Commit adad6c35 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Updated tests for new filenames

parent b950466d

tests/test_bam_scaling.yml

+1 −1
Original line number Diff line number Diff line
@@ -57,6 +57,6 @@ 
    - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph

      contains:

        - "chr20	171984	172009	1607.72"

    - path: results/03_peak_calling/01_bam_to_bedgraph/igg_R1.sorted.bedGraph

    - path: results/03_peak_calling/01_bam_to_bedgraph/igg_ctrl_R1.sorted.bedGraph

      contains:

        - "chr20	606391	606415	285.714"

tests/test_verify_output_align_intermed.yml

+4 −4
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ 
    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.filtered.bam

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

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

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

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

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

    - path: results/02_alignment/bowtie2/target/igg_R1.target.sorted.bam
 
    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.filtered.bam

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam

tests/test_verify_output_duplicates.yml

+9 −9
Original line number Diff line number Diff line
@@ -7,11 +7,11 @@ 
    - verify_output_align_duplicates_mark

  files:

    - 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/igg_ctrl_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/igg_ctrl_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

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.flagstat



- name: test_verify_output_duplicates_remove

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads false
@@ -22,11 +22,11 @@ 
    - verify_output_align_duplicates_remove

  files:

    - 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/igg_ctrl_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/igg_ctrl_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/igg_ctrl_R1.target.dedup.bam.flagstat

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

      should_exist: false
@@ -39,8 +39,8 @@ 
    - verify_output_align_duplicates_remove_target

  files:

    - 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/igg_ctrl_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/igg_ctrl_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
 
    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam.flagstat

tests/test_verify_output_only_align.yml

+3 −3
Original line number Diff line number Diff line
@@ -6,8 +6,8 @@ 
    - 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

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam

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

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

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam.bai

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

    - path: results/02_alignment/bowtie2/target/igg_R1.target.sorted.bam.flagstat
 
    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam.flagstat

tests/test_verify_output_only_filtering.yml

+3 −3
Original line number Diff line number Diff line
@@ -7,6 +7,6 @@ 
    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam

    - path: results/02_alignment/bowtie2/target/h3k27me3_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

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

    - path: results/02_alignment/bowtie2/target/igg_R1.target.markdup.bam.flagstat
 
    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.bai

    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.flagstat

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