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Missing input files for rule generate_web_visualization #139

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carlottaolivero opened this issue Mar 8, 2023 · 0 comments
Open

Missing input files for rule generate_web_visualization #139

carlottaolivero opened this issue Mar 8, 2023 · 0 comments

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@carlottaolivero
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Hi,
I have installed v-pipe and modified the config.yaml and created the folder "samples".
I tried the ./vpipe --dryrun and I've got:

VPIPE_BASEDIR = /Users/opentrons-b10/V-pipe/workflow
Using base configuration virus SARS-CoV-2
WARNING: protocols YAML look-up file </Users/opentrons-b10/V-pipe/workflow/../resources/sars-cov-2/primers.yaml> specified, but no sample ever uses it: fourth column absent from samples TSV file.
Building DAG of jobs...
MissingInputException in rule generate_web_visualization in file /Users/opentrons-b10/V-pipe/workflow/rules/visualization.smk, line 10:
Missing input files for rule generate_web_visualization:
output: samples/20230220/torino/visualization/snv_calling.html, samples/20230220/torino/visualization/alignment.html, samples/20230220/torino/visualization/reference_uri_file, samples/20230220/torino/visualization/bam_uri_file
wildcards: dataset=samples/20230220/torino
affected files:
/Users/opentrons-b10/V-pipe/workflow/../resources/sars-cov-2/primers/v3/nCoV-2019.tsv

Could you please help me ion solving this issue?
many thanks for the help,
Carlotta Olivero

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