Timeline for Nextflow - Missing value declared as output parameter - output variable defined in script
Current License: CC BY-SA 4.0
7 events
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| Jul 19, 2023 at 21:56 | comment | added | Death Metal | Hi @Steve - can you please assist me on post bioinformatics.stackexchange.com/questions/21338/…. | |
| Jul 15, 2023 at 4:45 | comment | added | Steve |
@DeathMetal I might be starting to sound like a broken record, but understanding how queue channels and value channels work should make writing workflows much easier. Queue channels can be consumed, but value channels can be read an unlimited number of times. In your example above, the intervals (targets) file and reference file should be passed in using value channels like in my previous answer. Note that value channels are implicitly created when a process is invoked with a simple value, like a file object.
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| Jul 15, 2023 at 4:41 | comment | added | Steve |
@DeathMetal A better way, I think, would be to pass your sample_name variable (or pair_id or whatever) down to your mutect2 process. It's likely you'll need this variable later in your workflow, so defining it in your workflow block likely makes more sense.
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| Jul 14, 2023 at 19:27 | vote | accept | Death Metal | ||
| Jul 14, 2023 at 19:26 | comment | added | Death Metal | I have seen your reply few times on my posts as well on others, I don't quite follow queue channels, values channels link. What do I use when and for what? Sorry this is complicated then I can understand or/and follow. | |
| Jul 14, 2023 at 19:25 | comment | added | Death Metal |
Thank you. I removed def and it worked. My apologies I didn't quite understand: but usually what you'd want to do is to define your sample_name variable outside of your process block in your workflow block like What do I do? the example you shared is too difficult.
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| Jul 14, 2023 at 1:31 | history | answered | Steve | CC BY-SA 4.0 |