago
0
🔧 pass thru merge with only one bam
#91
dmiller15
closed
4 years ago
0
🐎 split agg metrics into individual tools
#90
dmiller15
closed
4 years ago
1
🏗 input agnostic pipeline
#89
dmiller15
closed
4 years ago
4
Mb add kf logo
#88
migbro
closed
4 years ago
0
:wrench: add set -eo pipefail
#87
zhangb1
closed
5 years ago
0
:wrench: add wes cram only workflow for bam input
#86
zhangb1
closed
5 years ago
1
add tools and wf for 3vcf-bqsr
#85
yuankunzhu
closed
5 years ago
0
:wrench: add wes cram only workflow and fix the output
#84
zhangb1
closed
5 years ago
0
:wrench: add pipefail to bamtofastq step
#83
yuankunzhu
closed
5 years ago
0
:wrench: update tools and add unmapped reads
#82
zhangb1
closed
5 years ago
0
:wrench: update all workflow add unmapped reads
#81
zhangb1
closed
5 years ago
1
:zap: revert to 4 vcf input for now...
#80
migbro
closed
5 years ago
1
added missing samblaster step back in!
#79
migbro
closed
5 years ago
0
added Yuakun's updates for pipefail and increased resource usage for bwa
#78
migbro
closed
5 years ago
0
Updates/pipefail fix
#77
yuankunzhu
closed
5 years ago
0
updates bqsr unmap indel
#76
yuankunzhu
closed
5 years ago
0
:memo: readme, update cwl-viewer link
#75
yuankunzhu
closed
5 years ago
0
Add cram2gvcf w contam
#74
migbro
closed
6 years ago
0
:wrench:update tools and workflow for cram input
#73
zhangb1
closed
6 years ago
0
Gvcf temp bam test
#72
migbro
closed
6 years ago
0
Update/gvcf only by mb
#71
migbro
closed
6 years ago
0
:wrench: Created workflow to run haplotype caller on Broad-based cram…
#70
migbro
closed
6 years ago
1
:sparkles: Add alignment workflow take fastq as input and output Cram…
#69
Haoxuan-Jin
closed
6 years ago
0
:sparkles: reheader cram to generate gvcf
#68
danria
closed
6 years ago
0
:sparkles: alignment workflow takes fastq as input
#67
danria
closed
6 years ago
0
:sparkles:add fastqs input into workflow
#66
zhangb1
closed
6 years ago
0
Cram only2
#65
Haoxuan-Jin
closed
6 years ago
0
:sparkles: Add cavatica workflows
#64
Haoxuan-Jin
closed
6 years ago
0
:wrench: update
#63
yuankunzhu
closed
6 years ago
0
Wip/updates
#62
yuankunzhu
closed
6 years ago
0
Wip/updates
#61
yuankunzhu
closed
6 years ago
0
:sparkles: add expression_preparerg.cwl
#60
yuankunzhu
closed
6 years ago
0
Wip/updates
#59
yuankunzhu
closed
6 years ago
0
Wip/updates
#58
yuankunzhu
closed
6 years ago
0
Wip/updates
#57
yuankunzhu
closed
6 years ago
0
Wip/updates
#56
yuankunzhu
closed
6 years ago
0
Update/optimization changes
#55
bogdang989
closed
6 years ago
0
📄 Add LICENSE file
#54
dankolbman
closed
6 years ago
0
updates
#53
yuankunzhu
closed
6 years ago
0
Optimal Instance Type
#52
bogdang989
opened
6 years ago
0
HaplotypeCaller RamMin parameter
#51
bogdang989
closed
6 years ago
0
BAM sorting optimization suggestion
#50
bogdang989
closed
6 years ago
0
BAM Preprocessing optimization suggestion
#49
bogdang989
closed
6 years ago
0
Wip/updates
#48
yuankunzhu
closed
6 years ago
0
alignment optimization suggestions
#47
yuankunzhu
opened
6 years ago
5
optimization suggestions list
#46
yuankunzhu
opened
6 years ago
1
:wrench:validategvcf scatter run and add collectgvcfcallingmetrics th…
#45
zhangb1
closed
6 years ago
0
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