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cbg-ethz / V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes
https://cbg-ethz.github.io/V-pipe/
Apache License 2.0
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Missing input files for rule generate_web_visualization #139

Open carlottaolivero opened 1 year ago

carlottaolivero commented 1 year ago

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