nf-core/rnaseq: nf-core/rnaseq v3.1 - Lead Alligator

[3.1] - 2021-05-13 :warning: Major enhancements Samplesheet format has changed from <code>group,replicate,fastq_1,fastq_2,strandedness</code> to <code>sample,fastq_1,fastq_2,strandedness</code> This gives users the flexibility to name their samples however they wish (see #550) PCA generated by DESeq2 will now be monochrome and will not be grouped by using the replicate id Updated Nextflow version to <code>v21.04.0</code> (see nextflow#572) Restructure pipeline scripts into <code>modules/</code>, <code>subworkflows/</code> and <code>workflows/</code> directories Enhancements &amp; fixes Updated pipeline template to nf-core/tools <code>1.14</code> Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation Only FastQ files that require to be concatenated will be passed to <code>CAT_FASTQ</code> process [#449] - <code>--genomeSAindexNbases</code> will now be auto-calculated before building STAR indices [#460] - Auto-detect and bypass featureCounts execution if biotype doesn't exist in GTF [#544] - Update test-dataset for pipeline [#553] - Make tximport output files using all the samples; identified by @j-andrews7 [#561] - Add gene symbols to merged output; identified by @grst [#563] - samplesheet.csv merge error [#567] - Update docs to mention trimgalore core usage nuances [#568] - <code>--star_index</code> argument is ignored with <code>--aligner star_rsem</code> option [#569] - nextflow edge release documentation for running 3.0 [#575] - Remove duplicated salmon output files [#576] - umi_tools dedup : Run before salmon to dedup counts [#582] - Generate a separate bigwig tracks for each strand [#583] - Samtools error during run requires use of BAM CSI index [#585] - Clarify salmon uncertainty for some transcripts [#604] - Additional fasta with GENCODE annotation results in biotype error [#610] - save R objects as RDS [#619] - implicit declaration of the workflow in main [#629] - Add and fix EditorConfig linting in entire pipeline [nf-core/modules#423] - Replace <code>publish_by_id</code> module option to <code>publish_by_meta</code> [nextflow#2060] - Pipeline execution hang when native task fail to be submitted Parameters Old parameter New parameter <code>--hisat_build_memory</code> <code>--hisat2_build_memory</code> <code>--gtf_count_type</code> <code>--featurecounts_feature_type</code> <code>--gtf_group_features_type</code> <code>--featurecounts_group_type</code> <code>--bam_csi_index</code> <code>--schema_ignore_params</code> <code>--show_hidden_params</code> <code>--validate_params</code> <code>--clusterOptions</code> <strong>NB:</strong> Parameter has been <strong>updated</strong> if both old and new parameter information is present. <strong>NB:</strong> Parameter has been <strong>added</strong> if just the new parameter information is present. <strong>NB:</strong> Parameter has been <strong>removed</strong> 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 <code>bedtools</code> 2.29.2 2.30.0 <code>multiqc</code> 1.9 1.10.1 <code>preseq</code> 2.0.3 3.1.2 <strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present. <strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present. <strong>NB:</strong> Dependency has been <strong>removed</strong> if version information isn't present.