icgc-argo workflow-roadmap issues

icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing

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Make public XML to VCF conversion documentation

#458 edsu7 opened 1 month ago
0
Add SNV and Indel split for short variants to XML to Vcf pipeline

#457 edsu7 closed 1 month ago
0
DR10 - MUTO-INTL Donor entityExceptions

#456 edsu7 opened 2 months ago
1
Test xml_variant_ingestion workflow with new test data from MONSTAR

#455 guanqiaofeng closed 1 month ago
2
Document MONSTAR xml to vcf conversion

#454 guanqiaofeng closed 1 month ago
3
Check how many MONSTAR variant fall in BED file regions

#453 edsu7 opened 3 months ago
0
🐛 🐛Running workflow of nf-core framework in RDPC-QA generates incorrect nextflow.config

#452 edsu7 opened 3 months ago
0
BED file for FMI Target-Seq Regions

#451 edsu7 closed 3 months ago
2
Compile the list of exceptions for MONSTAR

#450 lindaxiang closed 2 weeks ago
0
Get the dump of XML files from Monstar

#449 lindaxiang opened 4 months ago
1
Update payload workflow

#448 guanqiaofeng opened 4 months ago
0
List of data in SFTP to made public

#447 edsu7 opened 5 months ago
0
Add Reference file subworkflow to RNAseq alignment pipeline

#446 edsu7 closed 3 months ago
1
Upload transcriptome reference files into reference bucket

#445 edsu7 opened 5 months ago
3
DR10 : Data Release 10

#444 edsu7 opened 5 months ago
0
Test the example data in QA with exceptions applied

#443 lindaxiang closed 2 months ago
2
MONSTAR-1 data overview

#442 lindaxiang closed 2 months ago
0
Update prep/metrics module

#441 guanqiaofeng closed 3 months ago
1
Update Stage_input subworkflow to accommodate RNAseq data

#440 guanqiaofeng closed 5 months ago
2
Benchmark rnaaln workflow

#439 guanqiaofeng opened 5 months ago
6
Generate transcriptome reference file for STAR alignment

#438 guanqiaofeng closed 5 months ago
4
DR9 - QC P1000-US RNA-Seq

#437 edsu7 closed 5 months ago
10
Missing entity exceptions from POG & MUTO

#436 lindaxiang closed 5 months ago
3
Generate reference index files for new STAR version

#435 edsu7 opened 6 months ago
6
DR9 - SANGER MUTO-INTL/POG-CA/P1000-US ~1700

#431 edsu7 closed 5 months ago
1
Tracking communications with programs

#430 edsu7 closed 7 months ago
1
DR9 - QC ~1400 MUTO-INTL/POG-CA Donors

#429 edsu7 closed 5 months ago
8
DR9 - MUTO-INTL ~900 mutect

#428 edsu7 closed 7 months ago
1
DR9 - MUTO-INTL ~900 alignment

#427 edsu7 closed 7 months ago
3
DR9 : Data Release 9

#426 edsu7 closed 5 months ago
1
Target-Seq pipeline Dev - XML to VCF in nf-core framework

#425 edsu7 closed 3 months ago
8
Transfer PCAWG data from Azure to EGA

#424 edsu7 opened 8 months ago
1
P1000-US data QC reports

#423 edsu7 closed 8 months ago
2
POG-CA data QC reports

#422 edsu7 closed 8 months ago
1
Process POG-CA workflows

#421 edsu7 closed 8 months ago
2
Japanese MONSTAR 2000 donor - XML - understanding data type and content

#420 guanqiaofeng closed 7 months ago
4
P1000-US : Remove clinical data and genomic data

#419 edsu7 closed 8 months ago
3
Data release 8.0 - data QC

#418 lindaxiang closed 8 months ago
3
RNAseq alignment pipeline using nf-core modules

#417 guanqiaofeng opened 9 months ago
7
Correcting prod analyses object with data integrity issues

#416 edsu7 closed 7 months ago
1
Re-align 10 POG sequencing_experiment analysis

#415 lindaxiang closed 7 months ago
7
Data inconsistency in dashboard - Prod

#414 edsu7 opened 9 months ago
0
🐛 QA - Blocked from submitting treatment with existing missing entity applied

#413 edsu7 closed 7 months ago
1
Clinical and molecular data submission tests in QA

#412 lindaxiang closed 9 months ago
9
Update whole exome sequencing samples song analysis in QA/Dev

#411 lindaxiang closed 9 months ago
6
Enable weblog plugin for Nextflow pod to collect task metrics

#410 lindaxiang opened 10 months ago
0
Increase allowed max dna seq alignment jobs per workDir in Cumulus RDPC Prod

#409 lindaxiang closed 7 months ago
2
Cumulus RDPC workflows benchmark

#408 lindaxiang closed 5 months ago
3
Compare metrics for new alignments to past

#407 edsu7 closed 8 months ago
3
Run workflows in azure.

#406 UmmulkiramR closed 7 months ago
1