diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c77f50591fc2503b8598505a2a88783eb75fca9..30d202afaec719eb5bb67a71f5f9e10af240eca1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# v0.1.0 (in development) +# v1.0.0 (in development) **User Facing** * Add option to pull references from datahub * Add option to send email on workflow error, with pipeline error message @@ -17,6 +17,7 @@ * Error if pe and line count of R1 != R2 * Error if ambiguous species inference * Remove non fastq from inputBag from the export bag config level +* Add link to reference builder script **Background** * Remove (comment out) option to pull references from S3 diff --git a/README.md b/README.md index 65e4e738d735e350eacb5db194cb505d46cc9e19..b21653de3f2f5db482ffb86be07abe14d15ac0e7 100644 --- a/README.md +++ b/README.md @@ -75,6 +75,11 @@ FULL EXAMPLE: nextflow run workflow/rna-seq.nf --repRID Q-Y5JA --source production --deriva ./data/credential.json --bdbag ./data/cookies.txt --dev false --upload true -profile biohpc ``` +To generate you own references or new references: +------------------------------------------ +Download the [reference creation script](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/snippets/31). +This script will auto create human and mouse references from GENCODE. It can also create ERCC92 spike-in references as well as concatenate them to GENCODE references automatically. In addition, it can create references from manually downloaded FASTA and GTF files. + To run a set of replicates from study RID: ------------------------------------------ Run in repo root dir: