nextflow

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## Bug report ### Expected behavior and actual behavior I'd like to be able to stage a directory from S3 as input to task, but am getting a java.lang.UnsupportedOperationException error...

jeremykap

Behaviour of `.collect()` and `.toList()`

11

## Bug report The semantics of these two operators are poorly documented and counter intuitive. From the documentation its not clear what the different between `.collect()` and `.toList()`, as the...

cjw85

Spawned from the language improvements mega-discussion (#3107). The `file()` method can be used to load a single file or multiple files using a glob string, which means this function can...

bentsherman

## Usage scenario I'd like to be able to return a tuple with optional elements. For example, by defining the output as `tuple val(id), path("output.txt"), path("output2.txt" optional: true)`, I'd like...

rcannood

Support string indices for operators with `by` option

12

Spawned from the language improvements mega-discussion (#3107). Operators that combine or group channels based on an index (i.e. `by` option) currently only support integer indices. They should also support string...

bentsherman

Modifying a mutable object (like Map) in a duplicated channel affects all instances

5

## Bug report ### Expected behavior and actual behavior I don't know if this is a bug or just a huge gotcha. Either way, I've been affected by it multiple...

Midnighter

Automatically delete files marked as temp as soon as not needed anymore

54

To reduce the footprint of larger workflows it's very useful if temporary files (which are marked as such) could be **automatically** deleted once they are not used anymore. Yes, this...

andreas-wilm

Supporting Ignite and using Ceph S3 as working directory

6

Dear nextflow developers As stated in issue (https://github.com/nextflow-io/nextflow/issues/2564) opened by @cnexcale, we are interested in using nextflow in combination with the nextflow feature that allows us to use OpenStack S3...

pbelmann

Allow custom configs `params` to be parsed before nextflow.config

4

## New feature I'm not sure whether to classify this as a feature request or bug. The issue is that `params` configuration from custom configs (`-c`) appears to be read...

mahesh-panchal

`path from ...collect` on a channel length 1 leads to unexpected outcome

3

## Bug report I am using the pattern shown in https://nextflow-io.github.io/patterns/index.html#_process_all_outputs_altogether to merge files generated by an upstream process. In some cases this process only generates one file. The pattern...

meowcat