Skip to content
Snippets Groups Projects
Select Git revision
  • f51bf1e4d50dd21bfe4e01d9f4251c0fac2d2a9a
  • master default protected
  • dchalopi-master-patch-91545
  • tp_experimental_biologists
4 results

samtools.config

Blame
    • Forked from LBMC / nextflow
    Source project has a limited visibility.
    tests.sh 1.29 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
    43 
    

    

    

    ./nextflow src/nf_modules/bwa/indexing.nf \
  -c src/nf_modules/bwa/indexing.config \
  -profile docker \
  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
  -resume

# ./nextflow src/nf_modules/bwa/mapping_single.nf \
#   -c src/nf_modules/bwa/mapping_single.config \
#   -profile docker \
#   --index "results/mapping/index/tiny_v2.index" \
#   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"

./nextflow src/nf_modules/bwa/mapping_paired.nf \
  -c src/nf_modules/bwa/mapping_paired.config \
  -profile docker \
  --index "results/mapping/index/tiny_v2.*" \
  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
  -resume


if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bwa/indexing.nf \
  -c src/nf_modules/bwa/indexing.config \
  -profile singularity \
  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
  -resume


# ./nextflow src/nf_modules/bwa/mapping_single.nf \
#   -c src/nf_modules/bwa/mapping_single.config \
#   -profile singularity \
#   --index "results/mapping/index/tiny_v2.index" \
#   --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"

./nextflow src/nf_modules/bwa/mapping_paired.nf \
  -c src/nf_modules/bwa/mapping_paired.config \
  -profile singularity \
  --index "results/mapping/index/tiny_v2.*" \
  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
  -resume

fi