mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
abe025677c
* updated kraken2 module to include optional classification of each input reads, and make fastq outputs optional NB: this is a breaking change, because the output channels have been renamed as a consequence of changes * updated yml * pigz command made optional, in order to be executed only if fastq of classified/unclassified reads are saved * updated test yaml file for kraken2 * fixed TODOs and renamed variables and outputs * untar in conda cannot keep same md5sum of version, and therefore md5sum check removed * improved description of the options Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
43 lines
1.8 KiB
YAML
43 lines
1.8 KiB
YAML
- name: kraken2 kraken2 test_kraken2_kraken2_single_end
|
|
command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c tests/config/nextflow.config
|
|
tags:
|
|
- kraken2
|
|
- kraken2/kraken2
|
|
files:
|
|
- path: output/kraken2/test.classified.fastq.gz
|
|
- path: output/kraken2/test.kraken2.report.txt
|
|
md5sum: 4227755fe40478b8d7dc8634b489761e
|
|
- path: output/kraken2/test.unclassified.fastq.gz
|
|
- path: output/kraken2/versions.yml
|
|
md5sum: 6e3ad947ac8dee841a89216071c181cc
|
|
- path: output/untar/versions.yml
|
|
|
|
- name: kraken2 kraken2 test_kraken2_kraken2_paired_end
|
|
command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c tests/config/nextflow.config
|
|
tags:
|
|
- kraken2
|
|
- kraken2/kraken2
|
|
files:
|
|
- path: output/kraken2/test.classified_1.fastq.gz
|
|
- path: output/kraken2/test.classified_2.fastq.gz
|
|
- path: output/kraken2/test.kraken2.report.txt
|
|
md5sum: 4227755fe40478b8d7dc8634b489761e
|
|
- path: output/kraken2/test.unclassified_1.fastq.gz
|
|
- path: output/kraken2/test.unclassified_2.fastq.gz
|
|
- path: output/kraken2/versions.yml
|
|
md5sum: 604482fe7a4519f890fae9c8beb1bd6e
|
|
- path: output/untar/versions.yml
|
|
|
|
- name: kraken2 kraken2 test_kraken2_kraken2_classifyreads
|
|
command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_classifyreads -c tests/config/nextflow.config
|
|
tags:
|
|
- kraken2
|
|
- kraken2/kraken2
|
|
files:
|
|
- path: output/kraken2/test.kraken2.classifiedreads.txt
|
|
md5sum: e7a90531f0d8d777316515c36fe4cae0
|
|
- path: output/kraken2/test.kraken2.report.txt
|
|
md5sum: 4227755fe40478b8d7dc8634b489761e
|
|
- path: output/kraken2/versions.yml
|
|
md5sum: 3488c304259e83c5bea573403293fce9
|
|
- path: output/untar/versions.yml
|