subworkflow: fingerprint_gbcms - #222

Open

anoronh4 wants to merge 62 commits into

module/fingerprintparser

Commits on Aug 12, 2025

first commit for custom/fingerprintvcfparser
anoronh4
committed
15c15f6
update module and nf-test
anoronh4
committed
785cd7c

Commits on Aug 14, 2025

set enable_conda to false
anoronh4
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7f47996
update meta.yml
anoronh4
committed
af7d902
remove TODO lines
anoronh4
committed
ed05eb0
remove more TODO lines
anoronh4
committed
5dc010e
add module to skipped nf-tests for conda
anoronh4
committed
112ac67
bugfix
anoronh4
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e09936f
add subworkflow for generating fingerprints with gbcms
anoronh4
committed
a8805ae

Commits on Aug 15, 2025

add subworkflow to skipped nf-tests for conda
anoronh4
committed
c9cf10f

Commits on Sep 25, 2025

add fingerprint contamination module
anoronh4
committed
e3a7bed

Commits on Sep 26, 2025

add custom/fingerprintcombine module
anoronh4
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95548d1
add subworkflow fingerprint_gbcms_batch
anoronh4
committed
b6e5229
update subworkflow to designate a genome to each sample fingerprint file
anoronh4
committed
257e8f9
remove tag attribute on custom/fingerprintcombine
anoronh4
committed
33c6cbd
update fingerprint_gbcms subworkflow, including fingerprint_gbcms_batch subworkflow
anoronh4
committed
404b8ef
skip conda tests for fingerprint modules and subworkflows
anoronh4
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ebf5800
update version output of contamination script
anoronh4
committed
eb9e073
update snapshot
anoronh4
committed
e0cf039
update snapshot
anoronh4
committed
6691063

Commits on Nov 5, 2025

exclude X, Y chromosomes from contamination calculations
anoronh4
committed
de1c5f6

Commits on Nov 6, 2025

set index of table to 'Position'
anoronh4
committed
a461d1e

Commits on Nov 7, 2025

fixed filtering of table by index labels
anoronh4
committed
a280d30
fix indentation
anoronh4
committed
04ff5ad

Commits on Dec 17, 2025

fix file formatting and spacing
anoronh4
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e5fb9ed
add meta map to custom/fingerprintcombine
anoronh4
committed
0c3c341

Commits on Dec 18, 2025

Commits on Dec 19, 2025

update custom/fingerprintcorrelation to output table with correlation values
anoronh4
committed
8a596c9

Commits on Jan 9, 2026

add grouping logic for ordering samples in fingerprintcombine
NoronhaA
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51047f1
add logic to handle exception for when denominator of fraction is zero
NoronhaA
committed
f45b4d9
fix failing nf-tests
anoronh4
committed
18db500

Commits on Jan 30, 2026

put process tag in double quotes
NoronhaA
committed
d6ecf3c
change method of adding a column in order to handle empty table
NoronhaA
committed
6d6c0e1
change output channel to include mix of run-computed and previously-computed FPs
NoronhaA
committed
acfa784
Merge branch 'module/fingerprintparser' of github.com:mskcc-omics-workflows/modules into module/fingerprintparser
NoronhaA
committed
1939aca

Commits on Feb 12, 2026

updates
anoronh4
committed
baff4ae

Commits on Feb 24, 2026

fix grouping
anoronh4
committed
6c7624b

Commits on Feb 26, 2026

cleanup and fix filter for unpaired samples
anoronh4
committed
eeedcad

Commits on Feb 27, 2026

Commits on Mar 21, 2026

fix custom/fingerprintcorrelation snapshot file
anoronh4
committed
79c9cbf
add new module custom/fingerprintmislabels/
anoronh4
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f7f509b

Commits on Mar 23, 2026

Commits on Mar 24, 2026

rework logic
anoronh4
committed
69eddef

Commits on Mar 26, 2026

Commits on Mar 31, 2026

move fingerprint modules from custom/fingerprint* to fingerprint/*
anoronh4
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5dd6240
update snapshots
anoronh4
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baff2d1
update local paths for inputs in nf-tests
anoronh4
committed
357bf03

Commits on Apr 1, 2026

Merge branch 'develop' into module/fingerprintparser
anoronh4
authored
9d3b013

Commits on May 14, 2026

update environment.yml to be congruent with container images
anoronh4
committed
04ee0ed

Commits on Jun 25, 2026

update plotting script to to adjust size ratios when less than 3 samples are used
Anne Marie Noronha
committed
5f0c250

Commits on Jun 26, 2026

fix prefix bug
anoronh4
committed
66cbedd

Commits on Jul 1, 2026

fix missing script version for FINGERPRINT_CONTAMINATION
anoronh4
committed
b02547a

Commits on Jul 9, 2026

add self_contained argument to plotting script
anoronh4
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37e953d
set XDG_CACHE_HOME in process
anoronh4
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21e0d42

Commits on Jul 10, 2026

fix bug and add optional heatmap_html_bundle_files output channel
anoronh4
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31e135d
fix bug in output capture pattern
anoronh4
committed
31eb259