Skip to content
Snippets Groups Projects
Select Git revision
  • f4268137c8ee103a0c9253a20163dd41ae6bc976
  • main default protected
2 results

projects_validation.md

Blame
    • tests.sh 1.33 KiB
    1
    2
    3
    4
    5
    6
    7
    8
    9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27
    28
    29
    30
    31
    32
    33
    34
    35
    36
    37
    38
    39
    40
    41
    42 
    

    

    

    ./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