Added error free BAMs, optimized read processing and functions#35

Merged

farchaab merged 59 commits intomainfrom readproc

Nov 1, 2024

+232-296

Commits on Oct 22, 2024

add --errfree argument
Ryan Teo
committed
remove minimal_test.tsv
Ryan Teo
committed
update default value for --errfree
Ryan Teo
committed

Commits on Oct 24, 2024

add directory to store error-free bam files
Ryan Teo
committed
add targets for errfree bam files
Ryan Teo
committed
add separate rules for processing errfree bam
Ryan Teo
committed
update output file suffix for errfree sam file
Ryan Teo
committed
update errfree sam file name
Ryan Teo
committed
merge with upstream
Ryan Teo
committed

Commits on Oct 25, 2024

restore original minimal_test
Ryan Teo
committed
fix targets
Ryan Teo
committed
fix path for error free reads
Ryan Teo
committed
resole conflict
Ryan Teo
committed
resolve conflicts
Ryan Teo
committed

Commits on Oct 29, 2024

simplified list_reads
farchaab
committed
fixed logs
farchaab
committed
added xargs for fastq concat
farchaab
committed
Merge branch 'readproc' into dev
teojcryan
authored
fixed shuffle seed
farchaab
committed
added fasta in wildcard_constraints
farchaab
committed
print only 3 first fastqs in cat_fastqs
farchaab
committed
improved formatting
farchaab
committed
fixed aggregate
farchaab
committed
removed ccs_sam_to_bam log
farchaab
committed
fixed shuffle seed

farchaab
authored and
Ryan Teo
committed
added fasta in wildcard_constraints

farchaab
authored and
Ryan Teo
committed
print only 3 first fastqs in cat_fastqs

farchaab
authored and
Ryan Teo
committed
improved formatting

farchaab
authored and
Ryan Teo
committed
fixed aggregate

farchaab
authored and
Ryan Teo
committed
removed ccs_sam_to_bam log

farchaab
authored and
Ryan Teo
committed
update file extension
Ryan Teo
committed
remove fix_art_sam_ef and update usage of aggregate()
Ryan Teo
committed
update convert_sam_to_bam_ef rule to match updated convert_sam_to_bam rule
Ryan Teo
committed
update merge_bams_ef rule to match merge_bams rule
Ryan Teo
committed
update ef rules to match existing workflow
Ryan Teo
committed

Commits on Nov 1, 2024