Update #1
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Update #1
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…r spatial_filter and tag_metrics for subsampling)
Merging early for temporary development burst.
remove --reference flag from samtools split command partially deals with #242
…salmon_cmd Support single-end libraries and wrap salmon command for validation and clean exiting
merge-aware nchs
* move adapterfind node to be in parallel with phix alignment in stage1 * stage1 outputs (plexed ord lane-level) can be cram or bam * merge input files using samtools merge instead of bamcat (inputs can be either bam or cram) * stage1 output format for lane-level was hard-coded to bam - corrrected to use the s1_output_format parameter value
…ard format (F0x000 instead of F0x00)
add qc check for samtools_stats (package lane level stats as JSON)
- Supports sinle-end libraries - Uses scramble to convert output from SAM to BAM (use samtools instead?)
- Add a post-alignment name sort to eliminate a bam12auxmerge failure. - Fastq input files extension has to be ".fq.gz" (and not just ".fq").
Add HISAT2 alignment
Use compressed fastq inputs in STAR alignment
release 0.24.0 prep: merge devel to master
use hisat2 -U flag for single-end reads
single-end flag change for hisat2 (update release 0.24.0)
wtsi-npg/devel into srl147/devel
fixed Not enough reads to run Salmon check
merge from devel to master to create release 0.24.1
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] <support@github.com>
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] <support@github.com>
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] <support@github.com>
…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
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