nf-core_modules/tests/modules/srst2/srst2/test.yml

- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config
  tags:
    - srst2/srst2
    - srst2
  exit_code: 1

- name: srst2 srst2 test_srst2_srst2_mlst
  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config
  tags:
    - srst2/srst2
    - srst2
  files:
    - path: output/srst2/test__SRR9067271.MLST_DB.pileup
      contains:
        - "dnaJ-1	2	C	17	.........,.......	FFFFFFFFFFFFFFFFF"
    - path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
    - path: output/srst2/test__mlst__MLST_DB__results.txt
      md5sum: ec1b1f69933401d67c57f64cad11a098
    - path: output/srst2/versions.yml
      md5sum: a0c256a2fd3636069710b8ef22ee5ea7

- name: srst2 srst2 test_srst2_srst2_paired_end
  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config
  tags:
    - srst2/srst2
    - srst2
  files:
    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
      md5sum: 099aa6cacec5524b311f606debdfb3a9
    - path: output/srst2/test__test1.resFinder_20180221_srst2.pileup
      md5sum: 64b512ff495b828c456405ec7b676ad1
    - path: output/srst2/test__test1.resFinder_20180221_srst2.sorted.bam
    - path: output/srst2/versions.yml
      md5sum: b446a70f1a2b4f60757829bcd744a214

- name: srst2 srst2 test_srst2_srst2_single_end
  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config
  tags:
    - srst2/srst2
    - srst2
  files:
    - path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
      md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
      md5sum: b8850c6644406d8b131e471ecc3f9013
    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.pileup
      md5sum: 5f6279dc8124aa762a9dfe3d7a871277
    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
    - path: output/srst2/versions.yml
      md5sum: 790fe00493c6634d17801a930073218b
linting test.yml 2022-05-02 15:38:39 +00:00			`- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db`
Update tests/modules/srst2/srst2/test.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> 2022-05-02 16:26:56 +00:00			`command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config`
linting test.yml 2022-05-02 15:38:39 +00:00			`tags:`
			`- srst2/srst2`
			`- srst2`
			`exit_code: 1`

added tests 2022-05-02 15:30:19 +00:00			`- name: srst2 srst2 test_srst2_srst2_mlst`
			`command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config`
			`tags:`
			`- srst2/srst2`
			`- srst2`
			`files:`
			`- path: output/srst2/test__SRR9067271.MLST_DB.pileup`
Update test.yml 2022-05-02 22:20:54 +00:00			`contains:`
Update test.yml 2022-05-02 22:38:48 +00:00			`- "dnaJ-1 2 C 17 .........,....... FFFFFFFFFFFFFFFFF"`
added tests 2022-05-02 15:30:19 +00:00			`- path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam`
			`- path: output/srst2/test__mlst__MLST_DB__results.txt`
			`md5sum: ec1b1f69933401d67c57f64cad11a098`
Update test.yml 2022-05-02 22:27:01 +00:00			`- path: output/srst2/versions.yml`
added tests 2022-05-02 15:30:19 +00:00			`md5sum: a0c256a2fd3636069710b8ef22ee5ea7`

adding srst2 module 2022-04-27 22:01:28 +00:00			`- name: srst2 srst2 test_srst2_srst2_paired_end`
			`command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config`
			`tags:`
Update test.yml 2022-04-27 23:54:33 +00:00			`- srst2/srst2`
added tests 2022-05-02 15:30:19 +00:00			`- srst2`
adding srst2 module 2022-04-27 22:01:28 +00:00			`files:`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: 099aa6cacec5524b311f606debdfb3a9`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__test1.resFinder_20180221_srst2.pileup`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: 64b512ff495b828c456405ec7b676ad1`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__test1.resFinder_20180221_srst2.sorted.bam`
			`- path: output/srst2/versions.yml`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: b446a70f1a2b4f60757829bcd744a214`

			`- name: srst2 srst2 test_srst2_srst2_single_end`
			`command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config`
			`tags:`
Update test.yml 2022-04-27 23:54:33 +00:00			`- srst2/srst2`
added tests 2022-05-02 15:30:19 +00:00			`- srst2`
adding srst2 module 2022-04-27 22:01:28 +00:00			`files:`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: d0762ef8c38afd0e0a34cce52ed1a3db`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: b8850c6644406d8b131e471ecc3f9013`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__test1_1.resFinder_20180221_srst2.pileup`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: 5f6279dc8124aa762a9dfe3d7a871277`
tmp/ to changed to output/ 2022-04-28 00:21:41 +00:00			`- path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam`
			`- path: output/srst2/versions.yml`
adding srst2 module 2022-04-27 22:01:28 +00:00			`md5sum: 790fe00493c6634d17801a930073218b`