LongPlex-v3.3

1. Update main.nf to support cases where the lima process produces only one output file.

LongPlex-v3.2

1. The --peek-guess option was removed from the Lima process to ensure that less abundant reads are not missed during demultiplexing.

LongPlex-v3.1

1. remove lima report from MULTIQC report due to MULTIQC version bump.
2. use a new version of longplexpy (longplexpy@0.2.2), which fixed the lima count file parsing due to using new version of lima (2.7.0 to 2.13.0)

LongPlex-v3.0

change_log: change the lima version from lima:2.7.1 to lima:2.13.0 by using the docker image quay.io/biocontainers/lima:2.13.0--h9ee0642_0. The summary R file is updated correspondingly.

2.1.0

What's Changed

• feat: support deployment of this pipeline on Latch by @clintval in #2
• feat: add a conda profile and environment file by @znorgaard in #3
• feat: use longplexpy multiqc plugin by @znorgaard in #4
• chore: create new latch release by @znorgaard in #5

New Contributors

• @clintval made their first contribution in #2
• @znorgaard made their first contribution in #3

Full Changelog: LongPlex-v2.0...2.1.0

LongPlex-v2.0

LongPlex-v2.0 uses lima summary from the first-step lima process ( neighbor, both end) to remove chimeric hybrid from the unbarcoded bam file after the first-step lima process. BBduk filtering process is therefore removed.

LongPlex-v1.0: Update nextflow.config

This is the work flow in nextflow to do demultiplex on pacbio data for seqWell longplex kit. Released on 20240708.