The covid-assembly from scaramir

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Project 2 from SC2 @ FUB This project is currently still in progress, therefore the code is not cleaned yet and still contains some unnecessary comments.

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Error: Missing input files for rule pangolin:

Hey, thanks for the nice pipeline and manual ;)

I downloaded everything like shown in the README.md and also checked the default config file which seemed fine (but maybe I overlooked smt).

Then I did:

conda activate snakemake
snakemake --cores 8 --use-conda

which produces the output and error:

                                                         R1                                                 R2
sample
          data/sc2-nanopore-illumina-reads/illumina/._il...  data/sc2-nanopore-illumina-reads/illumina/._il...
illumina  data/sc2-nanopore-illumina-reads/illumina/illu...  data/sc2-nanopore-illumina-reads/illumina/illu...
                                                         R1
sample
          data/sc2-nanopore-illumina-reads/nanopore/._na...
nanopore  data/sc2-nanopore-illumina-reads/nanopore/nano...
Building DAG of jobs...
File path results/qualimap//qualimapReport.html contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path results/qualimap//qualimapReport.html contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
MissingInputException in rule pangolin in file /scratch/hoelzerm/projects/2023-09-29-fu-smk-test/Covid-Assembly/workflow/rules/consensus.smk, line 51:
Missing input files for rule pangolin:
    output: results/consensus/lineage.csv
    affected files:
        results/consensus/_consensus.fasta

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