Commands for testing software setup

[tavareshugo]

@cambioinfo below the code to test the setup for day 1:

# directory for day 1
cd M_tuberculosis/

# samplesheet
python scripts/fastq_dir_to_samplesheet.py data/reads \
    samplesheet.csv \
    -r1 _1.fastq.gz \
    -r2 _2.fastq.gz

# activate environment
eval "$(conda shell.bash hook)"
source $(mamba info --base)/etc/profile.d/mamba.sh
mamba activate nextflow

# bacQC - takes ~6 min
nextflow run avantonder/bacQC \
  -r main \
  -profile singularity \
  --max_memory '16.GB' --max_cpus 8 \
  --input samplesheet.csv \
  --outdir results/bacqc \
  --kraken2db databases/minikraken2_v1_8GB \
  --brackendb databases/minikraken2_v1_8GB \
  --genome_size 4300000

# bactmap ~ takes ~10 min
nextflow run nf-core/bactmap \
  -profile singularity \
  --max_memory '16.GB' --max_cpus 8 \
  --input samplesheet.csv \
  --outdir results/bactmap \
  --reference resources/reference/MTBC0.fasta \
  --genome_size 4.3M

# activate new env
mamba activate seqtk

# seqtk script - <1 min
bash scripts/03-pseudogenome_check.sh

# activate new env
mamba activate remove_blocks

# masking script - <1 min
bash scripts/04-mask_pseudogenome.sh

[cambioinfo]

All working on current course environment for 11/12/23