sequana-rnaseq 0.9.17

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 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 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 of the aligner being used.

• salmon now integrated and feature counts created (still WIP in sequana)

0.9.15

• FastQC on raw data skipped by default (FastQC for processed data is still available)

• Added paired options (-p) for featureCounts

• Switch back markduplicates to False for now.

0.9.14

• Use only R1 with bowtie1

• set the memory requirements for mark_duplicates in cluster_config file

• Set temporary directory for mark_duplicates to be local ./tmp

0.9.13

• set mark_duplicate to true by default

• use new sequana pipeline manager

• export all features counts in a single file

• custom HTML report

• faster –help calls

• –from-project option added

0.9.12

• include salmon tool as an alternative to star/bowtie2

• include rnadiff directory with required input for Differential 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.

• 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 exists in the GFF

• schema is now used to check the config file values

• add a data test for testing and documentation

0.9.7

• fix typo found in version 0.9.6

0.9.6

• Fixed empty read tag in the configuration file

• 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 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 section ON automatically

0.9.0

Major refactorisation.

• 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.

• 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 a differential analysis.