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Update nextflow_wgs to DSL2 #274

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Update nextflow_wgs to DSL2 #274

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@alkc alkc commented Dec 16, 2024 •
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Description and reviewer info

Closes #255

TODO:

  • Work thru all lsp errors
  • workflows
  • subworkflows
  • stub run finishes
  • onco run finishes
  • wgs run finishes
  • tracefiles comparison
  • pipeeval

Type of change

  • Documentation
  • Patch
  • Minor change
  • Major change

Checklist

  • Self-review of my code
  • Update the CHANGELOG
  • Tag the latest commit (vX.Y.Z format)

Major / Minor change

  • Stub run completes without errors or new warnings
  • GIAB single (wgs) finishes and differences to current master branch have been investigated (using PipeEval)
  • GIAB trio (wgs) finishes and differences to current master branch have been investigated
  • Seracare (onco) sample finishes and differences to current master branch have been investigated
  • Output from processes with altered code have been inspected (i.e. in the work folder: .command.sh, .command.log, .command.err and result files)
  • All three samples can be loaded into Scout
  • At least one other person has reviewed and approved my code
  • I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

  • Alexander
  • Jakob
  • Paul
  • Ryan
  • Viktor

(Add if missing)

Testing performed by

  • Alexander
  • Jakob
  • Paul
  • Ryan
  • Viktor

@alkc alkc self-assigned this Dec 16, 2024
@alkc alkc marked this pull request as draft December 16, 2024 10:56
@alkc alkc added status: draft epic Theme of work that contains subtasks labels Dec 16, 2024
alkc added 25 commits December 17, 2024 14:55
@alkc
remove bwa_sharded
d18daa4
@alkc
wip: sweeping dsl2 changes
05ba891
@alkc
Merge branch 'master' into alkc/dsl2
254b0cb
@alkc
move when: statements after input-output
779064a
@alkc
add some TODOs
c185510
@alkc
define params outside of closure
df03da0
@alkc
mode to params.mode
63a308a
@alkc
remove some bam choice channel
2a5b1d2
@alkc
fix remaining mode -> params.mode
ffd09a3
@alkc
update changelog
c7b9c3f
@alkc
minimal wip workflows
07e73bb
@alkc
rename fq var in fastp
1bb244a
@alkc
move params declaration to top
f4564db
@alkc
temp disable most code
9f01db7
@alkc
set csv to params.csv
bb42366
@alkc
stray curly brace
4cc5ef0
@alkc
println to loggers
98f9535
@alkc
log subdir
c989042
@alkc
debug to info log
2a8a3a6
@alkc
define params inside main workflow
3934ed6
@alkc
new param for final output dirpath
2dafbdd
@alkc
remove tuple spec from single val output
99fd805
@alkc
bwa_align + switch order of group and id in output
d563717
@alkc
re-enable markdup
ab4c154
@alkc
fix dedup input/output spec
021de21
alkc added 30 commits January 9, 2025 12:02
@alkc
annotsv
2783591
@alkc
add annotsv and vep_sv
ce2eafe
@alkc
move channel out of sv block
df5cec3
@alkc
forgout output sepc
1597b2e
@alkc
add sv annotation procs
7a14de4
@alkc
add prescore ped channel wizardry
7f07acb
@alkc
fix join w/ multichannel
be0da72
@alkc
input order ruins the day again
ef38f6a
@alkc
more input order fixes
0a63b62
@alkc
view ped prescore
7c0b79b
@alkc
remove view statements
a4ca400
@alkc
reorder map
d313ebc
@alkc
add some debug loggers
735b875
@alkc
activate _fa and _ma peds?
4b26f3e
@alkc
fix parenthesis paralysis
7785e5d
@alkc
remove mix of already mixed ch
02b403e
@alkc
add script block to melt_qc_val
6552f84
@alkc
add up tp compound finder
0da231b
@alkc
melt_qc_val changes
cde0526
@alkc
convert path to file
a53ccfe
@alkc
add bamtoyaml
acd4f96
@alkc
merge intersected melt vcf
379fa6f
@alkc
respect qc_json as file instead of path
e4e029f 
might be required for the groovy code to work,
as readLines is used on a file and not path
and converting the qc_json path to file in the
groovy script produces a file not found error
@alkc
forgot to add melt processes
2adff15
@alkc
mix of edits
bb91add 
re-enable process, whitespace, documentation
@alkc
melt_qc_val debugging
ad282fa
@alkc
try emitting and inputting file
5a4d0c1
@alkc
do not run verifybamid for non-wgs
c1cdf52
@alkc
back to path and super explicitly to File
23abb1a
@alkc
try converting path to file again
1d9d1a6
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Rewrite pipeline into DSL2
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