Commit 6e1e82ca authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Updated q-filter test

parent 3fb47bbd

tests/test_verify_output_only_q_filter.yml

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

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true minimum_alignment_q_score 10 --skip_markduplicates true --skip_removeduplicates true -c tests/config/nextflow.config

  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true minimum_alignment_q_score 10 --skip_removeduplicates true -c tests/config/nextflow.config

  tags:

    - verify_output

    - verify_output_align

workflows/cutandrun.nf

+2 −1
Original line number Diff line number Diff line
@@ -86,7 +86,6 @@ if(params.skip_reporting) { 
    run_peak_plotting = false

}





if(params.only_input) {

    run_genome_prep        = false

    run_cat_fastq          = false
@@ -134,6 +133,8 @@ if(params.only_alignment) { 
}



if(params.only_filtering) {

    run_mark_dups    = false

    run_remove_dups  = false

    run_peak_calling = false

    run_reporting    = false

    run_multiqc      = false

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