Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

umicollapse #1368

Closed
wants to merge 807 commits into from
Closed
Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
807 commits
Select commit Hold shift + click to select a range
d338f00
Revert "Remove problem multiqc setting"
pinin4fjords Jun 21, 2024
858cd5d
add stub for local/deseq2_qc
maxulysse Jun 21, 2024
451483b
add stubs for all + test for most
maxulysse Jun 21, 2024
5bb52da
Merge branch 'updates' of github.com:drpatelh/nf-core-rnaseq into upd…
pinin4fjords Jun 25, 2024
e640eea
Update all nf-core/modules again
drpatelh Jun 27, 2024
6035f5b
Rename custom content keys as required in MultiQC v1.22.3
drpatelh Jun 27, 2024
0aaf228
Update snapshots for default pipeline test
drpatelh Jun 27, 2024
5818d6c
Merge branch 'updates' of github.com:drpatelh/nf-core-rnaseq into upd…
pinin4fjords Jun 27, 2024
489e7fd
patch dupradar
pinin4fjords Jun 27, 2024
2d314bf
Fix syntax
pinin4fjords Jun 27, 2024
e7ba0cf
update snapshot
pinin4fjords Jun 28, 2024
a29e775
Merge pull request #1330 from drpatelh/updates
pinin4fjords Jun 28, 2024
7af2a7f
Update CHANGELOG.md
maxulysse Jul 2, 2024
fa2f92b
Merge branch 'dev' into dev
maxulysse Jul 2, 2024
7e9077e
update snaps
maxulysse Jul 2, 2024
b901cbe
Merge pull request #1331 from maxulysse/dev
maxulysse Jul 2, 2024
b965ced
update all modules
maxulysse Jul 2, 2024
b796fc0
update all subworkflows
maxulysse Jul 2, 2024
ad73fc3
no more tags.yml
maxulysse Jul 3, 2024
9f98489
no more tags.yml
maxulysse Jul 3, 2024
bdb6e31
remove tag within tests
maxulysse Jul 3, 2024
ec409aa
update CHANGELOG
maxulysse Jul 3, 2024
1af00b9
Merge pull request #1334 from maxulysse/stubs
maxulysse Jul 3, 2024
0620d21
stub for align_star + a single snapshot match per test
maxulysse Jul 3, 2024
573ca90
add stubs + code polish + Harshil align
maxulysse Jul 3, 2024
3efcb84
add stub
maxulysse Jul 3, 2024
345d1f8
update all nf-core modules and subworkflows and do not include tags
maxulysse Jul 3, 2024
eb08f2f
simplify snapshot for stub
maxulysse Jul 3, 2024
c956f6f
add stubs for subworkflow local quantify_rsem
maxulysse Jul 3, 2024
bf5797f
update default snapshot
maxulysse Jul 3, 2024
a2443e7
Modify FastQC output publishing to comply with the paths in MultiQC c…
MatthiasZepper May 22, 2024
00d6113
MultiQC config updates.
MatthiasZepper May 29, 2024
7dade35
Linting.
MatthiasZepper Jun 3, 2024
1bf9390
Use the correct module names to supress the Percent Duplicate column …
MatthiasZepper Jun 3, 2024
850cb4c
Publish logfiles from umi-tools dedup steps.
MatthiasZepper Jun 5, 2024
2cb8eff
Modify subworkflow bam_dedup_stats_samtools_umitools to publish dedup…
MatthiasZepper Jun 5, 2024
6648b35
Update bam_dedup_stats_samtools_umitools subworkflow and MultiQC module.
MatthiasZepper Jun 10, 2024
2924f9e
Add UMI information for Watchmaker mRNA Library Prep Kit.
MatthiasZepper Jun 10, 2024
8a4aa8a
Publish the UMI-tools extract logs for MultiQC.
MatthiasZepper Jun 11, 2024
af1b91c
The output channel of fastq_fastqc_umitools_trimgalore/fastp is calle…
MatthiasZepper Jun 11, 2024
df31182
Mark FASTQC outputs with suffixes
pinin4fjords Jun 20, 2024
8bca15a
@aanil (Anandashankar Anil) correctly pointed out that some MultiQC …
MatthiasZepper Jul 2, 2024
6178e8c
Linting
MatthiasZepper Jul 3, 2024
4dc5b67
Changelog
MatthiasZepper Jul 4, 2024
37780ad
add plugin
maxulysse Jul 4, 2024
150ac0b
update all subworkflows
maxulysse Jul 4, 2024
9fd07da
do not snapshot fastq in stub
maxulysse Jul 4, 2024
2cdeea1
pipeline level stub
maxulysse Jul 4, 2024
3c78a6a
fix stub test for prepare_genome
maxulysse Jul 4, 2024
c572fc0
update all subworkflows
maxulysse Jul 4, 2024
df9efba
correctly align
maxulysse Jul 5, 2024
3edd994
Use nf-core/setup-nf-test action for portability
adamrtalbot Jul 5, 2024
9f3bd8a
changelog
adamrtalbot Jul 5, 2024
bc7d7a5
update all modules
maxulysse Jul 9, 2024
4555a27
Undo changes to modules/nf-core/dupradar/templates/dupradar.r from Ha…
MatthiasZepper Jul 9, 2024
eb4e362
Update Azure Batch guidance
adamrtalbot Jul 9, 2024
c6c8bcc
Add suggestions from @MatthiasZepper
lazappi Jul 10, 2024
5f3c471
bump module and temporarily patch for https://github.com/nf-core/modu…
pinin4fjords Jul 10, 2024
1931c05
Correct the diff
pinin4fjords Jul 10, 2024
9230216
Update MultiQC to v1.23
MatthiasZepper Jul 10, 2024
bb39866
Demote titles to return structure to previous
pinin4fjords Jul 11, 2024
8e42ab1
Update dupradar from modules repo and remove patch.
MatthiasZepper Jul 11, 2024
b78a653
use seqera containers
maxulysse Jul 11, 2024
d2d21cf
Update module for snapshot fix
pinin4fjords Jul 11, 2024
1c75669
Fix prefixes for FASTQC
pinin4fjords Jul 11, 2024
18d8d10
Merge pull request #1308 from MatthiasZepper/MultiQC_FastQC_bug
MatthiasZepper Jul 12, 2024
98cf1fa
Merge branch 'dev' into stubs_everywhere
maxulysse Jul 12, 2024
8759ed7
update all modules/subworkflows + remove tags
maxulysse Jul 12, 2024
cb31b88
Apply a blanket renaming in multiqc to catch inconsistent naming pair…
pinin4fjords Jul 12, 2024
6dcf3fd
Switch renaming to exact matches
pinin4fjords Jul 12, 2024
5c1db07
update snapshot
maxulysse Jul 12, 2024
e12ea63
Bump multiqc module
pinin4fjords Jul 12, 2024
47484f6
Separate rename patterns for forward and reverse
pinin4fjords Jul 12, 2024
6fccd13
update CHANGELOG
pinin4fjords Jul 12, 2024
c465f90
Remove Azure specific guidance
adamrtalbot Jul 12, 2024
e057134
Merge branch 'dev' into update-azure-batch-guidance
adamrtalbot Jul 12, 2024
17444ff
Update CHANGELOG.md
adamrtalbot Jul 12, 2024
39071b9
simplify logic to generate renaming table
pinin4fjords Jul 15, 2024
ccd95ab
Merge pull request #1340 from nf-core/update-azure-batch-guidance
pinin4fjords Jul 15, 2024
9135a7a
Merge branch 'dev' into rename_samples
pinin4fjords Jul 15, 2024
c016418
Update CHANGELOG
MatthiasZepper Jul 15, 2024
99fb7ef
Merge pull request #1314 from lazappi/annotation-documentation
MatthiasZepper Jul 15, 2024
a090530
Make name replacement specific to samples without tech reps
pinin4fjords Jul 15, 2024
c1e179b
Merge branch 'rename_samples' of https://github.com/nf-core/rnaseq in…
pinin4fjords Jul 15, 2024
182f523
Clarify comment
pinin4fjords Jul 15, 2024
d7ed353
Update main.nf
pinin4fjords Jul 15, 2024
f35f51b
Update CHANGELOG.md
pinin4fjords Jul 15, 2024
e1b2ef7
Merge pull request #1341 from nf-core/rename_samples
pinin4fjords Jul 15, 2024
b9ae33c
Merge branch 'dev' into use_nf_test_action
pinin4fjords Jul 15, 2024
66f3594
Merge pull request #1336 from adamrtalbot/use_nf_test_action
pinin4fjords Jul 15, 2024
3c9250d
Merge branch 'dev' into stubs_everywhere
maxulysse Jul 16, 2024
7315386
Factor out preprocessing logic to nf-core subworkflow
pinin4fjords Jul 16, 2024
2389882
update changelog
pinin4fjords Jul 16, 2024
4d30844
Update RNAseq preprocessing swf
pinin4fjords Jul 17, 2024
9e8f1e0
update modules.json
pinin4fjords Jul 17, 2024
6a22103
fix up ribo db wiring
pinin4fjords Jul 17, 2024
2447c6b
Install swf from branch for now
pinin4fjords Jul 17, 2024
3da0bc3
Fix tests
pinin4fjords Jul 17, 2024
259dccf
Update modules.json
pinin4fjords Jul 17, 2024
fe950ba
Move strandedness function testing to swf
pinin4fjords Jul 17, 2024
6bb1a79
Install from modules master
pinin4fjords Jul 17, 2024
1049fa5
Strip preprocessing components relocated to subworkflows
pinin4fjords Jul 17, 2024
5507a6d
Merge branch 'factor_out_preprocessing' of https://github.com/nf-core…
pinin4fjords Jul 17, 2024
5bd04b4
Merge pull request #1342 from nf-core/factor_out_preprocessing
pinin4fjords Jul 17, 2024
42d80fa
Fix the new call to preprocessing subworkflow
pinin4fjords Jul 19, 2024
b8160d4
Fix the new call to preprocessing subworkflow
pinin4fjords Jul 19, 2024
3e293a8
Fix the new call to preprocessing subworkflow
pinin4fjords Jul 19, 2024
141fa45
Merge branch 'fix_preprocessing_call' of github.com:nf-core/rnaseq in…
pinin4fjords Jul 19, 2024
6c8aa0b
Remove print
pinin4fjords Jul 19, 2024
4ed0cc6
update changelog
pinin4fjords Jul 19, 2024
809f060
Merge pull request #1345 from nf-core/fix_preprocessing_call
pinin4fjords Jul 19, 2024
8052b6b
Merge branch 'dev' into stubs_everywhere
maxulysse Jul 22, 2024
8b28fee
update nf-test to 0.9.0
maxulysse Jul 22, 2024
3eaf7a4
sort
maxulysse Jul 22, 2024
86bac63
update all modules/subworkflows + remove tags
maxulysse Jul 22, 2024
ee285c8
remove tags
maxulysse Jul 22, 2024
88286cd
keep card 3.1.1 that does not break CI due to weird RG
maxulysse Jul 22, 2024
f5adb7a
update snapshot
maxulysse Jul 22, 2024
d1c19be
update snapshot
maxulysse Jul 22, 2024
f94beb3
update all modules + subworkflows / remove tags + path markduplicates
maxulysse Jul 22, 2024
784aeb2
update snapshots
maxulysse Jul 22, 2024
30afc0e
update stringtie_stringtie
maxulysse Jul 22, 2024
58cee58
update snapshots for fastq_align_hisat2
maxulysse Jul 22, 2024
586058b
add proper stubs and tests for local star_*_igenomes modules
maxulysse Jul 22, 2024
61def16
Bump resource bucket for genomecov
pinin4fjords Aug 7, 2024
1e611b1
Revert "Bump resource bucket for genomecov"
pinin4fjords Aug 7, 2024
0af6da7
Update bedtools/genomecov for lower-resource sort
pinin4fjords Aug 7, 2024
add81e8
Update changelog
pinin4fjords Aug 7, 2024
6a508f0
Merge pull request #1350 from nf-core/bump_bedtools_mem
pinin4fjords Aug 7, 2024
5c0adce
Try multiqc fixes
pinin4fjords Aug 7, 2024
97a4530
Fix rename patterns
pinin4fjords Aug 8, 2024
25f3628
Import tsv func from nf-core subworkflow
pinin4fjords Aug 8, 2024
5663692
Better define ordering
pinin4fjords Aug 8, 2024
7dc68d6
Add new header, define some sections, reinstate trimming status repor…
pinin4fjords Aug 8, 2024
56a8d77
Fix up methods and versions passed to MultiQC
pinin4fjords Aug 9, 2024
be5825c
Attempt a rational fixed ordering of sections
pinin4fjords Aug 9, 2024
f87b645
Temp fix pending suworkflow update
pinin4fjords Aug 9, 2024
e5c0207
update subworkflow from nf-core
pinin4fjords Aug 9, 2024
d858577
update changelog
pinin4fjords Aug 9, 2024
4abc514
correct conditional for salmon indexing in proprocessing workflow
pinin4fjords Aug 15, 2024
0e6d601
Update CHANGELOG.md
pinin4fjords Aug 15, 2024
c1809d1
Merge pull request #1353 from nf-core/prepro_indexing_fix
pinin4fjords Aug 16, 2024
32a6440
Merge branch 'dev' into stubs_everywhere
maxulysse Aug 16, 2024
f77e714
proper sha for module bedtools/genomecov
maxulysse Aug 16, 2024
200d4bd
update samtools/stats module + rm tags
maxulysse Aug 16, 2024
addb735
Merge branch 'dev' into harmonize_new_for_multiqc
pinin4fjords Aug 16, 2024
cdbfcda
Update multiqc for prefix usage
pinin4fjords Aug 19, 2024
23717f3
tiny updates on subway map
maxulysse Aug 19, 2024
07c81e8
realign
maxulysse Aug 19, 2024
49fb5a8
tiny fixes
maxulysse Aug 19, 2024
fd5ba8c
update CHANGELOG
maxulysse Aug 19, 2024
bd83a81
Update CHANGELOG.md
maxulysse Aug 19, 2024
cbbe64a
Bump multiqc
pinin4fjords Aug 20, 2024
03daccd
Unset multiqc prefix for testing
pinin4fjords Aug 20, 2024
ad67c51
Merge pull request #1355 from maxulysse/subway_map_one_more_time
maxulysse Aug 20, 2024
dabbdaa
Merge branch 'dev' into harmonize_new_for_multiqc
pinin4fjords Aug 20, 2024
10a73f5
Update workflows/rnaseq/main.nf
pinin4fjords Aug 20, 2024
cb53ef3
Merge pull request #1352 from nf-core/harmonize_new_for_multiqc
pinin4fjords Aug 20, 2024
34fecc9
Merge branch 'dev' into stubs_everywhere
maxulysse Aug 20, 2024
3088bde
clean up stub tests
maxulysse Aug 20, 2024
93bb601
Fix anchor issue in multiqc
pinin4fjords Aug 20, 2024
9a00dbe
Update CHANGELOG.md
pinin4fjords Aug 20, 2024
75995bf
Merge pull request #1357 from nf-core/fix_anchor_issue
pinin4fjords Aug 20, 2024
a0499c8
Merge branch 'dev' into stubs_everywhere
maxulysse Aug 20, 2024
56539ac
update CHANGELOG
maxulysse Aug 20, 2024
7c189de
Animate subway map
maxulysse Aug 20, 2024
a68cb69
update snapshot
maxulysse Aug 20, 2024
1b34d1e
update snapshot
maxulysse Aug 21, 2024
ad43736
Merge pull request #1335 from maxulysse/stubs_everywhere
maxulysse Aug 21, 2024
4028290
Update test_full.config to restore a static URI for megatests
pinin4fjords Aug 21, 2024
d5da4bc
Update CHANGELOG.md
pinin4fjords Aug 21, 2024
bef25b6
use permalink
pinin4fjords Aug 21, 2024
065f5ad
Same for minimal tests
pinin4fjords Aug 21, 2024
04b147b
Update CHANGELOG.md
pinin4fjords Aug 21, 2024
8d11ea1
fix double reference
pinin4fjords Aug 21, 2024
9c52b08
Merge branch 'static_uri_megatests' of github.com:nf-core/rnaseq into…
pinin4fjords Aug 21, 2024
eff73a9
Fix input
pinin4fjords Aug 21, 2024
4a01a63
Merge pull request #1358 from nf-core/static_uri_megatests
pinin4fjords Aug 21, 2024
4464227
Revert multiqc workaround due to fix
pinin4fjords Aug 21, 2024
9130eea
Update changelog
pinin4fjords Aug 21, 2024
27d8091
Update changelog
pinin4fjords Aug 21, 2024
852dae1
snapshot all files contents by default
maxulysse Aug 21, 2024
1087b26
animate metro map
maxulysse Aug 21, 2024
7339ac8
Merge branch 'dev' into moar_snapshots
maxulysse Aug 21, 2024
b622978
Merge branch 'dev' into animate_subway
maxulysse Aug 21, 2024
8eb1311
fix MultiQC paths
maxulysse Aug 22, 2024
52de9f6
Install properly
pinin4fjords Aug 22, 2024
f6af6d9
Merge pull request #1359 from nf-core/revert_multiqc_workaround
pinin4fjords Aug 22, 2024
5708f7a
Merge branch 'dev' into animate_subway
maxulysse Aug 22, 2024
9e8f6cb
Tidy up multiqc test config
pinin4fjords Aug 22, 2024
8553a92
Add module config
pinin4fjords Aug 22, 2024
1632f4e
Update changelog
pinin4fjords Aug 22, 2024
ee0ad86
Install changes from modules
pinin4fjords Aug 22, 2024
6588b06
Merge pull request #1362 from nf-core/multiqc_test_config
maxulysse Aug 22, 2024
2265fac
update test and snapshot
maxulysse Aug 22, 2024
bf92d59
Merge branch 'dev' into moar_snapshots
maxulysse Aug 22, 2024
434a440
update MultiQC paths
maxulysse Aug 22, 2024
b7c780f
sort files
maxulysse Aug 22, 2024
aa1e6a9
update test and snapshot
maxulysse Aug 22, 2024
60ca773
update test and snapshot
maxulysse Aug 22, 2024
f8b1d3f
more snapshots
maxulysse Aug 22, 2024
c1d2f6a
update test and snapshot
maxulysse Aug 22, 2024
d03451e
update CHANGELOG
maxulysse Aug 22, 2024
c4a3dde
update test and snapshot
maxulysse Aug 22, 2024
e8cd2ac
update test and snapshot
maxulysse Aug 22, 2024
861c084
revert update CHANGELOG
maxulysse Aug 22, 2024
46e75d7
update test and snapshot
maxulysse Aug 22, 2024
914565f
Merge branch 'dev' into animate_subway
maxulysse Aug 22, 2024
09922ea
update CHANGELOG
maxulysse Aug 22, 2024
eedeb4f
text to path
maxulysse Aug 22, 2024
162c8b2
typo
maxulysse Aug 22, 2024
9a04059
more snapshots
maxulysse Aug 22, 2024
ab00caa
text to path
maxulysse Aug 22, 2024
f1867ad
update snapshots
maxulysse Aug 23, 2024
8802e2b
fastqc html are not stable
maxulysse Aug 23, 2024
85cf31e
update tests and snapshots
maxulysse Aug 23, 2024
12dfaed
update tests and snapshots
maxulysse Aug 23, 2024
01fadc1
update tests and snapshots
maxulysse Aug 23, 2024
f0f13fe
update tests and snapshots
maxulysse Aug 23, 2024
93cb05e
kallisto
maxulysse Aug 23, 2024
3c8bc75
Add link to static version
maxulysse Aug 23, 2024
c64c033
kallisto with snapshots
maxulysse Aug 23, 2024
0c296e5
kallisto updated snapshots
maxulysse Aug 23, 2024
792c809
min_mapped_reads snapshots
maxulysse Aug 23, 2024
8c7aa24
min_mapped_reads better snapshots
maxulysse Aug 23, 2024
33b34e7
fix stub snap
maxulysse Aug 23, 2024
8dd8c01
remove_ribo_rna snapshots
maxulysse Aug 23, 2024
8f9f874
update remove_ribo_rna snapshots
maxulysse Aug 26, 2024
715adf1
Merge pull request #1361 from maxulysse/animate_subway
maxulysse Aug 26, 2024
35c78e7
Merge branch 'dev' into moar_snapshots
maxulysse Aug 26, 2024
51b1b0f
salmon snapshots + update moar snapshots
maxulysse Aug 26, 2024
1426616
skip_qc snapshots
maxulysse Aug 26, 2024
3cf398a
update tests and snapshots
maxulysse Aug 26, 2024
439ae75
fix tests and snapshots
maxulysse Aug 26, 2024
c5f26a9
skip_trimming test and snapshots
maxulysse Aug 26, 2024
96b4369
update test and snapshots
maxulysse Aug 26, 2024
515f182
fix linting + star_rsem tests and snapshots
maxulysse Aug 26, 2024
14c5118
update CHANGELOG
maxulysse Aug 26, 2024
1ad7865
fix merge conflicts
maxulysse Aug 26, 2024
056ce81
update tests
maxulysse Aug 26, 2024
e4cfa09
update tests and snapshots
maxulysse Aug 26, 2024
8679eda
Merge pull request #1360 from maxulysse/moar_snapshots
maxulysse Aug 27, 2024
faabb90
update fastqc module
maxulysse Aug 28, 2024
96e3034
update utils subworkflows
maxulysse Aug 28, 2024
d513df5
use proper script for dupradar
maxulysse Aug 28, 2024
4f35611
no need for tags
maxulysse Aug 28, 2024
6688d46
no need for tags
maxulysse Aug 28, 2024
73504a6
update CHANGELOG
maxulysse Aug 28, 2024
b59f27f
Merge pull request #1363 from maxulysse/last_fix_before_3-15
maxulysse Aug 28, 2024
fc13650
Add umicollapse as an alternative to umi-tools
siddharthab Sep 3, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
update all subworkflows
  • Loading branch information
maxulysse committed Jul 2, 2024
commit b796fc0304558a0b40fbeb3df95272c6271c7453
2 changes: 1 addition & 1 deletion modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -310,7 +310,7 @@
},
"fastq_align_hisat2": {
"branch": "master",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
Expand Down
1 change: 0 additions & 1 deletion subworkflows/nf-core/fastq_align_hisat2/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

15 changes: 15 additions & 0 deletions subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 2 additions & 0 deletions subworkflows/nf-core/fastq_align_hisat2/tests/tags.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading