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apeltzerTCLamnidis
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Update .github/workflows/ci.yml
Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
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.github/workflows/ci.yml

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@@ -103,7 +103,7 @@ jobs:
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- name: MAPPER_BT2 Test running with BowTie2
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
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- name: HOST REMOVAL_FASTQ Run the basic pipeline with output unmapped reads as fastq
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- name: HOST_REMOVAL_FASTQ Run the basic pipeline with output unmapped reads as fastq
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --hostremoval_input_fastq
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- name: BAM_FILTERING Run basic mapping pipeline with mapping quality filtering, and unmapped export

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