Commit a3a920b2 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Updated testing names

parent e46a7359

.github/workflows/ci.yml

+13 −9
Original line number Diff line number Diff line
@@ -146,21 +146,25 @@ jobs: 
      matrix:

        nxf_version: ['21.10.3', '']

        tags:

          - params

          - samplesheet

          - verify_output_input

          - verify_output_peak_calling

          - verify_output_reporting

          - verify_output_save

          - verify_output_skip

          - verify_output_align_only_q_filter

          - verify_output_align_duplicates_mark

          - verify_output_align_duplicates_remove

          - verify_output_align_duplicates_remove_target

          - verify_output_save_ref

          - verify_output_only_input

          - verify_output_save_merged

          - verify_output_skip_fastqc

          - verify_output_save_trimmed

          - verify_output_skip_trimming

          - verify_output_align_intermed

          - verify_output_align_only_align

          - verify_output_align_save_spikein_align

          - verify_output_align_save_unaligned

          - verify_output_only_filtering

          - verify_output_align_duplicates_mark

          - verify_output_align_duplicates_remove

          - verify_output_align_duplicates_remove_target

          - verify_output_peak_calling_only_peak_calling

          - test_peak_callers

          - verify_output_reporting

    steps:

      - uses: actions/checkout@v2

conf/base.config

+3 −3
Original line number Diff line number Diff line
@@ -45,7 +45,7 @@ process { 
        errorStrategy = 'retry'

        maxRetries    = 2

    }

    withName:CUSTOM_DUMPSOFTWAREVERSIONS {

        cache = false

    }

    // withName:CUSTOM_DUMPSOFTWAREVERSIONS {

    //     cache = false

    // }

}

tests/test_verify_output_align_intermed.yml

+0 −1
Original line number Diff line number Diff line
@@ -3,7 +3,6 @@ 
  tags:

    - verify_output

    - verify_output_align

    - verify_output_align_long

    - verify_output_align_intermed

  files:

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

tests/test_verify_output_duplicates.yml

+22 −23
Original line number Diff line number Diff line 
- name: test_verify_output_duplicates_mark

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

  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

    - verify_output_align_long

    - 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

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

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

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

    - path: results/02_alignment/bowtie2/target/markdup/samtools_stats/igg_R1.target.markdup.bam.flagstat

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

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

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

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

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

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



- name: test_verify_output_duplicates_remove

  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --dedup_target_reads false

  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

  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

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

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

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

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

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

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

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

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

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

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

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

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

      should_exist: false



- name: test_verify_output_duplicates_remove_target

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

  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

  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

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

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

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

    - path: results/02_alignment/bowtie2/target/dedup/samtools_stats/igg_R1.target.dedup.bam.flagstat
 
 No newline at end of file
 
    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.bam

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

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

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

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

    - path: results/02_alignment/bowtie2/target/igg_R1.target.dedup.bam.flagstat
 
 No newline at end of file

tests/test_verify_output_only_align.yml

+0 −1
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@@ -3,7 +3,6 @@ 
  tags:

    - verify_output

    - verify_output_align

    - verify_output_align_short

    - verify_output_align_only_align

  files:

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

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