Question on SQANTI3 Argument Differences Between Conda and Singularity

[Motoufiq]

Hi,

I previously ran SQANTI3 using a Conda environment set up by a previous lab member. Since I no longer have access to that environment, I downloaded the latest Singularity image from the official SQANTI3 repository (installation guide) and plan to run it using Singularity.

I noticed a difference in the command-line arguments: in the Conda setup, we used --gtf to specify the transcript file, whereas the Singularity version appears to use --filter_gtf. I wanted to confirm does this difference in argument naming affect how SQANTI3 runs within the Singularity container, or is it simply a version-specific change?

Run SQANTI3 filter using conda

cd $SLURM_SUBMIT_DIR

source /projects/programs/miniconda3/etc/profile.d/conda.sh
conda activate SQANTI3.env
export PYTHONPATH=$PYTHONPATH:/projects/programs/SQANTI3-5.2/cDNA_Cupcake/sequence/
export PYTHONPATH=$PYTHONPATH:/projects/programs/SQANTI3-5.2/cDNA_Cupcake/

SQANTI_CLASS="/projects/sqanti3_qc_outputs/LUAD_v3_classification.txt"
GTF="/projects/LR_Analysis/collapse/LUAD_v2.collapsed.gff"
OUTPUT_NAME="LUAD_v3"
OUTPUT_DIR="/projects/sqanti3_filter_outputs"
FILTER_RULES="/projects/rulesFilter.json"

python /projects/programs/SQANTI3-5.2/sqanti3_filter.py rules\
 "$SQANTI_CLASS"\
 --gtf "$GTF"\
 -o "$OUTPUT_NAME"\
 -d "$OUTPUT_DIR"\
 -j "$FILTER_RULES"

Run SQANTI3 filter using singularity

singularity run /projects/palucka-lab/toufim/Tools/sqanti3.sif \
    sqanti3_filter.py rules \
    --sqanti_class "$SQANTI_CLASS" \
    --filter_gtf "$GTF" \
    -o "$OUTPUT_NAME" \
    -d "$OUTPUT_DIR" \
    -j "$FILTER_RULES"

Thanks in advance for your guidance!

Best Regards,
Toufiq

[pabloati]

Hi Toufiq,

The change in the argument is due to a version upgrade. Since the implementation of the wrapper, the --gtf argument has changesd to be --filter_gtf. If you want to have some more info on other changes, check the releases page :)

[Motoufiq]

Hello @pabloati thanks for the prompt response.

OK, SQANTI3 where the argument from --gtf to --filter_gtf was version upgrade. I understand that I can still input my gff file in the --filter_gtf argument and it does not impact the output results due to the argument change. Is my understanding correct?

module load singularity

SQANTI_CLASS="/projects/sqanti3_qc_outputs/LUAD_v3_classification.txt"
GTF="/projects/LR_Analysis/collapse/LUAD_v2.collapsed.gff"
OUTPUT_NAME="LUAD_v3"
OUTPUT_DIR="/projects/sqanti3_filter_outputs"
FILTER_RULES="/projects/rulesFilter.json"

# Run SQANTI3 filter using singularity
singularity run /projects/Tools/sqanti3.sif \
    sqanti3_filter.py rules \
    --sqanti_class "$SQANTI_CLASS" \
    --filter_gtf "$GTF" \
    -o "$OUTPUT_NAME" \
    -d "$OUTPUT_DIR" \
    -j "$FILTER_RULES"

[pabloati]

Yes Toufiq, you can change the argument and use it as you did before. It was only an "aesthetics" change ;)