v2.1.0

• Inputs can now include multiple fastqs per replicate. Due to this the fastq input is given as Array[Array[File]].

v2.0.0

• An arbitrary number of spikein files, as gzipped fasta, can be used.
• No need to specify splice junction file in the input anymore, it is automatically generated.
• TALON updated to version v5.0.
• Added flagging of internal priming events using TALON subcommand talon_label_reads.
• Complete refactoring of testing. Using pytest-workflow now, simplifying local test runs.
• WDL version 1.0.
• Resource specification simplified.

v1.3.1

• Output from create_gtf_from_talon_db is now gzipped.

v1.3

• Uses the complete rewrite of TranscriptClean version 2.0.2 enhancing the speed, and especially memory performance.
• canonical_only option added to TranscriptClean step.
• New TranscriptClean requires matching chromosome names in the reference, and in the variants file (if using one). dbSNP derived compatible variants file available at https://www.encodeproject.org/files/ENCFF911UGW/

v1.2

• Upgrade Transcriptclean to v1.0.8 fixing a bug related to non-canonical splice junction correction (mortazavilab/TranscriptClean#14).
• Fix bug related to filtering quantitation output, causing errors in calculation of replicates correlation (this was underestimated), and number of detected gencode genes (this was overestimated).
• Add output organizer output definition into the main pipeline wdl to simplify croo usage.

v1.1

Changes:

• Talon database initialization is now integrated into the pipeline.
• Talon upgraded to version 4.2 providing bugfixes.
• GTF reflecting the state of the TALON database is created from every replicate.