SPADES changed flag for single-read in illumina reads

[aidaanva]

PR checklist

Changed flag for single-read illumina reads to --s, since -s is used in spades for singletons from a pair-end library (see Input data in https://github.com/ablab/spades/blob/spades_3.15.5/README.md)

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[aidaanva]

Is this actually correct? --s comes under the 'multiple libraries' section, where my understanding of the implementation of this module is that it only ever accepts a single library (i.e. -1 vs -2, rather than --pe-1 -0pe-2 etc.?

The docs below would imply to me that for single-end libraries you would just give -1?

I tried to add the -1 flag as suggested by @jfy133, however when I used the -1 flag for the single-end alone the following error occurs:

== Error ==  the number of files with left paired reads is not equal to the number of
         files with right paired reads (library number: 1, library type: paired-end)! 

When I used the `--s1`` the input is interpreted correctly:

Dataset parameters:
  RNA virus assembly mode
  Metagenomic mode
  Reads:
    Library number: 1, library type: single
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/private/var/folders/1c/72tb52hs181_9xn2l2s9xt4m0000gp/T/tmp51itgo6g/63/1b394bce5e84e0aff90f28e1af303c/test_2.fastq.gz']
      merged reads: not specified

But I agree that the documentation seems to indicate otherwise

[SPPearce]

@aidaanva , do you need some help to get this finished off?

[aidaanva]

Hi @SPPearce, I just returned from maternity leave, I will try to get to this within the next month.

[luisas]

@aidaanva We are doing some nf-core cleaning and trying to close PRs when not used anymore (they can be reopened in the future ofc). Just to know, are you planning to work on this one? :)

[aidaanva]

I donor have the time to work on this one right now. I will reopen it when I have the time. Thank you for asking.

[luisas]

@aidaanva All cool! Thanks for replying.

I will close it then :)