=================
Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 12.x
- **BACKWARD INCOMPATIBLE:** Remove obsolete processes: ``assembler-abyss``,
``cutadapt-amplicon``, ``feature_location``, ``microarray-affy-qc``,
``reads-merge``, ``reference_compatibility``, ``transmart-expressions``,
``upload-hmmer-db``, ``upload-mappability-bigwig``,
``upload-microarray-affy``.
- **BACKWARD INCOMPATIBLE:** Remove obsolete descriptor schema: ``transmart``.
- **BACKWARD INCOMPATIBLE:** Remove tools which are not used by any process:
``clustering_leaf_ordering.py``, ``go_genesets.py``, ``VCF_ad_extract.py``,
``volcanoplot.py``, ``xgff.py``, ``xgtf2gff.py``.
- **BACKWARD INCOMPATIBLE:** Management command for inserting features and
mappings requires PostgreSQL version 9.5 or newer
- Update the meta data like name, description, category, etc. of most of the
processes
- Speed-up management command for inserting mappings
- Change location of cufflinks to Google Drive for resolwebio/rnaseq Docker
build
- Calculate alignment statistics for the uploaded alignment (.bam) file in the
``upload-bam``, ``upload-bam-indexed`` and ``upload-bam-secondary`` processes.
- Annotation (GTF/GFF3) file input is now optional for the creation of the
STAR genome index files. Annotation file can be used at the alignment stage
to supplement the genome indices with the set of known features.
- Trigger process warning instead of process error in the case when
``bamtobigwig.sh`` scripts detects an empty .bam file.
- Set the default reads length filtering parameter to 30 bp in the
``rna-seq-bbduk-star-featurecounts`` and ``kapa-rna-seq-bbduk-star-featurecounts``
experiment descriptor schema. Expand the kit selection choice options in the
latter descriptor schema.
Added
-----
- Add ``MultiQC (1.6.0)`` and ``Seqtk (1.2-r94)`` to the
``resolwebio/utils:1.5.0`` Docker image
- Add ``sample2`` descriptor schema which is the successor of the original
``sample`` and ``reads`` descriptor schemas
- Add bedToBigBed and Tabix to resolwebio/rnaseq:3.7.0 docker image
- Add ``HS Panel`` choice option to the ``amplicon-master-file`` descriptor
schema
- Add MultiQC process
- Add process for the Seqtk tool ``sample`` sub-command. This process allows
sub-sampling of ``.fastq`` files using either a fixed number of reads or the
ratio of the input file.
- Add MultiQC analysis step to the ``workflow-bbduk-star-featurecounts-single``
and ``workflow-bbduk-star-featurecounts-single`` processes.
- Add ``workflow-bbduk-star-featurecounts-qc-single`` and
``workflow-bbduk-star-featurecounts-qc-paired`` processes which support
MultiQC analysis, input reads down-sampling (using Seqtk) and rRNA
sequence detection using STAR aligner.
- Add to ``resolwebio/chipseq`` Docker image:
- ``bedtools (2.25.0-1)``
- ``gawk (1:4.1.3+dfsg-0.1)``
- ``picard-tools (1.113-2)``
- ``run_spp.R (1.2) (as spp)``
- ``SPP (1.14)``
- Add ``regtools-junctions-annotate`` process that annotates novel splice
junctions.
- Add ``background`` relation type to fixtures
Fixed
-----
- Track ``source`` information in the ``upload-fasta-nucl`` process.
- When STAR aligner produces an empty alignment file, re-sort the alignment
file to allow successful indexing of the output ``.bam`` file.
- Create a symbolic link to the alignment file in the ``feature_counts`` process,
so that relative path is used in the quantification results. This prevent the
FeatureCounts output to be listed as a separate sample in the MultiQC reports.
- Fix handling of expression objects in ``archive-samples`` process
===================