First release PR (version bumped to 1.0.0)

[vagkaratzas]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• [✓ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• [✓ ] If necessary, also make a PR on the nf-core/proteinfamilies branch on the nf-core/test-datasets repository.
• [✓ ] Make sure your code lints (nf-core pipelines lint).
• [✓ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [✓ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• [✓ ] Usage Documentation in docs/usage.md is updated.
• [✓ ] Output Documentation in docs/output.md is updated.
• [✓ ] CHANGELOG.md is updated.
• [✓ ] README.md is updated (including new tool citations and authors/contributors).

[jfy133]

Last couple of very minor comments on the pseudo PR but all my points addressed, this is good to go!

[jfy133]

I just noticed GitHub ACtions were entirely deactivated on this repository!?!?!

I've activated them now, and I have triggered an AWS full test to double check this is working

[jfy133]

OK the AWS test failed:

https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/BIbANt3VdGPQX

Error executing process > 'NFCORE_PROTEINFAMILIES:PROTEINFAMILIES:UPDATE_FAMILIES:CAT_HMM (mgnifams_update)'

Caused by:
  Cannot invoke method lastIndexOf() on null object -- Check script '.nextflow/assets/nf-core/proteinfamilies/./workflows/../subworkflows/local/remove_redundancy/../../../modules/nf-core/cat/cat/main.nf' at line: 77


Source block:
  def args = task.ext.args ?: ''
  def args2 = task.ext.args2 ?: ''
  def file_list = files_in.collect { it.toString() }
  prefix   = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}"
  out_zip  = prefix.endsWith('.gz')
  in_zip   = file_list[0].endsWith('.gz')
  command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
  command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
  if(file_list.contains(prefix.trim())) {
      error "The name of the input file can't be the same as for the output prefix in the " +
      "module CAT_CAT (currently `$prefix`). Please choose a different one."
  }
  """
  $command1 \\
      $args \\
      ${file_list.join(' ')} \\
      $command2 \\
      > ${prefix}
  
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS
  """

Container:
  wave.seqera.io/wt/2c9d512a8942/biocontainers/pigz:2.3.4

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

[jfy133]

@nf-core-bot fix linting

[edmundmiller]

LGTM!