Hi, I'm using the bedtools "Intersect intervals find overlapping intervals in various ways" tool. I used it in a workflow and am trying to (1) change the output filename and data-type, (2) only show the output (with the name changed) and (3) use (2) as an input to another tool in the workflow.
These are the settings:
BED/VCF/GFF/BAM file Output dataset 'output' from step 1 One or more BAM/BED/GFF/VCF file(s) Output dataset 'output' from step 2 Calculation based on strandedness? Overlaps on either strand What should be written to the output file? Write the original entry in A for each overlap (-wa) Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage. False Minimum overlap required as a fraction of the BAM alignment Require that the fraction of overlap be reciprocal for A and B False Report only those alignments that *do not overlap the BED file False Write the original A entry _once_ if _any_ overlaps found in B. True For each entry in A, report the number of overlaps with B. False Print the header from the A file prior to results False Actions: Rename output 'output' to 'log2ratio_DamID'. Set the datatype of output 'output' to 'bedgraph'*
It doesn't say that the output should be hidden even though it's selected to be hidden in the workflow canvas.
I have done this alot of times with other tools and it works but not now, with the bedtools. For some reason, it hides the one with the right name and display the pre-changed file AND somehow maybe does not get recognized as an input to the next tool and the workflow does not continue ie next tool always remain gray.
Any help would be appreciated!