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New tool: biobambam/bamsormadup #1478

Merged
merged 27 commits into from
Apr 6, 2022
Merged

New tool: biobambam/bamsormadup #1478

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453a13c
add bamsormadup
matthdsm Apr 1, 2022
7fc5834
fix yaml
matthdsm Apr 1, 2022
596afb3
add test.yml
matthdsm Apr 1, 2022
dc2b038
Update tests/modules/biobambam/bamsormadup/test.yml
matthdsm Apr 4, 2022
e8e2674
Merge branch 'master' into tool/bamsormadup
matthdsm Apr 4, 2022
1e3ee75
test meta.yaml: remove md5sums
matthdsm Apr 4, 2022
4908f1e
Tool bamsormadup:
matthdsm Apr 4, 2022
4b1d7cb
Merge branch 'master' into tool/bamsormadup
matthdsm Apr 4, 2022
6c338a1
fix input and output formats
matthdsm Apr 4, 2022
bf015bb
update input file description
matthdsm Apr 4, 2022
b97ebb9
drop sam output, goes against nf-core regs; add input check for cram …
matthdsm Apr 4, 2022
b936a5d
fix typo
matthdsm Apr 4, 2022
2d6231a
Merge branch 'master' into tool/bamsormadup
matthdsm Apr 4, 2022
bac3951
Update modules/biobambam/bamsormadup/main.nf
matthdsm Apr 4, 2022
be386c8
improve ref fasta name
matthdsm Apr 4, 2022
156a9ab
fix if else shorthand
matthdsm Apr 4, 2022
96b4460
fix syntax error
matthdsm Apr 4, 2022
baead3c
kind of fix tests
matthdsm Apr 4, 2022
e609147
Merge branch 'master' into tool/bamsormadup
matthdsm Apr 5, 2022
ed379a8
set fixed suffix for metrics file to keep it in line with picard and …
matthdsm Apr 5, 2022
cd5fd67
Merge branch 'master' into tool/bamsormadup
matthdsm Apr 5, 2022
50b835b
fix command line
matthdsm Apr 5, 2022
78ee44a
update test.yml
matthdsm Apr 5, 2022
389c804
add support for multiple input bams
matthdsm Apr 5, 2022
a788720
Update modules/biobambam/bamsormadup/meta.yml
matthdsm Apr 6, 2022
269eedc
Update modules/biobambam/bamsormadup/meta.yml
matthdsm Apr 6, 2022
9c88514
Update tests/modules/biobambam/bamsormadup/test.yml
matthdsm Apr 6, 2022
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Merge branch 'master' into tool/bamsormadup
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@matthdsm
matthdsm committed Apr 4, 2022
commit e8e26744ee3385843fb7e4ab13ae2f1b32d1eb1b

This merge commit was added into this branch cleanly.

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