A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I’m curious if anyone has a valdiated set of flags for running on Plasmidsaurus “raw” FASTQs. This service saves a ton of money based on our in-house sequencing but they are a bit opaque on methods. Based on their <https://plasmidsaurus.com/technical-documentation/rna|documentation>, it seems that ideally:
1. Length correction should be disabled (because it is 3' sequencing)
2. PolyA trimming should _maybe_ be performed
3. UMI deduplication should be performed
So something along these lines?

```extflow run nf-core/rnaseq -r 3.26.0 \
    --input samplesheet.csv \
    --outdir results \
    --fasta genome.fa.gz \
    --gtf annotation.gtf.gz \
    --aligner star_salmon \
    --extra_salmon_quant_args "--noLengthCorrection" \
    --extra_star_align_args "--outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA" \
    --with_umi \
    --umi_dedup_tool umicollapse \
    &lt;PLASMIDSAURUS_SPECIFIC_UMI_ARGUMENTS&gt;```
If anyone has a working submission script I would very much appreciate!

In case anyone runs into the same question: based on conversations with their technical support and some experimentation, these parameters appear to work

```trimmer: "fastp"
extra_fastp_args: "--trim_poly_x"
extra_salmon_quant_args: "--noLengthCorrection"

with_umi: true
skip_umi_extract: true
umi_dedup_tool: "umicollapse"
umitools_umi_separator: "_"```