CCBR / TRANQUIL

TRANQUIL (TRna AbundaNce QUantification pIpeLine)

Background

TRANQUIL or "TRna AbundaNce QUantification pIpeLine" is a Snakemake pipeline which quantifies tRNA using the mim-tRNAseq tool.

mim-tRNAseq is dockerized using this recipe. The docker is pushed to dockerhub for general consumption.

The pipeline is developed with the intention of executing it on Biowulf or FRCE clusters. Hence, may have some Biowulf/FRCE specific hardcoding.

Running on FRCE

Pipeline code has been checked out at /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL and is available for all users of FRCE.

$ /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil
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Pipeline Dir: 		 /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL
Snakefile: 		 /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/workflow/Snakefile
Git Commit/Tag: 	 678ccfc1f3c0013690c2d09100619b9a5b7259ee
Host: 			 FRCE
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Running /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil ...
TRANQUIL (TRna AbundaNce QUantification pIpeLine)
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USAGE:
  bash /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
Required Arguments:
1.  RUNMODE: [Type: String] Valid options:
    *) init : initialize workdir
    *) run : run with slurm
    *) reset : DELETE workdir dir and re-init it
    *) dryrun : dry run snakemake to generate DAG
    *) unlock : unlock workdir if locked by snakemake
    *) runlocal : run without submitting to sbatch
2.  WORKDIR: [Type: String]: Absolute or relative path to the
             output folder with write permissions.
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In order to run the pipeline, there are 3 steps:

1. Initialize: Use the init mode to setup the output folder:

$ bash /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -w=/scratch/cluster_scratch/$USER/TRANQUIL_test -m=init
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Pipeline Dir: 		 /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL
Snakefile: 		 /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/workflow/Snakefile
Git Commit/Tag: 	 678ccfc1f3c0013690c2d09100619b9a5b7259ee
Host: 			 FRCE
COPYING resources ...
COPYING scripts ...
Logs Dir: 		 /scratch/cluster_scratch/kopardevn/TRANQUIL_test/logs
Stats Dir: 		 /scratch/cluster_scratch/kopardevn/TRANQUIL_test/stats
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Done Initializing /scratch/cluster_scratch/kopardevn/TRANQUIL_test.
You can now edit
/scratch/cluster_scratch/kopardevn/TRANQUIL_test/config.yaml
/scratch/cluster_scratch/kopardevn/TRANQUIL_test/samples.tsv
and
/scratch/cluster_scratch/kopardevn/TRANQUIL_test/contrasts.tsv
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2. Enter Sample Manifest: Now edit the samples.tsv and contrasts.tsv in the output folder to reflect the names/locations of the sample input files and the desired contrasts.

samples.tsv has the following tab-delimited columns:

- sampleName
- replicateNumber	
- path_to_R1_fastq

contrasts.tsv has the following tab-delimited columns:

- group1
- group2

The group1 w.r.t. group2 contrast is run.

NOTE: By default the samples.tsv and contrasts.tsv will be pointing to the test dataset in the .tests folder.

3. Dry-run (and Run) : The following command will run the dry-run and generate a dryrun.log in the output folder

$ /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -w=/scratch/cluster_scratch/$USER/TRANQUIL_test -m=dry

Once everything looks ok, the job can be run on the cluster by switching the mode from dry to run, like so:

$ /mnt/projects/CCBR-Pipelines/pipelines/TRANQUIL/tranquil -w=/scratch/cluster_scratch/$USER/TRANQUIL_test -m=run

Outputs:

• The output folder has a results subfolder which has a fastqs subfolder with

  • trimmed fastqs prepared for mim-tRNAseq
  • readstats.txt tab-delimited file with trimming statistics

• The results folder also contains one subfolder for each of the contrasts in the contrasts.tsv with the naming convention of "<group1>_vs_<group2>". This folder has the mim-tRNAseq outputs.

Please send any comments/suggestions/requests to Vishal Koparde via email.