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Update cat module (#1469)

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* fix cat stub

* add test

* commit suggestions

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
This commit is contained in:
Ramprasad Neethiraj 2022-03-31 13:42:44 +02:00 committed by GitHub
parent 233f2e728b
commit eeda4136c0
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2 changed files with 42 additions and 0 deletions
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2
modules/cat/cat/main.nf
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@ -49,6 +49,8 @@ process CAT_CAT {
""" """
stub: stub:
def file_list = files_in.collect { it.toString() }
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
""" """
touch $prefix touch $prefix

40
tests/modules/cat/cat/test.yml
View file

@ -7,6 +7,14 @@
- path: output/cat/test.fasta - path: output/cat/test.fasta
md5sum: f44b33a0e441ad58b2d3700270e2dbe2 md5sum: f44b33a0e441ad58b2d3700270e2dbe2
- name: cat unzipped unzipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/test.fasta
- name: cat zipped zipped - name: cat zipped zipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags: tags:
@ -15,6 +23,14 @@
files: files:
- path: output/cat/test.gz - path: output/cat/test.gz
- name: cat zipped zipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/test.gz
- name: cat zipped unzipped - name: cat zipped unzipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags: tags:
@ -24,6 +40,14 @@
- path: output/cat/cat.txt - path: output/cat/cat.txt
md5sum: c439d3b60e7bc03e8802a451a0d9a5d9 md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
- name: cat zipped unzipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/cat.txt
- name: cat unzipped zipped - name: cat unzipped zipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags: tags:
@ -32,6 +56,14 @@
files: files:
- path: output/cat/cat.txt.gz - path: output/cat/cat.txt.gz
- name: cat unzipped zipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/cat.txt.gz
- name: cat one file unzipped zipped - name: cat one file unzipped zipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags: tags:
@ -39,3 +71,11 @@
- cat/cat - cat/cat
files: files:
- path: output/cat/cat.txt.gz - path: output/cat/cat.txt.gz
- name: cat one file unzipped zipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/cat.txt.gz