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Md cram #735

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merged 76 commits into from
Oct 12, 2022
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2500878
update markduplicates module
FriederikeHanssen Sep 7, 2022
fff88f5
use it in subworkflows
FriederikeHanssen Sep 7, 2022
2e3431f
update changelog
FriederikeHanssen Sep 7, 2022
d97c228
merge upstream/dev
FriederikeHanssen Sep 7, 2022
708dd6f
prefix must use output file name
FriederikeHanssen Sep 7, 2022
5d3fcd9
use samtools index, because the md index is not working
FriederikeHanssen Sep 7, 2022
ec57d1e
fix bam output
FriederikeHanssen Sep 8, 2022
5f10df0
check estimatelib can run on cram
FriederikeHanssen Sep 8, 2022
07c7ba9
merge upstream/dev
FriederikeHanssen Sep 8, 2022
e8fab9e
remove merge conflict markers
FriederikeHanssen Sep 8, 2022
8476c78
remove merge conflict markers
FriederikeHanssen Sep 8, 2022
e53164c
fix metrics path
FriederikeHanssen Sep 8, 2022
5eae260
fix output names
FriederikeHanssen Sep 8, 2022
afc794a
update usage docs
FriederikeHanssen Sep 8, 2022
aa05776
update output docs
FriederikeHanssen Sep 8, 2022
dbdf861
Update CHANGELOG.md
FriederikeHanssen Sep 8, 2022
b28a3b3
revert module chagnes
FriederikeHanssen Sep 8, 2022
90eed33
Merge remote-tracking branch 'origin/md_cram' into md_cram
FriederikeHanssen Sep 8, 2022
695949e
update json
FriederikeHanssen Sep 8, 2022
2e5ac3c
fix ending of stats file
FriederikeHanssen Sep 8, 2022
55d5c65
fix skip_md
FriederikeHanssen Sep 8, 2022
4340ad5
rename samtools imports
FriederikeHanssen Sep 8, 2022
a69c6cf
indent things
FriederikeHanssen Sep 8, 2022
483e37b
remove weird bam publication
FriederikeHanssen Sep 8, 2022
8763bee
fix naming
FriederikeHanssen Sep 8, 2022
894f149
fix naming
FriederikeHanssen Sep 8, 2022
fab6ea3
fix publish dir
FriederikeHanssen Sep 8, 2022
c65029d
fix path
FriederikeHanssen Sep 8, 2022
1ebe4ec
fix checksums
FriederikeHanssen Sep 8, 2022
a142955
mapped should be bam
FriederikeHanssen Sep 8, 2022
686f80d
fix output file look
FriederikeHanssen Sep 9, 2022
97f2760
remove view statements
FriederikeHanssen Sep 9, 2022
8edd3ee
add estimatelincom back
FriederikeHanssen Sep 9, 2022
5c17302
fix md5sums
FriederikeHanssen Sep 9, 2022
72fa282
check that mapped subdir is not added
FriederikeHanssen Sep 9, 2022
7c703b9
make test name unique
FriederikeHanssen Sep 9, 2022
c0f1d58
fix caridanlity
FriederikeHanssen Sep 9, 2022
6334c5e
write csv when output bam
FriederikeHanssen Sep 9, 2022
fbb2c31
fix checksums
FriederikeHanssen Sep 9, 2022
660dda8
fix mapped bam publishing
FriederikeHanssen Sep 9, 2022
848e858
fix start from prepare recal
FriederikeHanssen Sep 9, 2022
0260933
rename save_bam_mapped to save_mapped to reflect change to store as CRAM
FriederikeHanssen Sep 10, 2022
971e5a1
on save_mapped alone only publish CRAMs
FriederikeHanssen Sep 10, 2022
54518b2
remove space
FriederikeHanssen Sep 10, 2022
d9b63c8
refactor logic for bam/cram input through mapping and MD
FriederikeHanssen Sep 11, 2022
81e9dab
finish refactoring
FriederikeHanssen Sep 11, 2022
daa4776
explicelty name cram_qc for recal
FriederikeHanssen Sep 11, 2022
fa71638
explicelty name cram_qc for recal
FriederikeHanssen Sep 11, 2022
461f791
fix name
FriederikeHanssen Sep 11, 2022
4b720e6
remove duplicated file
FriederikeHanssen Sep 11, 2022
532f6fe
fix file duplication
FriederikeHanssen Sep 11, 2022
86e590c
remove unused files
FriederikeHanssen Sep 11, 2022
2752aeb
fix samtools stats out name
FriederikeHanssen Sep 11, 2022
33f5843
fix channel output
FriederikeHanssen Sep 12, 2022
176e20c
publish converted cram files to a converted subdir
FriederikeHanssen Sep 12, 2022
655f4b9
fix file name
FriederikeHanssen Sep 12, 2022
4651c36
address review comments
FriederikeHanssen Sep 12, 2022
25e810f
fix md5sums
FriederikeHanssen Sep 12, 2022
8469ec8
workaround weird meta map thing
FriederikeHanssen Sep 13, 2022
72dcf0b
checksum fixes
FriederikeHanssen Sep 13, 2022
011be69
add more md5sums
FriederikeHanssen Sep 22, 2022
9caa37c
Merge branch 'dev' into md_cram
FriederikeHanssen Sep 23, 2022
63749bf
remove merge conflict markers
FriederikeHanssen Sep 23, 2022
48c70ba
Merge upstream/dev
FriederikeHanssen Oct 10, 2022
8f7605f
fix paths
FriederikeHanssen Oct 10, 2022
447da0b
remove merge markers
FriederikeHanssen Oct 10, 2022
2ad3704
fix module imports
FriederikeHanssen Oct 10, 2022
04212c8
add process import back in that I removed when merging
FriederikeHanssen Oct 10, 2022
9be3627
fix skip_md tests
FriederikeHanssen Oct 11, 2022
2e5e484
fix saveoutputbam tests
FriederikeHanssen Oct 11, 2022
b1325d7
fix haplotypecaller checksums
FriederikeHanssen Oct 11, 2022
e8df4b5
some variabel md5sums
FriederikeHanssen Oct 11, 2022
2600ba7
some more checksum checks
FriederikeHanssen Oct 11, 2022
4843179
Add tests for saveoutputbam + saveoutputmapped & docs
FriederikeHanssen Oct 11, 2022
1b6e14d
Merge remote-tracking branch 'upstream/dev' into md_cram
FriederikeHanssen Oct 11, 2022
90d252c
fix edmunds linting
FriederikeHanssen Oct 11, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#730](https://github.com/nf-core/sarek/pull/730) - Reduce number of tests
- [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic`
- [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len
- [#735](https://github.com/nf-core/sarek/pull/735) - GATK Markduplciates now natively supports CRAM output
FriederikeHanssen marked this conversation as resolved.
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### Fixed

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21 changes: 16 additions & 5 deletions modules/nf-core/modules/gatk4/markduplicates/main.nf

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20 changes: 20 additions & 0 deletions modules/nf-core/modules/gatk4/markduplicates/meta.yml

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12 changes: 7 additions & 5 deletions subworkflows/nf-core/gatk4/markduplicates/main.nf

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11 changes: 4 additions & 7 deletions subworkflows/nf-core/gatk4/markduplicates_spark/main.nf

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