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50 add skip parameter for sreads polishers and fix multiqc report names #65

Merged
merged 30 commits into from
Feb 25, 2024
Merged

50 add skip parameter for sreads polishers and fix multiqc report names #65

merged 30 commits into from
Feb 25, 2024

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fmalmeida
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Fixes #50

@fmalmeida fmalmeida self-assigned this Feb 16, 2024
@fmalmeida fmalmeida added the enhancement New feature or request label Feb 16, 2024
@fmalmeida fmalmeida linked an issue Feb 16, 2024 that may be closed by this pull request
Add skip parameter for sreads polishers and fix multiqc report names #50
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@fmalmeida
update shasum
22b4fb4
@fmalmeida
add busco instead of quast-busco
2c55341
@fmalmeida
fix quast mem/cpus variable
1b00a46
@fmalmeida
update param description
d62c994
@fmalmeida
update how busco params default is handled
cb86547
@fmalmeida
pre-download busco db
d18826e
@fmalmeida
update docker image
90cae14
@fmalmeida
define automatic busco lineage control
f007b41
@fmalmeida
add param to nextflow schema
3ece903
@fmalmeida
add parameter in documentation
898543f
@fmalmeida
add BUSCO in tools listing
3b5fadb
@fmalmeida
fix mqc module
1ec4eaf
@fmalmeida
add new parameter for skipping pilon or polypolish
9f9d548
@fmalmeida
add a checker to have at least one sreads polisher if running hb stra…
a12596a 
…tegy 2
@fmalmeida
fix BUSCO samplenames
9b44cd0
@fmalmeida
Update environment.yml
5e65cbc
@fmalmeida
generate a versions.yml for all modules
b2d6cd9
@fmalmeida
fix indentation
96c176f
@fmalmeida
include generation of versions yml
73ba7eb
@fmalmeida
add lines to avoid saving versions.yml files
5a036f5
@fmalmeida
all modules use my image
522f010
@fmalmeida
Update test.config
a108dc2
@fmalmeida
fixed execution of versions file generation
de97097
@fmalmeida
added a proper configuration for new MultiQC
dce365a
@fmalmeida
Update manual.md
af4b88a 
add params in documentation
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Parameters --skip_pilon and --skip_polypolish added to the pipeline. Also, MultiQC report was fixed and enhanced.
Docker image was also modified to download BUSCO standalone and pipeline perform the BUSCO standalone run instead of via quast.

@fmalmeida fmalmeida merged commit 19400bc into dev Feb 25, 2024
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@fmalmeida fmalmeida deleted the 50-add-skip-parameter-for-sreads-polishers-and-fix-multiqc-report-names branch February 25, 2024 19:48
@fmalmeida fmalmeida mentioned this pull request Feb 25, 2024
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Add skip parameter for sreads polishers and fix multiqc report names
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