v0.1.0

0.1.0 (2026-09-30)

Added

• adapter and quality trimming for the scRNA and scTIP arms (7981847)
• add the --stop_after stage flag (a83a30a), closes #8
• add the arm fan-out and the per-arm read-count gate (da31747), closes #5
• add the carmack_readprep subworkflow with R2 carry-through (a57a5b5), closes #4
• add the four carmack read-prep modules (1a1a8fd), closes #3
• add the scRNA arm with per-arm FastQC and STARsolo (b4a3c65), closes #6
• add the scTIP arm with QNAME retagging and umi_tools dedup (4d005c8), closes #7
• bump carmack to 6816691 and finish the MultiQC integration (5b8c7d8), closes #9
• carmack: run carmack from neurogenomics/carmack's published image (6e3e43b)
• carmack: run carmack from neurogenomics/carmack's published image (#49) (9cd96a7)
• core skeleton — carmack read prep, gated arm fan-out, alignment (3c58a74)
• input: merge a sample's flowcell lanes before read prep (68345de)
• input: merge a sample's flowcell lanes before read prep (#35) (81b6463)
• lineardedup: add the carmack linear-dedup module (ab5d214), closes #21
• require fastq_2 and add the SK609 test fixtures (8c87c29), closes #2
• scrna: expose STARsolo multimappers and an optional tagged BAM (#30, #31) (751beac)
• scrna: paired forward-stranded STARsolo counting, multimapper option and a tagged BAM (f650edd)
• sctip: run linear deduplication behind --skip_linear_dedup (18be204), closes #22
• sctip: single-cell linear deduplication for the scTIP arm (5a2a25d)
• trim the scRNA arm with fastp and resync its barcode read (855fd6d), closes #15
• trim the scTIP arm with fastp before alignment (e7d535f), closes #14

Fixed

• bump carmack to ffa5349 and resync the nf-test fixtures (5e52f8e), closes #17
• carmack: pin the image to the submodule's sha tag (#49) (93a00c6)
• close the gaps a whole-epic review found (cc5b8e8)
• fastp: lower the scTIP length floor to 20 and hide the insert-size plot (153ecb5)
• input: reject a FASTQ listed on two rows and log each lane merge (c55d4b5), closes #35
• multiqc: hide fastp's insert-size plot (#42) (6d99fe4)
• scrna: count the scRNA arm forward-stranded (#37) (70e9586)
• scrna: count unstranded reads with --soloStrand Unstranded (#29) (751beac), closes #30 #31
• scrna: map both cDNA mates in STARsolo (#38) (94376f0)
• sctip: keep bowtie2's output in input order (#46) (0dd1b4a)
• sctip: lower fastp's length floor from 25 to 20 (#41) (8dd8112)
• sctip: set bowtie2's alignment options and expose --min_mapq (69061b5)

Changed

• carmack: bump to 01f2d18, bounding linear dedup's memory by chromosome (b0116c7), closes #20

Documentation

• flag the pipeline as incomplete and under development (c59988d)