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

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merged 59 commits into from
Nov 1, 2024
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e68dcb3
add --errfree argument
Oct 22, 2024
7caf345
remove minimal_test.tsv
Oct 22, 2024
987a879
update default value for --errfree
Oct 22, 2024
b55a0c4
add directory to store error-free bam files
Oct 24, 2024
393a4b9
add targets for errfree bam files
Oct 24, 2024
796f7bb
add separate rules for processing errfree bam
Oct 24, 2024
b18bebd
update output file suffix for errfree sam file
Oct 24, 2024
acfb620
update errfree sam file name
Oct 24, 2024
970a3b1
merge with upstream
Oct 24, 2024
90a0af4
restore original minimal_test
Oct 25, 2024
be262d3
fix targets
Oct 25, 2024
1964365
fix path for error free reads
Oct 25, 2024
7c5c403
resole conflict
Oct 25, 2024
ae730f9
resolve conflicts
Oct 25, 2024
1253a4f
added sambamba env
farchaab Oct 26, 2024
939d5ec
added sambamba container
farchaab Oct 26, 2024
24928f5
added samtools
farchaab Oct 26, 2024
cae1017
simplified aggregate
farchaab Oct 26, 2024
4db4d03
removed redundant cat rules, added sambamba
farchaab Oct 26, 2024
4872558
added default flag for 0 lenth indels
farchaab Oct 26, 2024
023de5b
improved functions
farchaab Oct 28, 2024
c95b174
replaced sambamba and bioconvert with samtools
farchaab Oct 28, 2024
8e5db9e
added rustybam and wgatools
farchaab Oct 28, 2024
dc73f88
added bioconvert back
farchaab Oct 28, 2024
04d56cc
env cleanup
farchaab Oct 28, 2024
f4c4f96
containers cleanup
farchaab Oct 28, 2024
09efdef
added zip to avoid all fasta and contigs combinations
farchaab Oct 28, 2024
c8a4ad9
fixed aggregate function
farchaab Oct 28, 2024
4fc53f4
removed benchmarks
farchaab Oct 28, 2024
8c61950
updated assembly_finder
farchaab Oct 28, 2024
f792130
simplified list_reads
farchaab Oct 29, 2024
6eda049
fixed logs
farchaab Oct 29, 2024
65d0e9a
added xargs for fastq concat
farchaab Oct 29, 2024
2ba38c2
Merge branch 'readproc' into dev
teojcryan Oct 29, 2024
a519200
fixed shuffle seed
farchaab Oct 29, 2024
b188a7b
added fasta in wildcard_constraints
farchaab Oct 29, 2024
3d3ee46
print only 3 first fastqs in cat_fastqs
farchaab Oct 29, 2024
e14c7e4
improved formatting
farchaab Oct 29, 2024
926e002
fixed aggregate
farchaab Oct 29, 2024
fbf1b90
removed ccs_sam_to_bam log
farchaab Oct 29, 2024
804d165
fixed shuffle seed
farchaab Oct 29, 2024
7595b89
added fasta in wildcard_constraints
farchaab Oct 29, 2024
1e42020
print only 3 first fastqs in cat_fastqs
farchaab Oct 29, 2024
06acb19
improved formatting
farchaab Oct 29, 2024
dc3dd0f
fixed aggregate
farchaab Oct 29, 2024
34a412a
removed ccs_sam_to_bam log
farchaab Oct 29, 2024
ac5c470
update file extension
Oct 29, 2024
cdd8b0f
remove fix_art_sam_ef and update usage of aggregate()
Oct 29, 2024
5c849c0
update convert_sam_to_bam_ef rule to match updated convert_sam_to_bam…
Oct 29, 2024
e114103
update merge_bams_ef rule to match merge_bams rule
Oct 29, 2024
32e228c
update ef rules to match existing workflow
Oct 29, 2024
8ae2ceb
Merge pull request #33 from teojcryan/dev
farchaab Oct 30, 2024
c5866cc
moved error free bams in bam dir
farchaab Oct 30, 2024
4afff3c
added logs for samtools sort stderr
farchaab Oct 30, 2024
48ead09
linted options
farchaab Oct 30, 2024
db88db9
moved errfree option
farchaab Oct 30, 2024
9c9f417
removed bam coverage for ef bams, fixed logs
farchaab Nov 1, 2024
58c2d5d
improved sam output
farchaab Nov 1, 2024
568e080
added apptainer setup actions
farchaab Nov 1, 2024
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removed ccs_sam_to_bam log
farchaab authored and Ryan Teo committed Oct 29, 2024
commit 34a412a6247758457dd579126e2b9574bb4d52c4
2 changes: 1 addition & 1 deletion mess/workflow/rules/processing/reads.smk
Original file line number Diff line number Diff line change
@@ -44,7 +44,7 @@ if PASSES > 1:
shell:
"""
samtools view -@ {threads} -Sb {input} | \\
samtools sort -@ {threads} -o {output} 2> {log}
samtools sort -@ {threads} -o {output}
"""

rule ccs_bam_to_fastq: