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This fixes Issue52: Sync with latest pggb #57

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merged 2 commits into from
Mar 22, 2021
Merged

This fixes Issue52: Sync with latest pggb #57

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cfc9073
Merge pull request #12 from nf-core/dev
subwaystation Mar 22, 2021
20a1c9d
update with pggb docker image 20210311083535c7fe1e
subwaystation Mar 22, 2021
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM ghcr.io/pangenome/pggb:202103011405301384b0
FROM ghcr.io/pangenome/pggb:20210311083535c7fe1e
LABEL authors="Simon Heumos, Michael Heuer, Lukas Heumos, Erik Garrison, Andrea Guarracino" \
description="Docker image containing all software requirements for the nf-core/pangenome pipeline"

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4 changes: 3 additions & 1 deletion main.nf
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Expand Up @@ -236,7 +236,7 @@ process odgiChop {
path("${graph}.chop.og")

"""
odgi chop -i $graph -c 100 -o ${graph}.chop.og
odgi chop -i $graph -c 100 -o ${graph}.chop.og -t ${task.cpus}
"""
}

Expand Down Expand Up @@ -275,6 +275,7 @@ process odgiDraw {
"""
}

// TODO ONCE OUR CUSTOM MULTIQC VERSION IS IN A MULTIQC RELEASE, WE CAN CHANGE THIS
process multiQC {
publishDir "${params.outdir}", mode: "${params.publish_dir_mode}"

Expand Down Expand Up @@ -341,6 +342,7 @@ workflow {
// include { FASTQC } from './modules/nf-core/fastqc' params(params)
// include { MULTIQC } from './modules/nf-core/multiqc' params(params)

// TODO REMOVE THIS ONCE WE TOOK CARE OF nextflow_schema.json
def helpMessage() {
// TODO nf-core: Add to this help message with new command line parameters
log.info nfcoreHeader()
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4 changes: 4 additions & 0 deletions nextflow.config
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Expand Up @@ -58,6 +58,10 @@ params {
smoothxg_consensus_spec = "10,100,1000,10000"
smoothxg_block_id_min = 0
smoothxg_ratio_contain = 0
// poa param suggestions from minimap2
// - asm5, --poa-params 1,19,39,3,81,1, ~0.1 divergence
// - asm10, --poa-params 1,9,16,2,41,1, ~1 divergence
// - asm20, --poa-params 1,4,6,2,26,1, ~5% divergence
smoothxg_poa_params = "1,4,6,2,26,1"

// Boilerplate options
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