8000 Add FASTQ input and position-sorted, indexed BAM output by etal · Pull Request #28 · formbio/laava · GitHub
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Add FASTQ input and position-sorted, indexed BAM output #28

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Merged
merged 10 commits into from
Jun 21, 2024
Merged

Add FASTQ input and position-sorted, indexed BAM output #28

merged 10 commits into from
Jun 21, 2024

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etal
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@etal etal commented Jun 11, 2024 •
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Addresses #22, #23, #25, and other maintenance concerns.

@etal etal mentioned this pull request Jun 20, 2024
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etal added 2 commits June 20, 2024 17:42
@etal
Makefile: Add Nextflow test commands
17a1970 
Remove standalone local runner script.
@etal
Move a dataframe from the report template to calculate_rdata.R
ff0f3fa 
Now it's available to downstream consumers via .Rdata
@etal etal force-pushed the io-compat branch 2 times, most recently from 9f63fa5 to 4cf9188 Compare June 21, 2024 04:18
etal added 4 commits June 20, 2024 21:55
@etal
Add folder/file input options to Form UI
7da7f49
@etal
Output a position-sorted, indexed BAM for downstream use (closes #22)
3c47e58
@etal
Fix missing flipflop.tsv output
6a14f41 
Previously, the file flipflop_assignments.tsv wasn't reaching
calculate_rdata.R because the input's file extension hadn't been updated
from .txt, so flipflop.tsv wasn't generated.
@etal
calculate_rdata: no-op tidying
5e4aa74
@etal etal marked this pull request as ready for review June 21, 2024 05:24
@etal etal requested review from Magdoll and alphabdiallo June 21, 2024 05:24
alphabdiallo
alphabdiallo approved these changes Jun 21, 2024
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LGMT

@etal etal added this to the v2.6 milestone Jun 21, 2024
@etal etal merged commit 30ad6a2 into main Jun 21, 2024
3 checks passed
@etal etal deleted the io-compat branch June 21, 2024 15:46
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@alphabdiallo alphabdiallo alphabdiallo approved these changes

@Magdoll Magdoll Awaiting requested review from Magdoll

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