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Adding single-read functionality to PROFILE #84

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merged 63 commits into from
Jan 6, 2025
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c4b1f62
Updated subsetReads to optionally take in single reads. Added PROFILE…
simonleandergrimm Oct 28, 2024
193dd22
Added BBDUK single read script.
simonleandergrimm Oct 28, 2024
0e081f2
Added subsetting for single reads/
simonleandergrimm Oct 28, 2024
4e140aa
Added selection of single or paired end reads.
simonleandergrimm Oct 28, 2024
d270d3f
WIP edits to taxonomy main scripts (commenting, subselecting processe…
simonleandergrimm Oct 28, 2024
bad2787
Adding kraken path to run_dev_se.nf
simonleandergrimm Oct 28, 2024
79f9222
Adding WIP changes to test/nextflow.config to run on Simon's S3.
simonleandergrimm Oct 28, 2024
50adde1
fixed wrong indent in run_dev_se.nf
simonleandergrimm Nov 7, 2024
daa6c3e
Slight edit to inline commments in taxonomy/main.nf. Reverted emit st…
simonleandergrimm Nov 7, 2024
39c797c
Revert "Adding WIP changes to test/nextflow.config to run on Simon's …
simonleandergrimm Nov 7, 2024
2da99f1
removed white space in two files
simonleandergrimm Nov 7, 2024
1d30115
Removed unneeded comments in taxonomy/main.nf
simonleandergrimm Nov 7, 2024
0f8636e
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Nov 19, 2024
d4b7239
dropped params.*
simonleandergrimm Nov 20, 2024
487c6c5
added selection of correct concat_group process in extractViralReads
simonleandergrimm Nov 20, 2024
dd71ea8
added paired paired and single version for concat_group
simonleandergrimm Nov 20, 2024
329acb1
Adapted profile to be cleaner and take in changes introduced by Will.
simonleandergrimm Nov 20, 2024
ea74362
Cleaned up taxonomy and took into account changes of v2.5.0
simonleandergrimm Nov 20, 2024
bbced47
Fixed single-end flags in run.nf
simonleandergrimm Nov 20, 2024
4a1edda
added "params" to the single_end flags to run_dev_se.nf
simonleandergrimm Nov 20, 2024
753982d
Fixing run_dev_se.config file
simonleandergrimm Nov 20, 2024
5c3cb73
updated config in paired end test dataset
simonleandergrimm Nov 20, 2024
5c29398
added params to single end.
simonleandergrimm Nov 22, 2024
9b47532
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Nov 30, 2024
8fa88fa
Dropped params.* for single_end.
simonleandergrimm Nov 30, 2024
abe95bf
moved single_end parameter definition to .config files.
simonleandergrimm Dec 2, 2024
15facd1
moved order of single_end definition.
simonleandergrimm Dec 2, 2024
8f5afe8
Reformatted tests/run-dev-se.config to be thesame as tests/run.config
simonleandergrimm Dec 3, 2024
b0d6737
removed unneded whitespace
simonleandergrimm Dec 3, 2024
5827044
reset test-data/nextflowconfig to have settings set to will defaults.
simonleandergrimm Dec 3, 2024
8302f25
removed test-se configfile.
simonleandergrimm Dec 3, 2024
ac10124
placeholder comiit
simonleandergrimm Dec 3, 2024
30a2a6e
Merge pull request #116 from naobservatory/harmon_fix_copying_file_bug
willbradshaw Nov 27, 2024
cc5fd19
Changed version of nextflow, hopefully this works
harmonbhasin Dec 3, 2024
ab78257
Updated label to be correct
harmonbhasin Dec 3, 2024
1db7ba8
updated end-to-end.yml and run dev se config.
simonleandergrimm Dec 3, 2024
1751288
test commit
simonleandergrimm Dec 3, 2024
1aef130
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 3, 2024
236175b
Merge remote-tracking branch 'origin/harmon_fix_gh_actions_test' into…
simonleandergrimm Dec 3, 2024
2159431
Merge branch 'single-read-profile' of https://github.com/naobservator…
simonleandergrimm Dec 3, 2024
764cf9c
Merge remote-tracking branch 'origin/harmon_fix_gh_actions_test' into…
simonleandergrimm Dec 4, 2024
162fb19
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 4, 2024
6216f77
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 4, 2024
3648257
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 4, 2024
aa62e5a
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 4, 2024
5567568
dropped read type info from config files where its not needed.
simonleandergrimm Dec 4, 2024
a3af7db
Made rundevse index and outputs look the same as run.nf
simonleandergrimm Dec 4, 2024
d465db7
fixed memory issue in bbduk
simonleandergrimm Dec 5, 2024
4e74d7c
Fixing setup of run_dev_se test config.
simonleandergrimm Dec 5, 2024
d061c1d
fixed imports in taxonomy/main.nf
simonleandergrimm Dec 9, 2024
db187e6
Removed redundancy
simonleandergrimm Dec 9, 2024
ce74e2c
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 9, 2024
fcc2f4a
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 10, 2024
8a09b08
delete unexpected cahracter
simonleandergrimm Dec 10, 2024
11f2145
Merge branch 'single-read-raw-clean' into single-read-profile
simonleandergrimm Dec 11, 2024
55f75f8
moved kraken db location
simonleandergrimm Dec 11, 2024
1210a3c
Update main.nf
simonleandergrimm Dec 12, 2024
9113fd4
Update end-to-end.yml
simonleandergrimm Dec 20, 2024
dca3c30
Merge branch 'dev' into single-read-profile. Fixed remaining issues i…
simonleandergrimm Dec 20, 2024
4bfbc46
updated changelog. updated rundevse to have correct loadsamplesheet p…
simonleandergrimm Dec 20, 2024
d2826d2
removed whitespace
simonleandergrimm Dec 20, 2024
6b1da71
Merge branch 'single-read-profile' of https://github.com/naobservator…
simonleandergrimm Dec 20, 2024
ae1fe8a
Merge branch 'dev' into single-read-profile
willbradshaw Dec 21, 2024
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removed unneded whitespace
simonleandergrimm committed Dec 3, 2024

Verified

This commit was signed with the committer’s verified signature.
aalu1418 Aaron Lu
commit b0d67372a758817c1e163f8aa80e6fed8ca6889b
1 change: 0 additions & 1 deletion subworkflows/local/profile/main.nf
Original file line number Diff line number Diff line change
@@ -86,7 +86,6 @@ workflow PROFILE {
br_ribo = tax_ribo_ch.bracken.collectFile(name: "bracken_reports_ribo.tsv.gz")
br_noribo = tax_noribo_ch.bracken.collectFile(name: "bracken_reports_noribo.tsv.gz")
merge_ch = MERGE_TAXONOMY_RIBO(kr_ribo, kr_noribo, br_ribo, br_noribo)

emit:
bracken = merge_ch.bracken
kraken = merge_ch.kraken