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Updates in base code #148

Merged
merged 64 commits into from
Mar 4, 2024
Merged

Updates in base code #148

merged 64 commits into from
Mar 4, 2024

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caballero
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This PR is for:

  1. capture software versions from HTML or JSON
  2. merge bam files if available
  3. set smart triggers for basecall, align and modbed files
  4. change modbam2bed to modkit
  5. capture model used from report JSON
  6. dorado align using Fastq instead of BAM as input
  7. fix parsing of species in multiqc_data in final report

Linked issues:

thomasmanke and others added 30 commits December 13, 2023 10:39
@thomasmanke
Merge pull request #136 from maxplanck-ie/develop
5a76dee 
update ship_qcreport()
@WardDeb
GPU check > 10GB, not 20 to accomodate V100s
c423f3c
@WardDeb
10G check on dorado rule as well
8ca3ae9
@caballero
Merge pull request #137 from maxplanck-ie/gpu_check10G
709e4b0 
GPU check > 10GB, not 20 to accomodate V100s
code cleaning and formatting
53e1f5c
code cleaning, adding model and software capture
c8549b1
code clean-up
dfa72a4
code clean up
96a3228
adding step to merge BAM files
d1f5ff5
code clean up, removing parkour creds
682ea1a
code clean up, removing parkour creds
a0ba4a7
turn-off final data transfer for debugging
498a806
turn-off final data transfer for debugging
cf166ec
activating BAM merging step
ec8b15b
adding clean-up and fixing baseout
e4ca565
bam expansion rule
317ff15
bam expansion rule
bd29492
changing modbam2bed to modkit
a2db649
final bam name
4c5523a
conditional flag
8153ddb
conditional flag
b1d6090
conditional flag
89cb183
conditional flag
d57d437
conditional flag
99bd269
conditional flag
4f6b093
align skiping
80b2e37
align skiping
d5e5b3a
simple software version capture, adding dorado
a6d01b6
conditional align
2a0c096
conditional align
741532e
Juan Caballero added 28 commits January 9, 2024 10:36
conditional basecall and modbed
8d0e38b
conditional basecall and modbed
5cfe9ac
conditional basecall and modbed
b4d51b8
rules for merging
c77bdc3
exporting bam in prepare_bam
53c5e04
exporting bam in prepare_bam
98277bb
exporting bam in prepare_bam
f1efe01
updating python and snakemake
4d32f32
updating python and snakemake
79d3bcb
updating python and snakemake
cdc578d
updating python and snakemake
d4cc6fe
updating python and snakemake
8775e12
debug for bam export
740ad2d
swapping BAM to Fastq for dorado align
5755292
adding optional align step
be92c98
clean up and adding back transfer step
4915ddd
removed unused functions
403aedd
adding changes after review
5436db9
code cleaning
d42045e
separating BAM merge
d051494
separating BAM merge
272eaff
missing comma
c75f611
adding logical steps for basecall, align and modbed
a9a8415
adding html parsing for metadata
dc3d3b0
config basecall model when needed
c16bafe
adding html parsing for metadata
fa6a973
bug fix for reporting the species in termination email
0d6890d
setting undefined model from json metadata
62fb58f
@caballero caballero merged commit 3a0f3ae into develop Mar 4, 2024
@caballero caballero deleted the bam_merge branch March 4, 2024 10:44
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3 participants
@caballero @thomasmanke @WardDeb