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RELEASE_notes.md

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BAQCOM 0.1.1 - 02/20/2019

Pipeline released

baqcom_mapping Version 0.1.2 - 03/11/2019

Changed genomeDir parameter in baqcom_mapping. Now does not need to indicate the genome index path. The default is the same path to gtf_target.

baqcom_qc Version 0.1.2 - 03/11/2019

added FastQC plots

BAQCOM Version 0.2.0 - 03/19/2019

baqcom_mapping Version 0.2.0 - 03/19/2019

Now you can run samples in parallel

baqcom_qc Version 0.2.0 - 03/21/2019

Now you can run samples in parallel

baqcom_qc and baqcom_mapping Version 0.2.1 - 04/11/2019

Including multiqc analysis

baqcom_qc Version 0.2.2 - 04/15/2019

Including two more options on trimming: LEADING and TRAILING
Including pigz option

baqcom_mapping Version 0.2.2 - 04/22/2019

Including stranded options

baqcom_qc and baqcom_mapping Version 0.2.3 - 04/23/2019

Change the folder names pattern
Set up pigz as default of compressed files
Minor bugs fixed

baqcom_mapping Version 0.2.4 - 05/20/2019

Change requirements to genome generate, mapping and counting
Set up more parameters
Minor bugs fixed

BAQCOM 0.3.0 - 07/20/2019

baqcomSTARmapping

Change pattern folder names
Minor bugs fixed

baqcomTrimmomatic

Change pattern folder names
Minor bugs fixed

baqcomHisat2Mapping

release of a new pipeline to align sequences

baqcomFeaturesCount

release of a new pipeline to count reads

baqcomHtseqCounting

release of a new pipeline to count reads






BAQCOM 0.3.1 - 07/26/2019

baqcomSTARmapping

single-end analysis implemented
Minor bugs fixed

baqcomTrimmomatic

single-end analysis implemented
Minor bugs fixed

baqcomHisat2Mapping

single-end analysis implemented

baqcomFeaturesCount

single-end analysis implemented
Count reads using Star results

baqcomHtseqCounting

single-end analysis implemented






BAQCOM 0.3.2 - 08/08/2019

baqcomSTAR

Change the pipeline's name pattern
from baqcomSTARmapping.R to baqcomSTAR.R
Minor bugs fixed

baqcomTrimmomatic

Minor bugs fixed

baqcomHisat2Mapping

Change the pipeline's name pattern
from baqcomHisat2Mapping.R to baqcomHisat2.R
Minor bugs fixed

baqcomFeaturesCount

Change the pipeline's name pattern
from baqcomFeaturesCount.R to baqcomFeatureCounts.R
Minor bugs fixed

baqcomHtseqCounting

Change the pipeline's name pattern
from baqcomHtseqCounting.R to baqcomHtseq.R
Minor bugs fixed






BAQCOM 0.3.3 - 10/24/2019

baqcomSTAR

Changing single-end files pattern as input
baqcomSTAR now uses compressed fasta files (saving space on your disk)
Minor bugs fixed

baqcomTrimmomatic

Changing single-end files pattern as input ans output
Minor bugs fixed

baqcomHisat2

Changing single-end files pattern as input
baqcomHisat2 now uses compressed fasta files (saving space on your disk)
Minor bugs fixed

BAQCOM 0.3.4 - 01/09/2020

baqcomSTAR

baqcomSTAR now uses compressed annotation files (saving space on your disk)
Minor bugs fixed

BAQCOM 0.3.5 - 11/03/2020

Coding refactoring and update STAR version for baqcomSTAR
Update of Hisat2 version on baqcomHisat2
Update htseq-count version on baqcomHtseq for multithreads
Minor bugs fixed
Coding refactoring for baqcomTrimmomatic