I have created a workflow with 9 steps. When I run my workflow the first 2 steps are to input datasets. I have paired end matching data so ideally I would like to select all of the "read1".fastq files in step 1 and all of the "read2".fastq files in step 2. There is this button that looks like a magnet or linked chain next to the dataset. When I hover over it it reads, "This input is linked and will be run in matched order with other input datasets(ex: use this for matching forward and reverse reads). I thought, hooray my issue is solved, however the functionality of the button is not intuitive and when I try to use it it will run every sample in step 1 with every sample in step 2 , i.e.. sample1_read1.fastq with sample1_read1.fastq and also sample1_read1.fastq with sample3_read2.fastq. Has anyone figured this out or can provide a workaround?
HI I do successfully use this option to run on multiple parallel workflows on pairs of fasta files. I assume that you have two 'input dataset' steps one for the read1s and for read2s
1 First makes sure that your datasets are all in a consistent order in the same history (i.e. all read1s above read2s).
3 select the icon which looks like a pile of papers (ignore the icon that looks like a linked chain).
4 search the for all read 1s (using the search box at the bottom) in the read 1 input datasets-THEN SELECT ALL THE FILES using shift select- they will go green then grey.
5repeat step 3 but for read 2.
6 run workflow (sending each parallel workflow to separate histories, check box at the bottom, can make organisation easier).