Flatten Nanopore data

Annotation: From a list of lists (of FASTQ reads), create a list of concatenated FASTQ files and relabel them according to the input mapping table.

StepAnnotation
Step 1: Input dataset collection
select at runtime
This list a list of lists, where the first level of the list is the barcode names and the second level of the list is the FASTQ files within each barcode. Create this list of lists using the Rule Builder.
Step 2: Input dataset
select at runtime
A table (i.e. two columns, tab separated) with barcode on the left and sample name on the right.
Step 3: Concatenate datasets
Output dataset 'output' from step 1
Datasets
Step 4: Relabel identifiers
Output dataset 'out_file1' from step 3
Map original identifiers to new ones using a two column table.
Output dataset 'output' from step 2
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