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Add ApplyBQSR, SamtoolStats, BamQC #259

Merged
merged 14 commits into from
Aug 3, 2020
Merged

Add ApplyBQSR, SamtoolStats, BamQC #259

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70dcb1b
Add ApplyBQSR module
FriederikeHanssen Jul 30, 2020
4fcb25a
Add ApplyBQSR process in WF
FriederikeHanssen Jul 30, 2020
7c5f5b5
Make samtools index separate process and sort with merge_bam
FriederikeHanssen Jul 31, 2020
47636a8
Add qualimap and samtools stats, remove useless comments
FriederikeHanssen Jul 31, 2020
a876ba5
Add qc to workflow
FriederikeHanssen Jul 31, 2020
9f08a51
Remove everything sentenion, we can look it up later in the released …
FriederikeHanssen Jul 31, 2020
ed2fc42
Some more small changes and removal of used code
FriederikeHanssen Jul 31, 2020
00de14c
Add multiqc back in
FriederikeHanssen Jul 31, 2020
6d12fb3
Remove obsolet when statement
FriederikeHanssen Jul 31, 2020
fec9391
Comment tag back in
FriederikeHanssen Jul 31, 2020
18e242a
Add qualimap_bamqc back in
FriederikeHanssen Jul 31, 2020
0f6151b
Add conditional samtools stats
FriederikeHanssen Jul 31, 2020
f18ecda
Traced the error to target_bed, however also the bam files are report…
FriederikeHanssen Jul 31, 2020
40e2adb
Merge_Bam_recal bams are the problem, other bams are fine
FriederikeHanssen Jul 31, 2020
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