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18 results

indexing.nf

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  • Forked from LBMC / nextflow
    Source project has a limited visibility.
    tests.sh NaN GiB
    ./nextflow src/nf_modules/Bowtie/indexing.nf \
      -c src/nf_modules/Bowtie/indexing.config \
      -profile docker \
      --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
    
    ./nextflow src/nf_modules/Bowtie/mapping_single.nf \
      -c src/nf_modules/Bowtie/mapping_single.config \
      -profile docker \
      --index "results/mapping/index/*.ebwt" \
      --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
    
    ./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
      -c src/nf_modules/Bowtie/mapping_paired.config \
      -profile docker \
      --index "results/mapping/index/*.ebwt" \
      --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
    
    if [ -x "$(command -v singularity)" ]; then
    ./nextflow src/nf_modules/Bowtie/indexing.nf \
      -c src/nf_modules/Bowtie/indexing.config \
      -profile singularity \
      --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
    
    ./nextflow src/nf_modules/Bowtie/mapping_single.nf \
      -c src/nf_modules/Bowtie/mapping_single.config \
      -profile singularity \
      --index "results/mapping/index/*.ebwt" \
      --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
    
    ./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
      -c src/nf_modules/Bowtie/mapping_paired.config \
      -profile singularity \
      --index "results/mapping/index/*.ebwt" \
      --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
    fi