Releases · kids-first/kf-alignment-workflow

The primary highlight of this release is a new workflow named kfdrc_alignment_wf_cyoa.cwl. This workflow replaces all existing workflows, which have been moved to the workflows-deprecated folder.

Key features of this new workflow:

Accepts SE FASTQs, PE FASTQs, and BAMs (or any combination of these) as inputs
Minimally converts the input into a CRAM with the option to create a gVCF
Breaks up CollectMultipleMetrics step into individual metrics steps
See the README and workflow doc for more...

Additional fixes:

Tab characters in python_createsequencegroups.cwl tool have been replaced with their ASCII code equivalent (allows tool to be run using cwltool)
Bug fix for sambamba_merge_anylist.cwl tool where it would fail with only one BAM input. The tool now correctly passes the BAM when only one is input

All studies to date (as of May 2020) have been processed with the various workflows in the workflows directory. Each workflow either takes in different inputs (bam vs fastq) and/or produces more outputs (gvcf vs not).

What's Changed

add samtools to cram by @yuankunzhu in #1
Revert "add samtools to cram" by @yuankunzhu in #2
add gatk_hc cram by @zhangb1 in #3
Add CWL QC steps by @zhangb1 in #4
modified: picard_collectaggregationmetrics.cwl by @zhangb1 in #5
move sub-cmd to baseCommand by @yuankunzhu in #6
add/scatter-sortbam by @yuankunzhu in #7
Add tool to make 2d sequence group array for scatter bqsr by @yuankunzhu in #8
gatk and picard change by @zhangb1 in #9
change picard version 2.8.3 to 2.15.0 by @zhangb1 in #11
fix bugs for scatter bqsr by @yuankunzhu in #12
rm redundant file type declare by @yuankunzhu in #13
add scatter for GatherBqsrReport by @yuankunzhu in #14
new file: picard_collectreadgroupbamqualitymetrics.cwl by @zhangb1 in #15
upgrade/entire-scatter-bqsr by @yuankunzhu in #16
change for QC steps by @zhangb1 in #17
upgrade/add_wf_raw_bam_to_gvcf by @yuankunzhu in #18
Workflow for qc by @zhangb1 in #22
verifybamid-modify by @zhangb1 in #23
add/alignment_pipeline by @yuankunzhu in #24
add gvcf validation by @zhangb1 in #25
add/verifybamid by @yuankunzhu in #26
add HC input & CheckContamination tool by @yuankunzhu in #29
🔧 update/picard-dbsnp-index by @yuankunzhu in #32
fix glob file for output2 by @zhangb1 in #37
Doc/readme update by @yuankunzhu in #38
✅ add tools with addtional options by @yuankunzhu in #39
🔧clean up tool files by @yuankunzhu in #40
Update readme.md by @yuankunzhu in #41
Add/addtional option tools by @yuankunzhu in #42
🔧 updating from pilot run by @yuankunzhu in #43
🔧 update/add gatk35 & update checkcontam by @yuankunzhu in #44
🔧validategvcf scatter run and add collectgvcfcallingmetrics th… by @zhangb1 in #45
Wip/updates by @yuankunzhu in #48
📄 Add LICENSE file by @dankolbman in #54
updates by @yuankunzhu in #53
Update/optimization changes by @bogdang989 in #55
Wip/updates by @yuankunzhu in #56
Wip/updates by @yuankunzhu in #57
Wip/updates by @yuankunzhu in #58
Wip/updates by @yuankunzhu in #59
✨ add expression_preparerg.cwl by @yuankunzhu in #60
Wip/updates by @yuankunzhu in #61
Wip/updates by @yuankunzhu in #62
🔧 update by @yuankunzhu in #63
✨ Add cavatica workflows by @Haoxuan-Jin in #64
Cram only2 by @Haoxuan-Jin in #65
✨ alignment workflow takes fastq as input by @danria in #67
✨ Add alignment workflow take fastq as input and output Cram… by @Haoxuan-Jin in #69
✨ reheader cram to generate gvcf by @danria in #68
🔧 Created workflow to run haplotype caller on Broad-based cram… by @migbro in #70
Update/gvcf only by mb by @migbro in #71
Gvcf temp bam test by @migbro in #72
🔧update tools and workflow for cram input by @zhangb1 in #73
Add cram2gvcf w contam by @migbro in #74
📝 readme, update cwl-viewer link by @yuankunzhu in #75
updates bqsr unmap indel by @yuankunzhu in #76
Updates/pipefail fix by @yuankunzhu in #77
added Yuakun's updates for pipefail and increased resource usage for bwa by @migbro in #78
added missing samblaster step back in! by @migbro in #79
⚡ revert to 4 vcf input for now... by @migbro in #80
🔧 update all workflow add unmapped reads by @zhangb1 in #81
🔧 update tools and add unmapped reads by @zhangb1 in #82
🔧 add pipefail to bamtofastq step by @yuankunzhu in #83
🔧 add wes cram only workflow and fix the output by @zhangb1 in #84
add tools and wf for 3vcf-bqsr by @yuankunzhu in #85
🔧 add wes cram only workflow for bam input by @zhangb1 in #86
🔧 add set -eo pipefail by @zhangb1 in #87
Mb add kf logo by @migbro in #88