GeneLab_Data_Processing
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nasa
Converted the amplicon Illumina processing workflow from Snakemake to Nextflow and added README documentation.
## Description Some datasets may only have 1 replicate per factor group, so DE analysis would not be possible. ## Solution Add option (e.g., `--skipDE`) to run workflow without the...
Converted the amplicon 454 Ion Torrent processing workflow from Snakemake to Nextflow and added README documentation.
Converted the metagenomics processing workflow from Snakemake to Nextflow and added README documentation.
## Description `R.utils` is only used when data files are compressed (e.g., `.CEL.gz`) to unzip them. The following assertion fails with uncompressed data files (e.g., `.CEL`) because `R.utils` is not...
## Description When renaming factor group column names, some factors may be a substring of another, causing the substring to be replaced instead of the full group name if it...
Track updates to [generate_protocol.sh](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/modules/POST_PROCESSING/GENERATE_PROTOCOL/resources/usr/bin/generate_protocol.sh) for Affymetrix pipeline.
## Description The following error occurred when rendering `Affymetrix.qmd` for one dataset: ``` Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function...
## Description The following error occurred when rendering `Affymetrix.qmd` for one dataset (but same issue could potentially arise in `Agile1CMP.qmd` too): ``` Error in `dplyr::bind_rows()`: ! Can't combine `..1$ensembl_gene_id` and...
The pipeline specifies coordinate-sorted BAM as input for deduplicated_bismark (see [GL-DPPD-7113 Step 6](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md#6-deduplicate-skip-if-data-are-rrbs)), but the deduplicate_bismark tool requires readname sorted input files (see [Bismark documentation](http://felixkrueger.github.io/Bismark/bismark/deduplication/)).
