How to run `workflows original local nf` the temporary home nf-core #pathogenepidemiology

How to run `workflows/original_local.nf`, the temp...

Bilal Asser

09/04/2026, 12:47 PM

How to run

workflows/original_local.nf

, the temporary home of the code that wraps the rest of

nf-core/pathogenepidemiology

ncbi.nlm.nih.gov/Traces/study?acc=ERP158273&f=instrument_s%3An%3Bl…&… source attached: • SRA accession list/metadata for dataset I have been using (127 samples: 73 ONT, 54 ILL. See metadata because there are a couple of nuances we want to use later for testing) • shell script

get_dataset

to download subset of this dataset (just sets parameters for

nf-core/fetchngs

and makes use of the directory

testing

existing in

.gitignore

but you could use whatever ignored paths you like) Call I have been using to test the

<http://original_local.nf|original_local.nf>

executable:

nextflow run workflows/original_local.nf --threads 7 --clair3model r941_prom_hac_g360+g422    -profile docker,gpu --validation_monochromeLogs false

but you can surely just run:

nextflow run workflows/original_local.nf --threads 7 -profile docker

you'll get some harmless warnings, I expect

get_dataset SraRunTable.csv SRR_Acc_List.csv

Bilal Asser

09/04/2026, 12:57 PM

(not tested with any other environment manager than docker)

Bilal Asser

09/04/2026, 1:04 PM

I would also recommend sticking to a number of threads that leaves something free while the slowest step

bbduk

runs (with the number of threads supplied in the arg) 7 is what I chose because: 8-thread CPU -> 1x 7-threaded bbduk process and 1x free thread for faster processes 16-thread CPU -> 2x 7-threaded bbduk process and 2x free thread for faster processes etc.

Bilal Asser

09/24/2026, 5:59 PM

This version of the Acc list contains amplicon and WGS samples from short and long read techs. Unfortunately there is a problem column to the samplesheet it generates (at least one row contains a wall of text with special characters). The problem column can be removed with:

REPO=/path/to/your/pathogenepidemiology/nf-core-pathogenepidemiology

python3 -c "

import csv, os

src = '$REPO/path/to/samplesheet/samplesheet.csv'

dst = src + '.tmp'

with open(src, newline='') as f, open(dst, 'w', newline='') as g:

r = csv.reader(f); w = csv.writer(g)

header = next(r)

idx = header.index('sample_description')

w.writerow([x for i, x in enumerate(header) if i != idx])

for row in r:

if len(row) != len(header):

continue

w.writerow([x for i, x in enumerate(row) if i != idx])

os.replace(dst, src)

wc -l $REPO/path/to/samplesheet/samplesheet.csv

head -1 $REPO/path/to/samplesheet/samplesheet.csv | tr ',' '\n' | grep -c sample_description

SRR_Acc_List.csv

Bilal Asser

09/26/2026, 7:12 AM

https://github.com/nf-core/pathogenepidemiology/issues/26 please read, relates to sampleset choice

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