prep release 0.41.0 #359
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prep release 0.41.0 #359
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when pruning, only remove ports that do not appear in splice edges (aka replacement edges)
…_duplexseq param files
Stage2 init options
Samtools/htslib 1.21
Added dependabot.yml to auto-update GitHub actions
Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
…ns/checkout-4 Bump actions/checkout from 3 to 4
…ns/cache-4 Bump actions/cache from 3 to 4
…ns/upload-artifact-4 Bump actions/upload-artifact from 3 to 4
"standard" (samtools markdup method, no split, target alignment); non-consented human split (samtools markdup method, build37 human ref with bwa aln, target alignment); y-split with no target alignment (samtools markdup method, target alignments [to human] reset after y-split)
…duction version of bwa move time-consuming libmaus2 library build further down the list
Container analyses static data
remove blank lines from alignment_wtsi_stage2_template.json
add new P4 explainer README.md
add FASTQ input option to non-consented human split analysis
documenting alternative ways of visualising
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merge devel to master