Commit dd55eb05 authored by Spencer Barnes's avatar Spencer Barnes
Browse files

fix pe/se test designations

parent bf3b3d37
Pipeline #7217 failed with stages
in 43 minutes and 3 seconds
......@@ -27,10 +27,10 @@ GRCh38-0.0.1:
except:
- tags
script:
- nextflow run ./workflow/main.nf --pairedEnd --designFile "./test_data/test_design_pe.txt" --reads "./test_data/*fastq.gz"
- nextflow run ./workflow/main.nf --designFile "./test_data/test_design_se.txt" --reads "./test_data/*fastq.gz"
- pytest -m pairedend
- pytest -m methData_pe
- pytest -m trimData_pe
- pytest -m methData_se
- pytest -m trimData_se
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -48,10 +48,10 @@ mm10-0.0.1:
except:
- tags
script:
- nextflow run ./workflow/main.nf --designFile "./test_data/test_design_se.txt" --reads "./test_data/*fastq.gz"
- pytest -m methData_se
- nextflow run ./workflow/main.nf --pairedEnd --designFile "./test_data/test_design_pe.txt" --reads "./test_data/*fastq.gz"
- pytest -m methData_pe
- pytest -m singleend
- pytest -m trimData_se
- pytest -m trimData_pe
artifacts:
name: "$CI_JOB_NAME"
when: always
......
sample_id experiment_id biosample treatment replicate fastq_read1 fastq_read2
heart1 heart heart none 1 heart_a_S2_R1_001.fastq.gz heart_a_S2_R2_001.fastq.gz
heart2 heart heart none 2 heart_b_S4_R1_001.fastq.gz heart_b_S4_R2_001.fastq.gz
liver1 liver liver none 1 liver_a_S4_R1_001.fastq.gz liver_a_S4_R2_001.fastq.gz
liver2 liver liver none 2 Liver_b_S2_R1_001.fastq.gz Liver_b_S2_R2_001.fastq.gz
sample_id,experiment_id,biosample,treatment,replicate,fastq_read1,fastq_read2
liver1,liver,liver,none,1,ENCFF000MBY_hsap_hepato_rep1.fastq.gz,
liver2,liver,liver,none,2,ENCFF000MCD_hsap_hepato_rep2.fastq.gz,
lung1,lung,lung,none,1,ENCFF000MDS_hsap_lung_rrbs_rep1.fastq.gz,
lung2,lung,lung,none,2,ENCFF000MDT_hsap__lung_rep2.fastq.gz,
\ No newline at end of file
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