5. Pipeline Tutorial¶
Welcome to the CARLISLE Pipeline Tutorial!
5.1 Getting Started¶
Review the information on the Getting Started for a complete overview the pipeline. The tutorial below will use test data available on NIH Biowulf HPC only. All example code will assume you are running v1.0 of the pipeline, using test data available on GitHub.
A. Change working directory to the CARLISLE repository
B. Initialize Pipeline
bash ./path/to/dir/carlisle --runmode=init --workdir=/path/to/output/dir
5.2 Submit the test data¶
Test data is included in the .test directory as well as the config directory.
A Run the test command to prepare the data, perform a dry-run and submit to the cluster
bash ./path/to/dir/carlisle --runmode=runtest --workdir=/path/to/output/dir
- An expected output for the
runtestis as follows:
Job stats:
job count min threads max threads
----------------------------- ------- ------------- -------------
DESeq 24 1 1
align 9 56 56
alignstats 9 2 2
all 1 1 1
bam2bg 9 4 4
create_contrast_data_files 24 1 1
create_contrast_peakcaller_files 12 1 1
create_reference 1 32 32
create_replicate_sample_table 1 1 1
diffbb 24 1 1
filter 18 2 2
findMotif 96 6 6
gather_alignstats 1 1 1
go_enrichment 12 1 1
gopeaks_broad 16 2 2
gopeaks_narrow 16 2 2
macs2_broad 16 2 2
macs2_narrow 16 2 2
make_counts_matrix 24 1 1
multiqc 2 1 1
qc_fastqc 9 1 1
rose 96 2 2
seacr_relaxed 16 2 2
seacr_stringent 16 2 2
spikein_assessment 1 1 1
trim 9 56 56
total 478 1 56
5.3 Review outputs¶
Review the expected outputs on the Output page. If there are errors, review and performing stesp described on the Troubleshooting page as needed.
Last update: 2024-07-16