Merged dev into recipes

Author: ODiogoSilva

changelog.md

@@ -1,5 +1,52 @@
 # Changelog
 
+## Changes in upcoming release (`dev` branch) 
+
+### Components changes
+
+- Added new `disableRR` param in the `spades` component that disables repeat
+resolution
+
+### New components
+
+- Added component `abyss`.
+
+### Minor/Other changes
+
+- Added removal of duplicate IDs from `reads_download` component input.
+- Added seed parameter to `downsample_fastq` component.
+- Added default docker option to avoid docker permission errors.
+- Changed the default URL generated by inspect and report commands. 
+
+### Bug fixes
+
+- Fixed forks with same source process name.
+- Fixed `inspect` issue when tasks took more than a day in duration.
+
+## 1.3.1
+
+### Features
+
+- Added a new `clearInput` parameter to components that change their input.
+The aim of this option is to allow the controlled removal of temporary files,
+which is particularly useful in very large workflows.
+
+### Components changes
+
+- Updated images for components `mash_dist`, `mash_screen` and 
+`mapping_patlas`.
+
+### New components
+
+- Added component `fast_ani`.
+
+### Minor/Other changes
+
+- Added `--export-directives` option to `build` mode to export component's 
+directives in JSON format to standard output.
+- Added more date information in `inspect` mode, including the year and the
+locale of the executing system.
+
 ## 1.3.0
 
 ### Features

docker/Dockerfile

@@ -0,0 +1,18 @@
+FROM python:3.6-alpine3.7
+MAINTAINER Bruno Gonçalves <bfgoncalves@medicina.ulisboa.pt>
+
+RUN apk add --no-cache git
+
+WORKDIR /flowcraft
+
+# Clone FlowCraft
+RUN git clone https://github.com/assemblerflow/flowcraft.git
+WORKDIR ./flowcraft
+
+# Install flowcraft
+RUN python setup.py install
+
+WORKDIR /flowcraft
+
+# Remove unnecessary packages
+RUN apk del git

docs/user/available_components.rst

@@ -99,7 +99,13 @@ Distance Estimation
   plasmid database and generates a JSON input file for pATLAS. This component
   searches for containment of a given sequence in read sequencing data.
   However if a different database is provided it can use mash screen for other
-  purporses.
+  purposes.
+
+- :doc:`components/fast_ani`: Performs pairwise comparisons between fastas,
+given a multifasta as input for fastANI. It will split the multifasta into
+single fastas that will then be provided as a matrix. The output will be the
+all pairwise comparisons that pass the minimum of 50 aligned sequences with a
+default length of 200 bp.
 
 - :doc:`components/mash_sketch_fasta`: Performs mash sketch for fasta files.
 

docs/user/basic_usage.rst

@@ -393,7 +393,7 @@ Local visualization
 :::::::::::::::::::
 
 The FlowCraft report JSON file can also be visualized locally by drag and dropping
-it into the FlowCraft web application page, currently hosted at http://192.92.149.169/reports
+it into the FlowCraft web application page, currently hosted at http://www.flowcraft.live/reports
 
 Offline visualization
 :::::::::::::::::::::

docs/user/components/downsample_fastq.rst

@@ -23,6 +23,7 @@ Parameters
 - ``genomeSize``: Genome size estimate for the samples. It is used to
   estimate the coverage.
 - ``depth``: The target depth to which the reads should be subsampled.
+- ``seed``: The seed number for seqtk. By default it is 100.
 
 Published results
 -----------------

docs/user/components/fast_ani.rst

@@ -0,0 +1,47 @@
+fast_ani
+========
+
+Purpose
+-------
+
+This component performs pairwise comparisons between fastas,
+given a multifasta as input for fastANI. It will split the multifasta into
+single fastas that will then be provided as a matrix. The output will be the
+all pairwise comparisons that pass the minimum of 50 aligned sequences with a
+default length of 200 bp.
+
+Input/Output type
+------------------
+
+- Input type: ``fasta``
+- Output type: ``None``
+
+
+Parameters
+----------
+
+- ``fragLen``: Sets the minimum size of the fragment to be passed to
+`--fragLen` argument of fastANI.
+
+
+Published results
+-----------------
+
+- ``results/fast_ani/``: A text file with the extension `.out`, which has all
+the pairwise comparisons between sequences, reporting ANI.
+
+
+Published reports
+-----------------
+
+None.
+
+
+Default directives
+------------------
+
+- ``fastAniMatrix``:
+    - ``container``: flowcraft/fast_ani
+    - ``version``: 1.1.0-2
+    - ``cpus``: 20
+    - ``memory``: { 30.GB * task.attempt }

docs/user/components/mapping_patlas.rst

@@ -60,10 +60,10 @@ Default directives
 
 - ``mappingBowtie``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``samtoolsView``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``jsonDumpingMapping``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1

docs/user/components/mash_dist.rst

@@ -65,7 +65,7 @@ Default directives
 
 - ``runMashDist``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``mashDistOutputJson``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1

docs/user/components/mash_screen.rst

@@ -60,7 +60,7 @@ Default directives
 
 - ``mashScreen``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``mashOutputJson``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1

flowcraft/__init__.py

@@ -1,6 +1,6 @@
 
-__version__ = "1.3.0"
-__build__ = "21092018"
+__version__ = "1.3.1"
+__build__ = "27092018"
 __author__ = "Diogo N. Silva, Tiago F. Jesus, Ines Mendes, Bruno Ribeiro-Goncalves"
 __copyright__ = "Diogo N. Silva"
 __license__ = "GPL3"