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Handle single primer-trimming #80

Merged
merged 84 commits into from
Nov 11, 2021
Merged

Handle single primer-trimming #80

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633a336
Add handling of single primers
FelixMoelder Jun 17, 2021
72818d7
Adjust input
FelixMoelder Jun 17, 2021
f252280
Added liftover
FelixMoelder Jun 17, 2021
4d583a7
Fixed syntax
FelixMoelder Jun 17, 2021
caeca2c
snakefmt
FelixMoelder Jun 17, 2021
59f4414
Fix wildcard constraint
FelixMoelder Jun 17, 2021
a047d06
More automagic
FelixMoelder Jun 17, 2021
ea907ed
Add missing config
FelixMoelder Jun 17, 2021
3c0416a
Fixed script
FelixMoelder Jun 17, 2021
157810b
Fixed script
FelixMoelder Jun 17, 2021
5604cb7
Fixed script
FelixMoelder Jun 17, 2021
6155a63
Fix script
FelixMoelder Jun 21, 2021
d06aa2d
Update build_primer_regions script
FelixMoelder Jul 6, 2021
b4ec7d2
Updated for fgbio filtering
FelixMoelder Jul 6, 2021
300efa4
Merge branch 'master' into single_primer
FelixMoelder Jul 6, 2021
2cf74e9
Cleanup
FelixMoelder Jul 6, 2021
a5e50d7
Remove env
FelixMoelder Jul 6, 2021
17f34d9
Remove script
FelixMoelder Jul 6, 2021
024b7cd
Fix yara
FelixMoelder Jul 6, 2021
511c43e
Fixed script
FelixMoelder Jul 6, 2021
a7afcda
Add tmp fgbio build
FelixMoelder Jul 7, 2021
fb763b5
Add jar
FelixMoelder Jul 7, 2021
481cd63
Update rule
FelixMoelder Jul 7, 2021
1746d03
Update rule
FelixMoelder Jul 7, 2021
19cefb4
Fix target regions
FelixMoelder Jul 12, 2021
880ab7c
Removed primer ref
FelixMoelder Jul 12, 2021
5fd817b
Update primer config
FelixMoelder Jul 12, 2021
d982013
Snakemake fmt
FelixMoelder Jul 12, 2021
cce562a
Build regions always
FelixMoelder Jul 12, 2021
72dac72
Merge branch 'master' into single_primer
FelixMoelder Jul 12, 2021
05a9593
Cleanup
FelixMoelder Jul 12, 2021
7a71f64
Cleanup
FelixMoelder Jul 12, 2021
d7a38bb
Enhanced rules
FelixMoelder Jul 12, 2021
6c783e6
Update env
FelixMoelder Jul 13, 2021
4e2a6ba
Update env
FelixMoelder Jul 13, 2021
3975326
Undo env update
FelixMoelder Jul 14, 2021
10b9aab
Merge branch 'master' into single_primer
FelixMoelder Jul 14, 2021
1c77804
snakefmt
FelixMoelder Jul 14, 2021
2113140
Remove comments
FelixMoelder Aug 9, 2021
f5852e6
Merge branch 'master' into single_primer
FelixMoelder Aug 12, 2021
d5d0bc6
Update rbt
FelixMoelder Aug 12, 2021
37d0377
Add index
FelixMoelder Aug 12, 2021
4df7a58
Merge annotated variants
FelixMoelder Aug 12, 2021
ba489a2
Add multiple primers
FelixMoelder Aug 17, 2021
9fae202
Merge branch 'master' into single_primer
FelixMoelder Aug 17, 2021
c48fdc2
fixes
FelixMoelder Aug 17, 2021
b65013c
Set params corrently
FelixMoelder Aug 18, 2021
e322439
Reordered workflow
FelixMoelder Aug 18, 2021
c9547a8
Various minor fixes
FelixMoelder Aug 25, 2021
805c580
Merge branch 'master' into single_primer
FelixMoelder Sep 6, 2021
5010ac4
Merge branch 'master' into single_primer
FelixMoelder Sep 6, 2021
93762bf
Filter primers by assignment
FelixMoelder Sep 21, 2021
c78f91c
Add missing files
FelixMoelder Sep 21, 2021
0ca0faf
Pipe stderr
FelixMoelder Sep 21, 2021
0c25aa3
Setup SSH session
FelixMoelder Sep 21, 2021
d982bad
Setup SSH session
FelixMoelder Sep 21, 2021
53c51f7
Add debugging prints
FelixMoelder Sep 23, 2021
feb03a1
Update env
FelixMoelder Sep 29, 2021
057e9f9
Temporary disable tests
FelixMoelder Sep 29, 2021
9ec2823
Update workflow/envs/filter_reads.yaml
FelixMoelder Sep 29, 2021
b467102
Update workflow/scripts/filter_primers.rs
FelixMoelder Sep 29, 2021
3c6c3eb
Add dep
FelixMoelder Sep 29, 2021
a34b9e5
Add dep
FelixMoelder Sep 29, 2021
1a22d72
Reset tests
FelixMoelder Sep 29, 2021
85191fe
Reset tests
FelixMoelder Sep 29, 2021
9fc5bcd
Merge branch 'master' into single_primer
FelixMoelder Oct 5, 2021
14e1c7d
Cleanup
FelixMoelder Oct 5, 2021
ea1e708
Merge branch 'single_primer' of github.com:snakemake-workflows/dna-se…
FelixMoelder Oct 5, 2021
a994a73
Update to fgbio 1.4
FelixMoelder Oct 20, 2021
39cb26f
Removed precompiled fgbio.jar
FelixMoelder Oct 21, 2021
17892f8
Merge branch 'master' into single_primer
FelixMoelder Oct 28, 2021
56af408
Merge branch 'master' into single_primer
FelixMoelder Nov 11, 2021
1098640
Update rbt
FelixMoelder Nov 11, 2021
7e49040
Remove todos
FelixMoelder Nov 11, 2021
7457b87
snakefmt
FelixMoelder Nov 11, 2021
870887f
Cleanup
FelixMoelder Nov 11, 2021
8a3b5d8
Revert fmt
FelixMoelder Nov 11, 2021
89714d8
Fix varlociraptor_alignment_properties
FelixMoelder Nov 11, 2021
f3819be
Update readme
FelixMoelder Nov 11, 2021
f63fbc6
Merge branch 'master' into single_primer
FelixMoelder Nov 11, 2021
cc44cf9
Typos
FelixMoelder Nov 11, 2021
122a6c8
Merge branch 'single_primer' of github.com:snakemake-workflows/dna-se…
FelixMoelder Nov 11, 2021
14efc2d
Update readme
FelixMoelder Nov 11, 2021
dcecf5f
Typos
FelixMoelder Nov 11, 2021
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4 changes: 2 additions & 2 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -45,14 +45,14 @@ jobs:
directory: .test
snakefile: workflow/Snakefile
args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"

- name: Test workflow (local FASTQs, target regions)
uses: snakemake/snakemake-github-action@v1.22.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"

- name: Test report
uses: snakemake/snakemake-github-action@v1.22.0
with:
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