Skip to content
Snippets Groups Projects
Select Git revision
  • cbd23ab657eb28ecb515824d97fadf5144eed196
  • master default protected
  • carpin-master-patch-86884
  • dev
  • v2.0.0
  • v0.4.0
  • v0.3.0
  • v0.2.9
  • v0.2.8
  • v0.2.7
  • v0.2.6
  • v0.1.0
  • v0.2.5
  • v0.2.4
  • v0.2.3
  • v0.2.2
  • v0.2.1
  • v0.2.0
  • v0.1.2
19 results

tests.sh

Blame
  • Forked from LBMC / nextflow
    942 commits behind the upstream repository.
    tests.sh 1.33 KiB
    ./nextflow src/nf_modules/Bowtie2/indexing.nf \
      -c src/nf_modules/Bowtie2/indexing.config \
      -profile docker \
      --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
      -resume
    
    ./nextflow src/nf_modules/Bowtie2/mapping_single.nf \
      -c src/nf_modules/Bowtie2/mapping_single.config \
      -profile docker \
      --index "data/tiny_dataset/fasta/*.bt2" \
      --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
      -resume
    
    ./nextflow src/nf_modules/Bowtie2/mapping_paired.nf \
      -c src/nf_modules/Bowtie2/mapping_paired.config \
      -profile docker \
      --index "data/tiny_dataset/fasta/*.bt2" \
      --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
      -resume
    
    if [ -x "$(command -v singularity)" ]; then
    ./nextflow src/nf_modules/Bowtie2/indexing.nf \
      -c src/nf_modules/Bowtie2/indexing.config \
      -profile singularity \
      --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
      -resume
    
    ./nextflow src/nf_modules/Bowtie2/mapping_single.nf \
      -c src/nf_modules/Bowtie2/mapping_single.config \
      -profile singularity \
      --index "data/tiny_dataset/fasta/*.bt2" \
      --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
      -resume
    
    ./nextflow src/nf_modules/Bowtie2/mapping_paired.nf \
      -c src/nf_modules/Bowtie2/mapping_paired.config \
      -profile singularity \
      --index "data/tiny_dataset/fasta/*.bt2" \
      --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
      -resume
    fi