search

InPreD / tso500_nxf_workflow

Nextflow workflow to run Illumina LocalApp and TSOPPI on TSO500 data
MIT License
0 stars 1 forks source link

TruSight_Oncology_500_RUO.sh use cases #2

Open marrip opened 11 months ago

marrip commented 11 months ago

Here we gather all the use cases for TruSight_Oncology_500_RUO.sh:

# start from bcl
$ sudo bash TruSight_Oncology_500_RUO.sh --user ${USER_UID} --remove --resourcesFolder "${RESOURCE_DIR}" --runFolder "${SEQ_RUN_DIR}" --analysisFolder "${ANALYSIS_OUTPUT_DIR}" --sampleSheet "${SAMPLE_SHEET}"
# start from fastq
$ sudo bash TruSight_Oncology_500_RUO.sh --user ${USER_UID} --remove --resourcesFolder "${RESOURCE_DIR}" --fastqFolder "${FASTQ_DIR}" --analysisFolder "${ANALYSIS_OUTPUT_DIR}" --sampleSheet "${SAMPLE_SHEET}"
marrip commented 9 months ago

we had a meeting last week were we agreed on trying out if we could do a 3 way split of the LocalApp - Demultiplex for sequencing run -> DNA and RNA analysis per sample -> Gather of all results. We will see if this could potentially speed things up 😬