Add trimming, fastqc, software versions, email notifications from nf-core

[olgabot]

• FastQC: checks quality of input reads
• fastp Trims low quality reads and poly-Ns (thanks @samlhao for the tip!)
• MultiQC: summarizes fastqc and fastp output
• Email notifications - not sure how to get these exactly working but supposedly this can work

[olgabot]

Something is really weird with conda environments here. The Dockerfile explicitly does conda init $(basename $SHELL) and exec $SHELL so conda activate should totally work. But somehow it doesn't and either way if one uses source activate or conda activate, it errors out.

Using source activate

ERROR ~ Error executing process > 'output_documentation (null)'

Caused by:
  Process `output_documentation (null)` terminated with an error exit status (1)

Command executed:

  source activate r
  markdown_to_html.r output.md results_description.html

Command exit status:
  1

Command output:
  (empty)

Command error:
  /opt/conda/envs/r/etc/conda/activate.d/activate-binutils_linux-64.sh: line 67: HOST: unbound variable

Work dir:
  /Users/olgabot/code/nf-kmer-similarity/work/6b/b914914f94ecd450c9f7687faf4920

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Using conda activate

ERROR ~ Error executing process > 'output_documentation (null)'

Caused by:
  Process `output_documentation (null)` terminated with an error exit status (1)

Command executed:

  conda activate r
  markdown_to_html.r output.md results_description.html

Command exit status:
  1

Command output:
  (empty)

Command error:

  CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
  To initialize your shell, run

      $ conda init <SHELL_NAME>

  Currently supported shells are:
    - bash
    - fish
    - tcsh
    - xonsh
    - zsh
    - powershell

  See 'conda init --help' for more information and options.

  IMPORTANT: You may need to close and restart your shell after running 'conda init'.


Work dir:
  /Users/olgabot/code/nf-kmer-similarity/work/cc/7d3048bf6f6fc52631ea548079f945

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