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35 workflow runs

35 workflow runs

feat: include pseudogenes in GFF annotation parsing and featureCounts BactSeq CI #168: Commit db9232d pushed by adamd3

9m 25s main

main

9m 25s

feat: include pseudogenes in GFF annotation parsing and featureCounts BactSeq CI #167: Commit 713b15f pushed by adamd3

6m 39s develop

develop

6m 39s

Replace Trim Galore! with fastp for read trimming and QC BactSeq CI #166: Commit ee67838 pushed by adamd3

8m 5s develop

develop

8m 5s

Merge pull request #21 from adamd3/develop BactSeq CI #165: Commit 73442f2 pushed by adamd3

35m 31s develop

develop

35m 31s

Merge pull request #21 from adamd3/develop BactSeq CI #164: Commit 73442f2 pushed by adamd3

8m 37s main

main

8m 37s

Merge develop into main: TPM, efficient counting, sort CPU fix BactSeq CI #163: Pull request #21 opened by adamd3

2m 33s develop

develop

2m 33s

Merge remote-tracking branch 'origin/main' into develop BactSeq CI #162: Commit d4f0537 pushed by adamd3

9m 0s develop

develop

9m 0s

fix: prevent samtools sort being allocated 0 cpus when task cpus is 1 BactSeq CI #161: Commit d6801e6 pushed by adamd3

11m 2s develop

develop

11m 2s

feat: more efficient counting of mapped reads and fragments BactSeq CI #160: Commit b80d459 pushed by adamd3

9m 35s develop

develop

9m 35s

fix: output tpm from normalisation module BactSeq CI #159: Commit cee032a pushed by adamd3

6m 6s develop

develop

6m 6s

fix: implement log2 transformation when specified BactSeq CI #158: Commit 08437ac pushed by adamd3

7m 12s develop

develop

7m 12s

feat: change RPKM to TPM for gene length normalisation BactSeq CI #157: Commit cd2c762 pushed by adamd3

2m 3s develop

develop

2m 3s

Merge pull request #20 from adamd3/develop BactSeq CI #156: Commit d7b8661 pushed by adamd3

8m 54s main

main

8m 54s

Add paired-end test data, config profile, and CI matrix testing BactSeq CI #155: Pull request #20 opened by adamd3

2m 24s develop

develop

2m 24s

Add paired-end test data, config profile, and CI matrix testing BactSeq CI #154: Commit 0ca68d4 pushed by adamd3

3m 57s develop

develop

3m 57s

Automatically infer paired-end status from sample sheet BactSeq CI #153: Commit 39df351 pushed by adamd3

4m 8s develop

develop

4m 8s

Refactor count processing and differential expression (#19) BactSeq CI #152: Commit 4b69db5 pushed by adamd3

9m 1s develop

develop

9m 1s

Refactor count processing and differential expression (#19) BactSeq CI #151: Commit 4b69db5 pushed by adamd3

12m 11s main

main

12m 11s

Refactor count processing and differential expression BactSeq CI #150: Pull request #19 opened by adamd3

2m 20s develop

develop

2m 20s

fix: create contrast list cleanly BactSeq CI #149: Commit 8200c10 pushed by adamd3

5m 9s develop

develop

5m 9s

fix: make meta and counts match robustly BactSeq CI #148: Commit b0bc202 pushed by adamd3

4m 22s develop

develop

4m 22s

fix: sanitise names in counts data BactSeq CI #147: Commit 8c4954a pushed by adamd3

4m 25s develop

develop

4m 25s

fix: package loading for tidyverse BactSeq CI #146: Commit 2b5f58c pushed by adamd3

4m 32s develop

develop

4m 32s

refactor: extract locus tags and gene names BactSeq CI #145: Commit 199d256 pushed by adamd3

4m 38s develop

develop

4m 38s

refactor: tidy functional enrichment steps BactSeq CI #144: Commit 9179ffe pushed by adamd3

4m 30s develop

develop

4m 30s