# Collect sorting by key but keep only files/paths **URL:** \ **Category:** Ask for help\ **Tags:** nextflow\ **Created:** [April 14, 2026, 12:21pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632 "2026-04-14T12:21:03Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![rseraphin](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/rseraphin/32/2408_2.png) [@rseraphin](https://community.seqera.io/u/rseraphin)\ **Post date:** [April 14, 2026, 12:21pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632/1 "2026-04-14T12:21:03Z")
Hello, I have a process that works by chromosomes that output a tuple in the following format: `tuple val(chr_id), path(chr_vcf)`. In the following process i want to concatenate all my vcfs into a full genome vcf but i want to make sure my chromosomes are in the correct order. I managed to collect and sort by the key `chr_id` using either `collect(flat: false, sort: {it[0]})` or `toSortedList{ a, b -> a[0] <=> b[0] }` but then I struggle with the cardinality or to get a list with only the vcfs paths for the following process. A more concrete example: ```auto Channel.of(["1","test_1.vcf.gz"], ["MU123", "test_MU123.vcf.gz"], ["JA01.1", "test_JA01.1.vcf.gz"], ["2", "test_2.vcf.gz"], ["10", "test_10.vcf.gz"], ["MT", "test_MT.vcf.gz"]) .view() .set{ my_ch } // sorting works my_ch.collect(flat: false, sort: {it[0]}) .view() // sorting works my_ch.toSortedList{ a, b -> a[0] <=> b[0] } .view() // sorting works but how to get list of paths? => does nothing my_ch.collect(flat: false, sort: {it[0]}) .map{ it[][1] } .view() process CONCAT_TEST{ input: // or how to manage input cardinality? tuple val(chr_id), path(chr_vcfs) script: """ bcftools concat ... """ } workflow{ CONCAT_TEST(my_ch.collect(flat: false, sort: {it[0]})) } ``` Output: ```auto Launching `example_nf.nf` [distracted_legentil] DSL2 - revision: 3470727da3 [1, test_1.vcf.gz] [MU123, test_MU123.vcf.gz] [JA01.1, test_JA01.1.vcf.gz] [2, test_2.vcf.gz] [10, test_10.vcf.gz] [MT, test_MT.vcf.gz] // collect: [[1, test_1.vcf.gz], [10, test_10.vcf.gz], [2, test_2.vcf.gz], [JA01.1, test_JA01.1.vcf.gz], [MT, test_MT.vcf.gz], [MU123, test_MU123.vcf.gz]] // toSortedList: [['1', 'test_1.vcf.gz'], ['10', 'test_10.vcf.gz'], ['2', 'test_2.vcf.gz'], ['JA01.1', 'test_JA01.1.vcf.gz'], ['MT', 'test_MT.vcf.gz'], ['MU123', 'test_MU123.vcf.gz']] WARN: Input tuple does not match tuple declaration in process `CONCAT_TEST` -- offending value: [[1, test_1.vcf.gz], [10, test_10.vcf.gz], [2, test_2.vcf.gz], [JA01.1, test_JA01.1.vcf.gz], [MT, test_MT.vcf.gz], [MU123, test_MU123.vcf.gz]] ERROR ~ Error executing process > 'CONCAT_TEST' Caused by: Not a valid path value: '10' ``` ---
**Author:** ![bentsherman](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/bentsherman/32/52_2.png) [@bentsherman](https://community.seqera.io/u/bentsherman)\ **Post date:** [April 14, 2026, 3:46pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632/2 "2026-04-14T15:46:46Z")
You need a bit of extra operator logic to transform the list of tuples into a tuple of lists: ```auto process CONCAT_TEST { input: tuple val(chr_ids), path(chr_vcfs) script: """ bcftools concat ... """ } workflow{ my_ch = channel.of( ["1","test_1.vcf.gz"], ["MU123", "test_MU123.vcf.gz"], ["JA01.1", "test_JA01.1.vcf.gz"], ["2", "test_2.vcf.gz"], ["10", "test_10.vcf.gz"], ["MT", "test_MT.vcf.gz"] ) samples_val = my_ch.collect(flat: false) .map { samples -> samples = samples.toSorted { id, path -> id } def ids = samples.collect { id, path -> id } def files = samples.collect { id, path -> path } tuple(ids, files) } .view() CONCAT_TEST(samples_val) } ``` You can find all of the extra methods like `toSorted` and `collect` in the standard library docs: [Types | Seqera Docs](https://docs.seqera.io/nextflow/reference/stdlib-types#iterablee) ---
**Author:** ![Alexander\_Nater](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/alexander_nater/32/552_2.png) [@Alexander\_Nater](https://community.seqera.io/u/Alexander_Nater)\ **Post date:** [April 14, 2026, 3:57pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632/3 "2026-04-14T15:57:05Z")
I like to do this: ```auto my_ch .collect(flat: false, sort: {it[0]}) .map { def (ids, vcfs) = it.transpose() tuple(ids, vcfs) } .view() ``` ---
**Author:** ![rseraphin](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/rseraphin/32/2408_2.png) [@rseraphin](https://community.seqera.io/u/rseraphin)\ **Post date:** [April 14, 2026, 4:22pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632/4 "2026-04-14T16:22:11Z")
Thanks for the answer, when I try with nextflow version 25.10.4 i get an error with the `samples = samples.toSorted { id, path -> id }` line: `ERROR ~ Cannot cast object ‘[MU123, test_MU123.vcf.gz]’ with class ‘java.util.ArrayList’ to class ‘int’` but Alexander’s answer below seems to work using a similar logic! ---
**Author:** ![bentsherman](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/bentsherman/32/52_2.png) [@bentsherman](https://community.seqera.io/u/bentsherman)\ **Post date:** [April 14, 2026, 4:50pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632/5 "2026-04-14T16:50:30Z")
You’re right, the tuple unpacking won’t work with the toSorted closure. So I guess you would have to do `samples.toSorted { it -> it[0] }` (my answer is geared more towards setting you up for static typing in the future 😃 ) ---
**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\ **Post date:** [April 21, 2026, 4:51pm UTC](https://community.seqera.io/t/collect-sorting-by-key-but-keep-only-files-paths/2632/6 "2026-04-21T16:51:07Z")
Closed on April 21, 2026, 4:51pm UTC This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.