Commit 4d76c50b authored by Chris Cheshire's avatar Chris Cheshire
Browse files

added unit test config

parent caba95d1

tests/config/nextflow.config

0 → 100644
+10 −0
Original line number Diff line number Diff line 
params {

    outdir = "results/"

    publish_dir_mode = "copy"

}



process {

  cpus = 2

  memory = 6.GB

  time = 6.h

}
 
 No newline at end of file

tests/test_samplesheet_check.yml

+9 −9
Original line number Diff line number Diff line 
- name: test_samplesheet_check_test_id_1

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/rep_id_start_1.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/rep_id_start_1.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_start_1

  exit_code: 1



- name: test_samplesheet_check_noigg_pos

  command: nextflow run main.nf -profile docker,test --only_input true --igg_control false --input tests/data/samplesheets/no_igg.csv

  command: nextflow run main.nf -profile docker,test --only_input true --igg_control false --input tests/data/samplesheets/no_igg.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_no_igg
@@ -15,7 +15,7 @@ 
    - path: results/pipeline_info/samplesheet.valid.csv



- name: test_samplesheet_check_noigg_neg

  command: nextflow run main.nf -profile docker,test --only_input true --igg_control true --input tests/data/samplesheets/no_igg.csv

  command: nextflow run main.nf -profile docker,test --only_input true --igg_control true --input tests/data/samplesheets/no_igg.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_no_igg
@@ -23,7 +23,7 @@ 
  exit_code: 1



- name: test_samplesheet_check_1_1_pos

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_1_1
@@ -32,7 +32,7 @@ 
    - path: results/pipeline_info/samplesheet.valid.csv



- name: test_samplesheet_check_1_1_neg

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_neg.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_neg.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_1_1
@@ -40,7 +40,7 @@ 
  exit_code: 1



- name: test_samplesheet_check_1_2_group_match

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_non_matching_groups.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_non_matching_groups.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_1_2
@@ -48,7 +48,7 @@ 
  exit_code: 1



- name: test_samplesheet_check_2_2_group_match_tech_rep

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_non_matching_groups_tech_rep.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_non_matching_groups_tech_rep.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_2_2
@@ -56,7 +56,7 @@ 
  exit_code: 1



- name: test_samplesheet_check_multiple_sample_single_igg

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/multiple_sample_single_igg.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/multiple_sample_single_igg.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_M_1
@@ -64,7 +64,7 @@ 
    - path: results/pipeline_info/samplesheet.valid.csv



- name: test_samplesheet_check_multiple_sample_multiple_igg

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/multiple_sample_multiple_igg.csv

  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/multiple_sample_multiple_igg.csv -c tests/config/nextflow.config

  tags:

    - samplesheet

    - samplesheet_M_M

tests/test_verify_output_align_intermed.yml

+1 −1
Original line number Diff line number Diff line 
- name: test_verify_output_align_intermed

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --save_align_intermed true

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --save_align_intermed true -c tests/config/nextflow.config

  tags:

    - verify_output

    - verify_output_align

tests/test_verify_output_duplicates.yml

+1 −1
Original line number Diff line number Diff line 
- name: test_verify_output_duplicates_mark

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config

  tags:

    - verify_output

    - verify_output_align

tests/test_verify_output_only_align.yml

+1 −1
Original line number Diff line number Diff line 
- name: test_verify_output_only_align

  command: nextflow run main.nf -profile docker,test --only_alignment true --skip_fastqc true

  command: nextflow run main.nf -profile docker,test --only_alignment true --skip_fastqc true -c tests/config/nextflow.config

  tags:

    - verify_output

    - verify_output_align

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