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Merged
merged 226 commits into from
Feb 4, 2025
Merged

Before read from file commit #13

merged 226 commits into from
Feb 4, 2025

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bwlang
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@bwlang bwlang commented Oct 18, 2024

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aerijman and others added 30 commits April 21, 2023 12:25
@aerijman
scaffolded main modules and config
c97c0f0
@aerijman
scaffold main modules and config
1655a93
@aerijman
path_to_tiles,etc
41c974f
@aerijman
cheap solution to filter on regex
fe65df9
@aerijman
test aggregation step
d083974
@aerijman
file shouldn't be here
5e74ff0
@aerijman
WIP
3c614fd
@aerijman
Merge branch 'modular_dsl2' of github.com:nebiolabs/EM-seq into modul…
129f2cd 
…ar_dsl2
@aerijman
typos
d6a2716
@aerijman
quoted rg_id
3acb576
@aerijman
samtools fastq needs -n when feeded to bwameth
8fb53e8
@aerijman
nonconverted needed reference in args
a296093
@aerijman
working state keep comments
82da0e0
@aerijman
wip
917b130
@aerijman
except QC and outdated tools all good
a678135
@aerijman
ngs-agg stderr temporary saved
d9d472e
@aerijman
write ngs_agg out and err to files for record
8e43ce8
@aerijman
pysam needs python10 in conda
4eeff12
@aerijman
library should be created in first step
0ac0255
@aerijman
alignment broken
51b0876
@aerijman
WIP
5caa9b4
@aerijman
getting aggregation ready (not yet)
6eac454
@aerijman
passes tests
59b1cb8
@aerijman
removed unnecessary comment
f6daa69
@aerijman
organize nextflow.config
a52a640
@aerijman
publishdir should include flowcell in addition to library
b223f31
@aerijman
Merge branch 'modular_dsl2' of github.com:nebiolabs/EM-seq into modul…
eb0e66f 
…ar_dsl2
@aerijman
include module consistent with or without .nf
1f4838f
@aerijman
rails model expects no header for nonconverted_counts
f60938a
@aerijman
before filtering by mapq before methylation analysis
97ea8be
aerijman and others added 29 commits December 26, 2024 12:34
@aerijman
explicit bash not sh for github actions
4b9d3cc
@aerijman
github actions not working with exported functions
30e8c58
@aerijman
conda to work in github and customer local
62a88f4
@aerijman
silly mistakes
d8d8372
@aerijman
WIP: test conda in github actions
fbaf001
@aerijman
WIP: dependencies
9246fff
@aerijman
WIP: github actions dependencies
c6771d2
@aerijman
WIP: github actions dependencies...
813cf1f
@aerijman
WIP,...
1c017cd
@aerijman
WIP
f940efa
@aerijman
WIP
a60ffd5
@aerijman
WIP
605283a
@aerijman
WIP
baa007c
@aerijman
WIP
5a4a8b1
@aerijman
WIP
9858f6e
@aerijman
WIP
8f4088f
@aerijman
WIP
4b8d504
@aerijman
WIP
a673be1
@aerijman
WIP
99c2d88
@aerijman
revert test.yml and avoid mamba
72e0d4d
@aerijman
WIP
585508c
@aerijman
mamba has problems in github actions
415688f
@aerijman
export fx inside run_test script
64bacb4
@aerijman
perhaps mkfifo negatively impacted exported fx
8d293a8
@aerijman
WIP
d4e1850
@aerijman
WIP
85c72db
@aerijman
no /bin/bash if local. Only in github actions
b74952e
@lnblum
clarify default input
48cba79
@aerijman
added a little debugging
b376ede
@aerijman aerijman merged commit a6d15da into master Feb 4, 2025
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4 participants
@bwlang @adrianreich @aerijman @lnblum