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indexing.nf
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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