Skip to content

Commit

Permalink
Add rnaseqc container. cleanup rseqc section
Browse files Browse the repository at this point in the history 
also cleanup HTML report and added precommit
  • Loading branch information
@cokelaer
cokelaer committed Dec 13, 2023
1 parent c980933 commit 84ee640
Show file tree
Hide file tree
Showing 9 changed files with 263 additions and 243 deletions.
85 changes: 44 additions & 41 deletions README.rst
View file
Expand Up @@ -8,7 +8,7 @@
:alt: JOSS (journal of open source software) DOI

.. image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/rnaseq/actions/workflows/main.yaml
:target: https://github.com/sequana/rnaseq/actions/workflows/main.yaml



Expand All @@ -17,7 +17,7 @@ This is is the **RNA-seq** pipeline from the `Sequana <https://sequana.readthedo
:Overview: RNASeq analysis from raw data to feature counts
:Input: A set of Fastq Files and genome reference and annotation.
:Output: MultiQC and HTML reports, BAM and bigwig files, feature Counts, script to launch differential analysis
:Status: Production.
:Status: Production.
:Citation(sequana): Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
:Citation(pipeline):
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4047837.svg
Expand All @@ -40,13 +40,13 @@ Usage
sequana_rnaseq --help
sequana_rnaseq --input-directory DATAPATH --genome-directory genome --aligner star

This creates a directory with the pipeline and configuration file. You will then need
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline::

cd rnaseq
sh rnaseq.sh # for a local run

This launch a snakemake pipeline. If you are familiar with snakemake, you can
This launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::

snakemake -s rnaseq.rules -c config.yaml --cores 4 --stats stats.txt
Expand Down Expand Up @@ -80,7 +80,7 @@ Or use the conda.yaml file available in this repository. If you start a new
environment from scratch, those commands will create the environment and install
all dependencies for you::

conda create --name sequana_env python 3.7.3
conda create --name sequana_env python 3.7.3
conda activate sequana_env
conda install -c anaconda qt pyqt>5
pip install sequana
Expand All @@ -100,22 +100,22 @@ To use apptainer, initialise the pipeline with the --use-singularity option and
Details
~~~~~~~~~

This pipeline runs a **RNA-seq** analysis of sequencing data. It runs in
parallel on a set of input FastQ files (paired or not).
This pipeline runs a **RNA-seq** analysis of sequencing data. It runs in
parallel on a set of input FastQ files (paired or not).
A brief HTML report is produced together with a MultiQC report.

This pipeline is complex and requires some expertise for the interpretation.
Many online-resources are available and should help you deciphering the output.
Many online-resources are available and should help you deciphering the output.

Yet, it should be quite straigtforward to execute it as shown above. The
pipeline uses bowtie1 to look for ribosomal contamination (rRNA). Then,
pipeline uses bowtie1 to look for ribosomal contamination (rRNA). Then,
it cleans the data with cutapdat if you say so (your data may already be
pre-processed). If no adapters are provided (default), reads are
trimmed for low quality bases only. Then, mapping is performed with standard mappers such as
pre-processed). If no adapters are provided (default), reads are
trimmed for low quality bases only. Then, mapping is performed with standard mappers such as
star or bowtie2 (--aligner option). Finally,
feature counts are extracted from the previously generated BAM files. We guess
the strand and save the feature counts into the directoy
./rnadiff/feature_counts.
./rnadiff/feature_counts.

The pipelines stops there. However, RNA-seq analysis are followed by a different
analysis (DGE hereafter). Although the DGE is not part of the pipeline, you can
Expand All @@ -138,7 +138,7 @@ Rules and configuration details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_rnaseq/main/sequana_pipelines/rnaseq/config.yaml>`_
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.


.. warning:: the RNAseQC rule is switch off and is not currently functional in
Expand All @@ -158,6 +158,9 @@ Changelog
========= ====================================================================
Version Description
========= ====================================================================
0.19.1 * add rnaseqc container.
* Update rseqc rules (redirection)
* cleanup onsuccess rule
0.19.0 * Refactorisation to use click
0.18.1 * fastp multiqc regression. Fixed missing sample names by updating
multiqc_config and adding sample names in the output filename
Expand All @@ -166,28 +169,28 @@ Version Description
* BUG: Fix missing params (options) in star_mapping rule not taken
into account
0.17.1 * use new rulegraph / graphviz apptainer
0.17.0 * fastp step changed to use sequana-wrappers. Slight change in
0.17.0 * fastp step changed to use sequana-wrappers. Slight change in
config file. The reverse and forward adapter options called
rev and fwd have been dropped in favor of a single adapters option.
v0.17.0 config and schema are not compatible with previous
v0.17.0 config and schema are not compatible with previous
versions.
* Update singularity containers and add new one for fastp
0.16.1 * fix bug in feature counts automatic strand balance detection. Was
0.16.1 * fix bug in feature counts automatic strand balance detection. Was
always using the stranded case (2).
* add singularity workflow for testing
* fix documentation in config.yaml
0.16.0 * star, salmon, bam_coverage are now in sequana wrappers, updated
0.16.0 * star, salmon, bam_coverage are now in sequana wrappers, updated
the pipeline accordingly
* updated config file and schema to include resources inside the
* updated config file and schema to include resources inside the
config file (so as to use new --profile option)
* set singularity images in all rules
* star wrappers has changed significantly to use star
* star wrappers has changed significantly to use star
recommandation. To keep using previous way, a legacy option
is available and set to True in this version.
* bamCoverage renamed in bam_coverage in the config file
* multiqc_config removed redundant information and ordered
the output in a coherent way (QC and then analysis)
0.15.2 * Fix bowtie2 rule to use new wrappers. Use wrappers in
0.15.2 * Fix bowtie2 rule to use new wrappers. Use wrappers in
add_read_group and mark_duplicates
0.15.1 * Adapt to new bowtie2 align wrapper
0.15.0 * fix typo reported in https://github.com/sequana/rnaseq/issues/12
Expand All @@ -199,7 +202,7 @@ Version Description
same genome directory.
* Ribosomal is now estimated on the first 100,000 reads to speed up
analysis
* --indexing and --force-indexing options not required anymore.
* --indexing and --force-indexing options not required anymore.
Indexing will be done automatically and not redone if present.
* Use of the new sequana-wrappers repository
0.13.0 * Major update to use the new sequana version and the RNADiff tools.
Expand All @@ -210,7 +213,7 @@ Version Description
* user interface has now a --skip-gff-check option. Better handling of
input gff with more meaningful messages
* integration of rseqc tool
0.12.1 * indexing was always set to True in the config after 0.9.16 update.
0.12.1 * indexing was always set to True in the config after 0.9.16 update.
0.12.0 * BUG fix: Switch mark_duplicates correctly beore feature counts
0.11.0 * rnadiff one factor is simplified
* When initiating the pipeline, provide information about the GFF
Expand All @@ -226,7 +229,7 @@ Version Description
created and used
* fix the --do-igvtools and --do-bam-coverage with better doc
0.10.0 * 9/12/2020
* Fixed bug in sequana/star_indexing for small genomes (v0.9.7).
* Fixed bug in sequana/star_indexing for small genomes (v0.9.7).
Changed the rnaseq requirements to benefit from this bug-fix that
could lead to seg fault with star aligner for small genomes.
* Report improved with strand guess and plot
Expand All @@ -235,32 +238,32 @@ Version Description
* In config file, bowtie section 'do' option is removed. This is now
set automatically if rRNA_feature or rRNA_file is provided. This
allows us to skip the rRNA mapping entirely if needed.
* fastq_screen should be functional. Default behaviour is off. If
* fastq_screen should be functional. Default behaviour is off. If
set only phiX174 will be search for. Users should build their own
configuration file.
* star/bowtie1/bowtie2 have now their own sub-directories in the
genome directory.
* star/bowtie1/bowtie2 have now their own sub-directories in the
genome directory.
* added --run option to start pipeline automatically (if you know
what you are doing)
* rnadiff option has now a default value (one_factor)
* add strandness plot in the HTML summary page
0.9.19 * Remove the try/except around tolerance (guess of strandness) to
0.9.19 * Remove the try/except around tolerance (guess of strandness) to
make sure this is provided by the user. Final onsuccess benefits
from faster GFF function (sequana 0.9.4)
0.9.18 * Fix typo (regression bug) + add tolerance in schema + generic
0.9.18 * Fix typo (regression bug) + add tolerance in schema + generic
title in multiqc_config. (oct 2020)
0.9.17 * add the *tolerance* parameter in the feature_counts rule as a user
parameter (config and pipeline).
0.9.16 * Best feature_counts is now saved into rnadiff/feature_counts
parameter (config and pipeline).
0.9.16 * Best feature_counts is now saved into rnadiff/feature_counts
directory and rnadiff scripts have been updated accordingly
* the most probable feature count option is now computed more
effectivily and incorporated inside the Snakemake pipeline (not in
the onsuccess) so that multiqc picks the best one (not the 3
the onsuccess) so that multiqc picks the best one (not the 3
results)
* the target.txt file can be generated inside the pipeline if user
fill the rnadiff/conditions section in the config file
* indexing options are filled automatically when calling
sequana_rnaseq based on the presence/absence of the index
sequana_rnaseq based on the presence/absence of the index
of the aligner being used.
* salmon now integrated and feature counts created (still WIP in
sequana)
Expand All @@ -283,13 +286,13 @@ Version Description
analysis
0.9.11 * Automatic guessing of the strandness of the experiment
0.9.10 * Fix multiqc for RNAseQC rule
0.9.9 * Fix RNAseQC rule, which is now available.
0.9.9 * Fix RNAseQC rule, which is now available.
* Fix ability to use existing rRNA file as input
0.9.8 * Fix indexing for bowtie1 to not be done if aligner is different
* add new options: --feature-counts-options and --do-rnaseq-qc,
--rRNA-feature
* Based on the input GFF, we now check the validity of the rRNA
feature and feature counts options to check whether the feature
feature and feature counts options to check whether the feature
exists in the GFF
* schema is now used to check the config file values
* add a data test for testing and documentation
Expand All @@ -298,25 +301,25 @@ Version Description
* Possiblity to switch off cutadapt section
* Fixing bowtie2 rule in sequana and update the pipeline accordingly
* Include a schema file
* output-directory parameter renamed into output_directory (multiqc
* output-directory parameter renamed into output_directory (multiqc
section)
* handle stdout correctly in fastqc, bowtie1, bowtie2 rules
0.9.5 * Fixed https://github.com/sequana/sequana/issues/571
* More cutadapt commands and sanity checks
* Fixed bowtie2 options import in rnaseq.rules
0.9.4
0.9.3 if a fastq_screen.conf is provided, we switch the fastqc_screen
0.9.4
0.9.3 if a fastq_screen.conf is provided, we switch the fastqc_screen
section ON automatically
0.9.0 **Major refactorisation.**

* remove sartools, kraken rules.
* remove sartools, kraken rules.
* Indexing is now optional and can be set in the configuration.
* Configuration file is simplified with a general section to enter
the genome location and aligner.
the genome location and aligner.
* Fixed rules in sequana (0.8.0) that were not up-to-date with
several executables used in the pipeline including picard,
fastq_screen, etc. See Sequana Changelog for details with respect
to rules changes.
* Copying the feature counts in main directory ready to use for
to rules changes.
* Copying the feature counts in main directory ready to use for
a differential analysis.
========= ====================================================================
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "sequana-rnaseq"
version = "0.19.0"
version = "0.19.1"
description = "A RNAseq pipeline from raw reads to feature counts"
authors = ["Sequana Team"]
license = "BSD-3"
Expand Down
34 changes: 0 additions & 34 deletions sequana_pipelines/rnaseq/cluster_config.json
View file

This file was deleted.

4 changes: 3 additions & 1 deletion sequana_pipelines/rnaseq/config.yaml
View file
Expand Up @@ -26,7 +26,7 @@ apptainers:
igvtools: "https://zenodo.org/record/7022635/files/igvtools_2.12.0.img"
graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
multiqc: "https://zenodo.org/record/10205070/files/multiqc_1.16.0.img"

rnaseqc: "https://zenodo.org/record/5799564/files/rnaseqc_2.35.0.img"

# =========================================== Sections for the users

Expand Down Expand Up @@ -370,6 +370,8 @@ rnaseqc:
do: false
gtf_file:
options: --coverage
resources:
mem: 8G


# if be_file not provided, try to create one on the fly
Expand Down

0 comments on commit 84ee640

Please sign in to comment.