[3.0] - 2020-12-15 :warning: Major enhancements You will need to install Nextflow >=20.11.0-edge to run the pipeline. If you are using Singularity, then features introduced in that release now enable the pipeline to directly download Singularity images hosted by Biocontainers as opposed to performing a conversion from Docker images (see #496). The previous default of aligning BAM files using STAR and quantifying using featureCounts (--aligner star) has been removed. The new default is to align with STAR and quantify using Salmon (--aligner star_salmon). This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see Zhao et al., 2015 and Soneson et al., 2015). For similar reasons, quantification will not be performed if using --aligner hisat2 due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. This pipeline option is still available for those who have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2. No gene-level quantification results will be generated. In a future release we hope to add back quantitation for HISAT2 using different tools. Enhancements & fixes Updated pipeline template to nf-core/tools 1.12.1 Bumped Nextflow version 20.07.1 -> 20.11.0-edge Added UCSC bedClip module to restrict bedGraph file coordinates to chromosome boundaries Check if Bioconda and conda-forge channels are set-up correctly when running with -profile conda Use rsem-prepare-reference and not gffread to create transcriptome fasta file [#494] - Issue running rnaseq v2.0 (DSL2) with test profile [#496] - Direct download of Singularity images via HTTPS [#498] - Significantly different versions of STAR in star_rsem (2.7.6a) and star (2.6.1d) [#499] - Use of salmon counts for DESeq2 [#500, #509] - Error with AWS batch params [#511] - rsem/star index fails with large genome [#515] - Add decoy-aware indexing for salmon [#516] - Unexpected error [InvocationTargetException] [#525] - sra_ids_to_runinfo.py UnicodeEncodeError Parameters Old parameter New parameter --fc_extra_attributes --gtf_extra_attributes --fc_group_features --gtf_group_features --fc_count_type --gtf_count_type --fc_group_features_type --gtf_group_features_type --singularity_pull_docker_container --skip_featurecounts NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present. Software dependencies Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Dependency Old version New version bioconductor-summarizedexperiment 1.18.1 1.20.0 bioconductor-tximeta 1.6.3 1.8.0 picard 2.23.8 2.23.9 requests 2.24.0 salmon 1.3.0 1.4.0 ucsc-bedclip 377 umi_tools 1.0.1 1.1.1 NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.