- fix #3

up: basecalling, nextflow.config, nextflow parameters and readability

See merge request !10

fix typos and missing parameters in the documentation.

remove redundant parameters in the human_blood profiles (most were
the same as the default ones).

 - Updated multiple variables in nextflow.config to match them across the different processes and workflows;
 - Added profiles in nextflow to facilitate the steps;
 - Added --kit-name configuration (params.barcoding_kit) to improve trimming during basecalling;
 - Changed descriptions across variables in nextflow.config;
 - Improved output directory name to include the projects' name (params.project_name);
 - Updated params.basecall_speed to use latest available simplex/modification model for basecalling;
 - Reorganized demux process to be included in the basecalling process to improve code readability;
 - Corrected few typos.

up: basecalling.nf code optmization

See merge request !8

 - added the nvidia-conatiner-toolkit dependency info in README.md
 - modified basecall.nf to improve output handling

- added echo logs for each step

- removed CPU process from basecalling since it was not needed.

fix strict syntax mentioned in #1

Closes #1

See merge request !7

Adds Nanopore Pipeline Image

See merge request !5

Organization

See merge request !6

up: dorado, modkit, multiQC and pycoQC (duceppemo fork); fix: container definitions to reduce image size.

See merge request !4

up: dorado, modkit, multiQC and pycoQC (duceppemo fork); fix: container definitions to reduce image size;

removed miniconda and replaced installs with apt/pip
installed samtools, bedtools via apt; pod5 and multiQC via pip
used pip options:
 `--no-cache-dir` to reduce image size
 `--break-system-packages` to bypass debian PEP 668 issue
updated timezone to Sao_Paulo
fixed plotly version conflict between pycoQC and MultiQC:
  edited pycoQC's `setup.py` inside container using:
   `sed -i 's/plotly==5.16.1/plotly==5.18.0/' setup.py`

Correção de estilo

See merge request !3

# Conflicts:
#   workflow/nextflow.config