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fix: update CI workflow, snakemake wrappers and python / pandas code syntax #40

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fix: update CI workflow, snakemake wrappers and python / pandas code syntax #40

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10c4ba2
fix: stop using deprecated pd.read_table argument squeeze
dlaehnemann Jun 6, 2023
958f9ef
update GitHub Actions workflow to use newer Actions versions
dlaehnemann Jun 6, 2023
933cdb9
Merge branch 'update-ci' into fix-issue-39-read-table-squeeze-depreca…
dlaehnemann Jun 6, 2023
632c847
snakefmt
dlaehnemann Jun 6, 2023
1a0ba66
update multiqc wrapper version
dlaehnemann Jun 6, 2023
7d9a97e
update all wrappers to latest version
dlaehnemann Jun 7, 2023
2b72197
adjust .gitignore for easier workflow development
dlaehnemann Jun 7, 2023
d319afc
adjust tabix index wrapper to new tabix wrapper substrucutre
dlaehnemann Jun 7, 2023
ba2c18f
adjust bwa index wrapper syntax to newer version
dlaehnemann Jun 7, 2023
d38c2d3
update syntax for newer picard markduplicates wrapper
dlaehnemann Jun 7, 2023
69d4d82
update picard extra argument specification syntax
dlaehnemann Jun 7, 2023
9002ddf
further picard argument parsing syntax update
dlaehnemann Jun 7, 2023
6bee97c
explicitly specify sort order for picard markduplicates
dlaehnemann Jun 7, 2023
c9fa254
try `--VALIDATION_STRINGENCY LENIENT` for picard markduplicates
dlaehnemann Jun 7, 2023
85a3b64
reintroduce `--ASSUME_SORT_ORDER coordinate`
dlaehnemann Jun 8, 2023
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update picard extra argument specification syntax
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@dlaehnemann
dlaehnemann committed Jun 7, 2023
commit 69d4d82772ab528aaafd4910b50d7c4828e2c165
2 changes: 1 addition & 1 deletion .test/config/config.yaml
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Expand Up @@ -30,7 +30,7 @@ params:
GenotypeGVCFs: ""
VariantRecalibrator: ""
picard:
MarkDuplicates: "REMOVE_DUPLICATES=true"
MarkDuplicates: "--REMOVE_DUPLICATES=true"
trimmomatic:
pe:
trimmer:
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2 changes: 1 addition & 1 deletion config/config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ params:
GenotypeGVCFs: ""
VariantRecalibrator: ""
picard:
MarkDuplicates: "REMOVE_DUPLICATES=true"
MarkDuplicates: "--REMOVE_DUPLICATES=true"
trimmomatic:
pe:
trimmer:
Expand Down