Commit 2e6c9c53 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Changed tagging system in pytest to remove forward slahes

parent d8c5d919

.github/workflows/ci.yml

+1 −1
Original line number Diff line number Diff line
@@ -75,7 +75,7 @@ jobs: 
    strategy:

      matrix:

        nxf_version: ["21.04.0", '']

        tags: ["samplesheet", "verify_output/input", "verify_output/align", "verify_output/peak_calling", "verify_output/reporting", "verify_output/save", "verify_output/skip"]

        tags: ["samplesheet", "verify_output_input", "verify_output_align", "verify_output_peak_calling", "verify_output_reporting", "verify_output_save", "verify_output_skip"]

    steps:

      - uses: actions/checkout@v2

tests/test_samplesheet_check.yml

+15 −15
Original line number Diff line number Diff line
@@ -2,15 +2,15 @@ 
  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/rep_id_start_1.csv

  tags:

    - samplesheet

    - samplesheet/start_1

    - 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

  tags:

    - samplesheet

    - samplesheet/no_igg

    - samplesheet/no_igg/pos

    - samplesheet_no_igg

    - samplesheet_no_igg_pos

  files:

    - path: results/pipeline_info/samplesheet.valid.csv
@@ -18,16 +18,16 @@ 
  command: nextflow run main.nf -profile docker,test --only_input true --igg_control true --input tests/data/samplesheets/no_igg.csv

  tags:

    - samplesheet

    - samplesheet/no_igg

    - samplesheet/no_igg/neg

    - samplesheet_no_igg

    - samplesheet_no_igg_neg

  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

  tags:

    - samplesheet

    - samplesheet/1_1

    - samplesheet/1_1/pos

    - samplesheet_1_1

    - samplesheet_1_1_pos

  files:

    - path: results/pipeline_info/samplesheet.valid.csv
@@ -35,31 +35,31 @@ 
  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/single_sample_single_igg_neg.csv

  tags:

    - samplesheet

    - samplesheet/1_1

    - samplesheet/1_1/neg

    - samplesheet_1_1

    - samplesheet_1_1_neg

  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

  tags:

    - samplesheet

    - samplesheet/1_2

    - samplesheet/1_2/group_match

    - samplesheet_1_2

    - samplesheet_1_2_group_match

  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

  tags:

    - samplesheet

    - samplesheet/2_2

    - samplesheet/2_2/group_match_tech_rep

    - samplesheet_2_2

    - samplesheet-2_2_group_match_tech_rep

  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

  tags:

    - samplesheet

    - samplesheet/M_1

    - samplesheet_M_1

  files:

    - path: results/pipeline_info/samplesheet.valid.csv
@@ -67,6 +67,6 @@ 
  command: nextflow run main.nf -profile docker,test --only_input true --input tests/data/samplesheets/multiple_sample_multiple_igg.csv

  tags:

    - samplesheet

    - samplesheet/M_M

    - samplesheet_M_M

  files:

    - path: results/pipeline_info/samplesheet.valid.csv
 
 No newline at end of file

tests/test_verify_output_align_intermed.yml

+2 −2
Original line number Diff line number Diff line
@@ -2,8 +2,8 @@ 
  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --save_align_intermed true

  tags:

    - verify_output

    - verify_output/align

    - verify_output/align/intermed

    - verify_output_align

    - verify_output_align_intermed

  files:

    - path: results/02_alignment/bowtie2/target/intermed/align/h3k27me3_R1.target.sorted.bam

    - path: results/02_alignment/bowtie2/target/intermed/qfilter/h3k27me3_R1.target.filtered.bam

tests/test_verify_output_duplicates.yml

+9 −9
Original line number Diff line number Diff line
@@ -2,9 +2,9 @@ 
  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true

  tags:

    - verify_output

    - verify_output/align

    - verify_output/align/duplicates

    - verify_output/align/duplicates/mark

    - verify_output_align

    - verify_output_align_duplicates

    - verify_output_align_duplicates_mark

  files:

    - path: results/02_alignment/bowtie2/target/markdup/h3k27me3_R1.target.markdup.bam

    - path: results/02_alignment/bowtie2/target/markdup/igg_R1.target.markdup.bam
@@ -17,9 +17,9 @@ 
  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads false

  tags:

    - verify_output

    - verify_output/align

    - verify_output/align/duplicates

    - verify_output/align/duplicates/remove

    - verify_output_align

    - verify_output_align_duplicates

    - verify_output_align_duplicates_remove

  files:

    - path: results/02_alignment/bowtie2/target/markdup/h3k27me3_R1.target.markdup.bam

    - path: results/02_alignment/bowtie2/target/dedup/igg_R1.target.dedup.bam
@@ -34,9 +34,9 @@ 
  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads true

  tags:

    - verify_output

    - verify_output/align

    - verify_output/align/duplicates

    - verify_output/align/duplicates/remove_target

    - verify_output_align

    - verify_output_align_duplicates

    - verify_output_align_duplicates_remove_target

  files:

    - path: results/02_alignment/bowtie2/target/dedup/h3k27me3_R1.target.dedup.bam

    - path: results/02_alignment/bowtie2/target/dedup/igg_R1.target.dedup.bam

tests/test_verify_output_only_align.yml

+2 −2
Original line number Diff line number Diff line
@@ -2,8 +2,8 @@ 
  command: nextflow run main.nf -profile docker,test --only_alignment true --skip_fastqc true

  tags:

    - verify_output

    - verify_output/align

    - verify_output/align/only_align

    - verify_output_align

    - verify_output_align_only_align

  files:

    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.sorted.bam

    - path: results/02_alignment/bowtie2/target/igg_R1.target.sorted.bam

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