> snakemake --cores 2 -n
...
BAM_to_BED 2
Non_insertion_mapping 2
all 1
annotation_overlap_insertion 2
basic_insertion_plots 1
build_insertion_reference 1
calc_distance_to_elements 2
calculate_exact_insertion_coordinates 2
clean_postcut_by_maping_quality 2
collect_outputs 2
copy_config_version 1
detailed_fragmentation_length_plot 2
extract_by_length 2
extract_fastq_insertions 2
extract_mapping_quality 2
fasta_insertion_reads 2
finalize_mapping_quality 2
find_insertion_BLASTn 2
find_insertion_BLASTn_in_Ref 2
fragmentation_distribution_plots 2
generate_mapq_plot 2
get_coordinates_for_fasta 2
hardcode_blast_header 2
insertion_fragmentation 1
insertion_mapping 2
insertion_points 2
insertion_reads 2
make_blastn_DB 1
make_fasta_without_tags 2
minimap_index 1
multiqc 1
nanoplot 2
prepare_insertion 1
read_level_fastqc 2
sort_insertion_file 2
split_fasta 2
total 63
All of these jobs will be executed in the correct order by the workflow. So let's finally run it.
snakemake --cores 2 --use-conda!!! info
Depending on the number of cores and threads specified and whether the environments need to be built for the first time, this process may take a while. However, since the simulated data is very small, the expected runtime should not exceed 5-10 minutes.
If you see this message, the workflow has executed successfully and completed. If not, refer to the error handling section.
Finished job 0.
63 of 63 steps (100%) doneNow, run snakemake again with its built-in --report functionality to get a comprehensive overview of the workflow's runtime and output.
snakemake --report tutorial/report.html