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icgc-argo
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seq-tools
Command line tools for ARGO sequencing data validation
https://github.com/icgc-argo/seq-tools
GNU Affero General Public License v3.0
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Add skip for c140 to platform uniqueness
#113
edsu7
opened
10 months ago
0
add skip for c650
#112
edsu7
closed
1 year ago
0
Update c120_permissible_char_in_rg_id.py
#111
edsu7
closed
1 year ago
0
Fix `submitter_read_group_id`
#110
edsu7
closed
1 year ago
1
Add parallel
#109
edsu7
closed
1 year ago
0
allow for skipping of multiple tests
#108
edsu7
closed
1 year ago
3
Temporarily disable certain tests
#107
edsu7
closed
1 year ago
1
Performance improvements for`seq-tools`
#106
lindaxiang
opened
1 year ago
2
C691 update2
#105
edsu7
opened
1 year ago
0
merging updates
#104
edsu7
opened
2 years ago
0
C685 nested cram file md5sum and file size match
#103
edsu7
closed
2 years ago
0
Revert "initial commit and fix to c609"
#102
edsu7
closed
2 years ago
0
Update c609_fastq_sanity.py
#101
edsu7
closed
2 years ago
0
added extra check for payload post cram2bam
#100
edsu7
closed
2 years ago
0
initial commit and fix to c609
#99
edsu7
closed
2 years ago
1
Revert "c690 to check for rna-seq strandedness"
#98
edsu7
closed
2 years ago
0
Add expected running duration of each check for a given normal file size input
#97
lindaxiang
opened
2 years ago
0
initial commit of function and tests
#96
edsu7
closed
2 years ago
1
Add description for seq-tools checks
#95
edsu7
closed
2 years ago
6
FASTQ sanity check
#94
edsu7
closed
2 years ago
2
update version
#93
lindaxiang
closed
2 years ago
0
Detect `RNA-seq strandedness` in FASTQ
#92
edsu7
opened
2 years ago
9
c690 to check for rna-seq strandedness
#91
edsu7
closed
2 years ago
0
added c680 to detect repeat read names
#90
edsu7
closed
2 years ago
0
Add C670 test, anonymized test data, and update expected reports
#89
edsu7
closed
2 years ago
0
Update Seq-Tools Descriptions on ARGO Doc Site
#88
b-f-chan
closed
11 months ago
1
Build New Docker Container for Seq-Tools for Quay.io
#87
b-f-chan
opened
2 years ago
1
Add README.md for Validation Checks in the Seq-Tools
#86
lindaxiang
closed
2 years ago
6
C690 check strand specificity in bam
#85
edsu7
closed
2 years ago
0
C680 repeated read names per group in bam
#84
edsu7
closed
2 years ago
0
C670 rg is paired in bam
#83
edsu7
closed
2 years ago
0
C650 empty sm
#82
edsu7
closed
2 years ago
0
C120 permissible char update regex
#81
edsu7
closed
2 years ago
0
V2
#80
edsu7
closed
2 years ago
0
New check: for RNA-Seq BAM submit data, detect the `library_strandedness` and check whether it matches what's in the metadata
#79
lindaxiang
opened
2 years ago
3
🐛 Regex check not matching schema in c120_permissible_char_in_rg_id.py
#78
edsu7
closed
2 years ago
3
🐛 Failing c650 test due to empty SM
#77
edsu7
closed
2 years ago
3
display message when validation begins, addressing #70
#76
junjun-zhang
closed
3 years ago
0
PU check
#75
junjun-zhang
closed
3 years ago
0
C681 c683
#74
junjun-zhang
closed
3 years ago
0
🐛 Validation does not check empty string for required fields
#73
hknahal
closed
3 years ago
1
New feature: add a flag to skip md5sum check
#72
junjun-zhang
closed
3 years ago
1
New check: for BAM submission, detect whether it's paired end or not and whether it matches what's in the metadata
#71
junjun-zhang
closed
2 years ago
1
Improvement: print short message to inform user the total number of metadata files to be checked
#70
junjun-zhang
closed
3 years ago
1
Fix 650
#69
junjun-zhang
closed
3 years ago
0
Adjustments
#68
junjun-zhang
closed
3 years ago
0
Feature Request: QA from seq-tools
#67
rosibaj
closed
3 years ago
1
New check: repeated identical reads from different read groups
#66
junjun-zhang
closed
2 years ago
2
New checker (c260): fileName pattern check
#65
junjun-zhang
closed
3 years ago
1
improvement of exception handling in the base checker class
#64
junjun-zhang
closed
4 years ago
1
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