genome analysis-workflows issues

genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

MIT License

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update vt docker image

#1088 apaul7 closed 4 months ago
0
Also update the docs updater to python 3.10 and newer cwltool.

#1087 tmooney opened 1 year ago
0
Update python and cwltool version for testing CWL syntax

#1086 tmooney closed 1 year ago
0
Updates to immuno workflow for upcoming 4.0.0 release

#1085 susannasiebert opened 1 year ago
0
Port changes from tmooney/analysis-wdls#1.

#1084 tmooney opened 1 year ago
0
Upgrade pVACtools to version 3.1.1

#1083 susannasiebert closed 1 year ago
0
Use sambamba for duplicate marking.

#1082 tmooney opened 1 year ago
1
filter_vcf_depth.cwl problems handling DNPs?

#1081 zlskidmore opened 1 year ago
1
Update docker image to 0.5.4 for handling of case of 0-depth variant.

#1080 tmooney closed 2 years ago
0
FDA table generation: the output `table_file_name` is required

#1079 tmooney opened 2 years ago
1
Exome alignment example YAML files

#1078 jasonwalker80 closed 2 years ago
0
Fda metrics split on sequence

#1077 johnegarza closed 1 year ago
3
How to run immuno.cwl pipeline

#1076 dxkeac opened 2 years ago
1
Fda metrics bugfixes

#1075 johnegarza closed 2 years ago
0
Remove rnaseq from immuno pipeline

#1074 johnegarza closed 2 years ago
0
Upgrade mapq0 filter to v0.5.3

#1073 tmooney closed 2 years ago
0
Upgrade to pVACtools version 3.0.3

#1072 susannasiebert closed 2 years ago
0
actually allow nounset for tumor only mutect runs

#1071 apaul7 closed 1 year ago
1
Immuno FDA metrics

#1070 johnegarza closed 2 years ago
0
allow optional normal input in mutect tool

#1069 apaul7 closed 2 years ago
1
Immuno tweaks

#1068 johnegarza closed 2 years ago
0
Keep sample names in filenames

#1067 johnegarza closed 2 years ago
0
Upgrade to pVACtools version 3.0.1

#1066 susannasiebert closed 2 years ago
0
Broken

#1065 johnegarza closed 2 years ago
0
fix docm filter by passing decomposed vcf in tumor only mode

#1064 sridhar0605 closed 2 years ago
0
Patch case where clinical class II alleles are not provided

#1063 johnegarza closed 2 years ago
1
germline docm filter needs a decompose step

#1062 chrisamiller closed 2 years ago
0
update docker image

#1061 sridhar0605 closed 2 years ago
2
handle unparseable GT entries by skipping those lines

#1060 johnmaruska closed 2 years ago
0
removing pindel param that isn't used

#1059 chrisamiller closed 2 years ago
1
Immuno rnaseq fusion enhancements

#1058 johnegarza closed 2 years ago
2
Update pVACtools docker pulls to 2.0.5

#1057 susannasiebert closed 2 years ago
0
v4.1.8.1 weird behaviour, not seen in v4.2+

#1056 IrenaeusChan closed 2 years ago
0
Pangenome: RNA-seq Pipeline Requirements

#1055 jasonwalker80 opened 3 years ago
1
Pangenome: ATAC-seq Pipeline

#1054 jasonwalker80 opened 3 years ago
0
changing bam variable to sam for clarity

#1053 chrisamiller closed 3 years ago
0
Build HCC1395 test input for CNVKit

#1052 jasonwalker80 opened 3 years ago
0
Add cwltool requirement InlineJavascriptRequirement

#1051 jasonwalker80 opened 3 years ago
1
Location of FASTQ files

#1050 jasonwalker80 opened 3 years ago
1
Should we pass Omni to BQSR?

#1049 jasonwalker80 opened 3 years ago
0
Rnaseq sequence type input

#1048 johnegarza closed 2 years ago
2
Gather input files page has broken image links

#1047 chrisamiller closed 3 years ago
1
Update merge_bams.cwl to work with both cwltool and cromwell.

#1046 tmooney closed 3 years ago
1
Problem with merge_bams

#1045 tgambin opened 3 years ago
4
Add -m and -d options to vt decompose step to avoid splitting

#1044 susannasiebert closed 3 years ago
1
germline joint detect variants workflow

#1043 apaul7 opened 3 years ago
0
Set user name and email for documentation update commit.

#1042 tmooney closed 3 years ago
0
Migrate documentation generator to github actions.

#1041 tmooney closed 3 years ago
0
update germline workflows to produce genome vcfs and genotyped vcf

#1040 apaul7 opened 3 years ago
0
Initial github action for testing

#1039 tmooney closed 3 years ago
0