adding Megahit separate module

README.md

@@ -35,7 +35,7 @@ This pipeline wraps up the following software:
 
 || **Source** |
 |:- | :- |
-| **Assemblers** | [Canu](https://github.com/marbl/canu), [Flye](https://github.com/fenderglass/Flye), [Raven](https://github.com/lbcb-sci/raven), [Shasta](https://github.com/chanzuckerberg/shasta), [wtdbg2](https://github.com/ruanjue/wtdbg2), [Haslr](https://github.com/vpc-ccg/haslr), [Unicycler](https://github.com/rrwick/Unicycler), [Spades](https://github.com/ablab/spades), [Shovill](https://github.com/tseemann/shovill) |
+| **Assemblers** | [Canu](https://github.com/marbl/canu), [Flye](https://github.com/fenderglass/Flye), [Raven](https://github.com/lbcb-sci/raven), [Shasta](https://github.com/chanzuckerberg/shasta), [wtdbg2](https://github.com/ruanjue/wtdbg2), [Haslr](https://github.com/vpc-ccg/haslr), [Unicycler](https://github.com/rrwick/Unicycler), [Spades](https://github.com/ablab/spades), [Shovill](https://github.com/tseemann/shovill), [Megahit](https://github.com/voutcn/megahit) |
 | **Polishers** | [Nanopolish](https://github.com/jts/nanopolish), [Medaka](https://github.com/nanoporetech/medaka), [gcpp](https://github.com/PacificBiosciences/gcpp), [Pilon](https://github.com/broadinstitute/pilon) |
 | **Quality check** | [QUAST](https://github.com/ablab/quast), [MultiQC](https://multiqc.info/) |
 

conf/base.config

@@ -1,6 +1,6 @@
 process {
 
-    // The defaults for all processes
+    // The defaults for all processes (without labels)
     cpus   = { params.max_cpus   }
     memory = { params.max_memory }
     time   = { params.max_time   }

conf/defaults.config

@@ -103,6 +103,9 @@ params {
   skip_unicycler = false                      // Hybrid and shortreads only assemblies
   unicycler_additional_parameters = null      // Must be given as shown in Unicycler manual. E.g. " --mode conservative --no_correct "
 
+  skip_megahit = false                        // Shortreads only assemblies
+  megahit_additional_parameters = null        // Must be given as shown in Megahit manual. E.g. " --presets meta-large "
+
   skip_haslr     = false                      // Hybrid assemblies
   haslr_additional_parameters = null          // Must be given as shown in Haslr manual. E.g. " --cov-lr 30 "
 

docs/_html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 887e9b50bee95a35f552f1f87891fdbc
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_html/_sources/config.rst.txt

@@ -0,0 +1,18 @@
+.. _config:
+
+Configuration File
+==================
+
+.. code-block:: bash
+
+  # To download a configuration file template users just need to run:
+  nextflow run fmalmeida/mpgap [--get_config]
+
+  # Using a config file your code is a lot more clean and concise:
+  nextflow run fmalmeida/mpgap -c [path-to-config]
+
+Main config file
+----------------
+
+.. literalinclude:: ../nextflow.config
+   :language: groovy

docs/_html/_sources/index.rst.txt

@@ -0,0 +1,50 @@
+.. _index:
+
+.. image:: lOGO_3_transparente.png
+  :width: 250
+  :align: left
+  :alt: laboratory logo
+
+----
+
+MpGAP
+=====
+
+`MpGAP <https://github.com/fmalmeida/mpgap>`_ is a pipeline developed with `Nextflow <https://www.nextflow.io/docs/latest/index.html>`_ and `Docker <https://www.docker.com/>`_. It was designed to provide an easy-to-use framework for *de novo* genome assembly of Illumina, Pacbio and Oxford Nanopore sequencing data through illumina only, long reads only or hybrid modes.
+
+It wraps up the following tools:
+
+.. list-table::
+   :widths: 40 60
+   :header-rows: 1
+
+   * - Analysis steps
+     - Used software
+
+   * - Long reads assembly
+     - `Canu <https://github.com/marbl/canu>`_, `Flye <https://github.com/fenderglass/Flye>`_, `Unicycler <https://github.com/rrwick/Unicycler>`_, `Raven <https://github.com/lbcb-sci/raven>`_, `Shasta <https://github.com/chanzuckerberg/shasta>`_ and `wtdbg2 <https://github.com/ruanjue/wtdbg2>`_
+
+   * - Hybrid assembly
+     - `Haslr <https://github.com/vpc-ccg/haslr>`_, `Unicycler <https://github.com/rrwick/Unicycler>`_ and `SPAdes <https://github.com/ablab/spades>`_
+
+   * - Short reads assembly
+     - `Shovill <https://github.com/tseemann/shovill>`_, `Unicycler <https://github.com/rrwick/Unicycler>`_, `Megahit <https://github.com/voutcn/megahit>`_ and `SPAdes <https://github.com/ablab/spades>`_
+
+   * - Assembly polishing
+     - `Nanopolish <https://github.com/jts/nanopolish>`_, `Medaka <https://github.com/nanoporetech/medaka>`_, `gcpp <https://github.com/PacificBiosciences/gcpp>`_ and `Pilon <https://github.com/broadinstitute/pilon>`_
+
+   * - Assembly QC
+     - `Quast <https://github.com/ablab/quast>`_ and `MultiQC <https://multiqc.info/>`_
+
+.. toctree::
+   :hidden:
+
+   installation
+   quickstart
+   samplesheet
+   manual
+   config
+
+Support Contact
+---------------
+Whenever a doubt arise feel free to contact me at [email protected]

docs/_html/_sources/installation.rst.txt

@@ -0,0 +1,50 @@
+.. _installation:
+
+Installation
+============
+
+Dependencies
+------------
+
+This pipeline requires only `Docker <https://www.docker.com/>`_ or `Singularity <https://sylabs.io/docs/>`_ and `Nextflow <https://www.nextflow.io/docs/latest/index.html>`_ to run.
+
+1. Installing Docker or Singularity
+
+   + Read more in the `docker <https://docs.docker.com/>`_ and `singularity <https://sylabs.io/docs/>`_ manuals
+
+2. Installing Nextflow
+
+   ``curl -s https://get.nextflow.io | bash``
+
+3. Download the pipeline
+
+   ``./nextflow pull fmalmeida/mpgap``
+
+4. Test your installation
+
+   ``./nextflow run fmalmeida/mpgap --help``
+
+5. Download required Docker images
+
+   .. code-block:: bash
+
+      # for docker
+      docker pull fmalmeida/mpgap:v3.1
+
+      # for singularity
+      # remember to properly set NXF_SINGULARITY_LIBRARYDIR
+      # read more at https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
+      export NXF_SINGULARITY_LIBRARYDIR=MY_SINGULARITY_IMAGES
+      singularity pull --dir MY_SINGULARITY_IMAGES docker://fmalmeida/mpgap:v3.1
+
+   * To understand how to change between profiles please refer to https://github.com/fmalmeida/MpGAP/tree/master#selecting-between-profiles
+
+      * You can also run it with conda
+
+6. (Optional) Install nf-core
+
+   ``pip install nf-core>=1.10``
+
+.. tip::
+
+	The pipeline requires a UNIX system, therefore, Windows users may successfully use this pipeline via the `Linux subsystem for windows <https://www.nextflow.io/blog/2021/setup-nextflow-on-windows.html>`_.