adding MOP3

INSTALL.sh

@@ -4,31 +4,49 @@
 # params:
 # 1 guppy version
 
+if [ -e "./mop_preprocess/bin/guppy_basecaller" ] ; then
+	echo "unlinking previously installed versions"
+	cd mop_preprocess/bin; find . -maxdepth 1 -type l | xargs rm; cd ../../
+fi
+
 if [ x"$1" == x ]; then
         GUPPY_VER='3.4.5'
 else
 	GUPPY_VER=$1
 fi
 
 
-wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_${GUPPY_VER}_linux64.tar.gz 
+wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_${GUPPY_VER}_linux64.tar.gz
 if [ $? -eq 0 ]; then
 	echo "INSTALLING GUPPY VERSION ${GUPPY_VER}"
 else
-    echo "GUPPY VERSION ${GUPPY_VER} is not found" 
+    echo "GUPPY VERSION ${GUPPY_VER} is not found"
     exit
 fi
 
 tar -zvxf ont-guppy_${GUPPY_VER}_linux64.tar.gz
-mv ont-guppy mop_preprocess/bin/
+
+wget https://biocore.crg.eu/public/mop3_pub/models.tar
+mv models.tar mop_preprocess/guppy_models/
+cd mop_preprocess/guppy_models; tar -xvf  models.tar; rm models.tar; cd ../../
+
+mkdir -p mop_preprocess/bin/ont-guppy_${GUPPY_VER}
+mv ont-guppy/* mop_preprocess/bin/ont-guppy_${GUPPY_VER}
+for i in mop_preprocess/guppy_models/*.gz; do gzip -cd $i > mop_preprocess/bin/ont-guppy_${GUPPY_VER}/data/`basename $i .gz`; done
+rmdir ont-guppy
+
 cd mop_preprocess/bin
-ln -sf ont-guppy/bin/guppy_* .
-ln -sf ont-guppy/lib/* .
+ln -s ont-guppy_${GUPPY_VER}/bin/guppy_* .
+ln -s ont-guppy_${GUPPY_VER}/lib/* .
 cd ../../
-if [ ! -e "mop_preprocess/bin/ont-guppy/lib/libz.so" ] ; then
-        unlink mop_preprocess/bin/ont-guppy/lib/libz.so
-        cd mop_preprocess/bin/ont-guppy/lib/
-        ln -sf libz.so.1 libz.so
-        cd ../../../../
+
+if [ ! -e "./mop_preprocess/bin/ont-guppy_${GUPPY_VER}/lib/libz.so" ] ; then
+	if [ -e "./mop_preprocess/bin/ont-guppy_${GUPPY_VER}/lib/libz.so.1" ] ; then
+        	unlink mop_preprocess/bin/ont-guppy_${GUPPY_VER}/lib/libz.so
+        	cd mop_preprocess/bin/ont-guppy_${GUPPY_VER}/lib/
+        	ln -s libz.so.1 libz.so
+        	cd ../../../../
+	fi
 fi
-rm ont-guppy_${GUPPY_VER}_linux64.tar.gz
+
+rm ./ont-guppy_${GUPPY_VER}_linux64.tar.gz

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Biocore@CRG
+Copyright (c) 2022 Biocore@CRG
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,47 +1,67 @@
-# MoP2- DSL2 version of Master of Pores
+# MoP3 - Master of Pores 3
 [![Docker Build Status](https://img.shields.io/docker/automated/biocorecrg/nanopore.svg)](https://cloud.docker.com/u/biocorecrg/repository/docker/biocorecrg/nanopore/builds)
-[![mop2-CI](https://github.com/biocorecrg/MoP2/actions/workflows/build.yml/badge.svg)](https://github.com/biocorecrg/MoP2/actions/workflows/build.yml)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![mop3-CI](https://github.com/biocorecrg/master_of_pores/actions/workflows/build.yml/badge.svg)](https://github.com/biocorecrg/master_of_pores/actions/workflows/build.yml)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Nextflow version](https://img.shields.io/badge/Nextflow-21.04.1-brightgreen)](https://www.nextflow.io/)
 [![Nextflow DSL2](https://img.shields.io/badge/Nextflow-DSL2-brightgreen)](https://www.nextflow.io/)
 [![Singularity version](https://img.shields.io/badge/Singularity-v3.2.1-green.svg)](https://www.sylabs.io/)
 [![Docker version](https://img.shields.io/badge/Docker-v20.10.8-blue)](https://www.docker.com/)
 
 <br/>
 
-![MOP2](https://github.com/biocorecrg/MoP2/blob/main/img/master_red.jpg?raw=true)
 
 
-Inspired by Metallica's [Master Of Puppets](https://www.youtube.com/watch?v=S7blkui3nQc)
+<img align="right" href="https://biocore.crg.eu/" src="https://raw.githubusercontent.com/CRG-CNAG/BioCoreMiscOpen/master/logo/biocore-logo_small.png" />
+
+
+Master of Pores is a pipeline written in Nextflow DSL2 for the analysis of Nanopore data.
+<br/>
+
+It can handle reads from direct RNAseq, cDNAseq, DNAseq etc.
+
+<br/>
+
+
+![MOP3](https://github.com/biocorecrg/master_of_pores/blob/v3.0/img/goku3.png?raw=true)
+
+The name is inspired by the Metallica's [Master Of Puppets](https://www.youtube.com/watch?v=S7blkui3nQc)
 
 ## Install
 Please install nextflow and singularity or docker before.
 
 Then download the repo:
 
 ```
-git clone --depth 1 --recurse-submodules [email protected]:biocorecrg/MOP2.git
-```
-
-or
-```
-git clone --depth 1 --recurse-submodules https://github.com/biocorecrg/MOP2.git
+git clone --depth 1 --recurse-submodules https://github.com/biocorecrg/master_of_pores.git
 ```
 
-You can use INSTALL.sh to download the version 3.4.5 of guppy or you can replace it with the version you prefer. Please consider that the support of VBZ compression of fast5 started with version 3.4.X. 
+You can use INSTALL.sh to download the version 3.4.5 of guppy or you can replace it with the version you prefer. Please consider that the support of VBZ compression of fast5 started with version 3.4.X.
 
 ```
-cd MOP2; sh INSTALL.sh 3.4.5
+cd master_of_pores; sh INSTALL.sh
 ```
 
 ## Testing
 You can replace ```-with-singularity``` with ```-with-docker``` if you want to use the docker engine.
 
 ```
 cd mop_preprocess
-nextflow run mop_preprocess.nf -with-singularity -bg -profile local > log
+nextflow run mop_preprocess.nf -with-singularity -bg -profile local -params-file params.yaml > log
+```
+
+## Upgrading
+To upgrade the tool you can type:
 
 ```
+git pull --recurse-submodules
+```
+
+## Documentation
+The documentation is available at [https://biocorecrg.github.io/master_of_pores/](https://biocorecrg.github.io/master_of_pores/)
+
+## Contact
+Please open an [issue](https://github.com/biocorecrg/master_of_pores/issues) if you encounter any issues/troubles.
+However, please go over the previous issues (including closed issues) before opening a new issue, as your same exact question might have been already answered previously. Thank you!
+
 
 ## Reference
 If you use this tool, please cite our papers:
@@ -52,7 +72,3 @@ Cozzuto L, Delgado-Tejedor A, Hermoso Pulido T, Novoa EM, Ponomarenko J. *N. Met
 ["MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets"
 Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva Maria Novoa.
 *Front. Genet., 17 March 2020.* https://doi.org/10.3389/fgene.2020.00211](https://www.frontiersin.org/articles/10.3389/fgene.2020.00211/full)
-
-
-## Documentation
-The documentation is available at [https://biocorecrg.github.io/MOP2/docs/](https://biocorecrg.github.io/MOP2/docs/about.html)

conf.py

@@ -0,0 +1,183 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = u'Master of Pores 3'
+copyright = u'2019, CRG'
+author = u'Luca Cozzuto'
+author = u'Anna Delgado'
+author = u'Eva Novoa'
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u''
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.githubpages'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+#source_suffix = ['.rst', '.html']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'docs/index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_copy_source = False
+html_show_sourcelink = False
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'SphinxGitHubActionTestdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'SphinxGitHubActionTest.tex', u'Sphinx GitHub Action Test Documentation',
+     u'Sean Zheng', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'sphinxgithubactiontest', u'Sphinx GitHub Action Test Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'SphinxGitHubActionTest', u'Sphinx GitHub Action Test Documentation',
+     author, 'SphinxGitHubActionTest', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

conf/awsbatch.config

@@ -3,6 +3,7 @@ aws.region = 'eu-central-1'
 aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 
 process {
+        shell = ['/bin/bash', '-euo', 'pipefail']
 	executor = 'awsbatch'
         queue = 'mop'
 	cpus = 1
@@ -13,40 +14,35 @@ process {
         containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g)': null}
 
 	withLabel: big_cpus {
-		cpus = 2
-		memory = '2G'
+		cpus = 8
+		memory = '12G'
 	}
 
         withLabel: big_cpus_ignore {
                 errorStrategy = 'ignore'
-                cpus = 2
-                memory = '2G'
+                cpus = 8
+                memory = '12G'
         }
 
 	withLabel: big_mem_cpus {
 		time = '6h'
-		cpus = 3
-		memory = '2G'
-	}
-
-	withLabel: big_time_cpus {
-		time = '24h'
-		cpus = 3
-		memory = '2G'
+		cpus = 8
+		memory = '20G'
 	}
 
 	 withLabel: demulti_gpus {
 	     accelerator = 1
 	     queue = 'mop-gpu'
 	     memory = '2G'
+	     // clusterOptions = {" -l gpu=1 -l virtual_free=${task.memory.toString().replaceAll(/[\sB]/,'')}"}
 			 containerOptions = { workflow.containerEngine == "singularity" ? '--nv':
 			 ( workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g) --gpus all': null ) }	 }
 	  withLabel: basecall_gpus {
 	  	accelerator = 1
    		queue = 'mop-gpu'
    		memory = '2G'
    		clusterOptions = '-l gpu=1'
-		containerOptions = { workflow.containerEngine == "singularity" ? '--nv':
+			containerOptions = { workflow.containerEngine == "singularity" ? '--nv':
       		( workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g) --gpus all': null ) }
 	}
 }