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Snakebite-RNAseq_server_config.yaml
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Snakebite-RNAseq_server_config.yaml
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__default__:
time: 00:30:00
job-name: RNAseq
account: project_2002561
ntasks: 1
cpus-per-task: 1
mem-per-cpu: 4000
partition: small
working-directory: /scratch/project_2002561/MastitisChallenge/logs/
nvme: 0
# Step1 - Preparations
################################################################################
star_create_index:
job-name: star_index
time: 08:00:00
mem-per-cpu: 4000
cpus-per-task: 20
rsem_create_index:
job-name: rsem_index
time: 0-10:00:00
cpus-per-task: 20
# Step2 - Preprocessing
################################################################################
fastp_trim_reads:
job-name: fastp
time: 01:00:00
cpus-per-task: 10
# Step3 - QC
################################################################################
fastqc_quality_control_raw_data:
job-name: fastqc_raw_data
time: 05:00:00
cpus-per-task: 20
multiqc_quality_control_raw_data:
job-name: multiqc_raw_data
time: 02:30:00
cpus-per-task: 1
mem-per-cpu: 16000
fastqc_quality_control_concatenated_data:
job-name: fastqc_concatenated_data
time: 05:00:00
cpus-per-task: 20
multiqc_quality_control_concatenated_data:
job-name: multiqc_concatenated_data
time: 02:30:00
cpus-per-task: 1
mem-per-cpu: 16000
fastqc_quality_control_trimmed_data:
job-name: fastqc_trimmed_data
time: 05:00:00
cpus-per-task: 20
multiqc_quality_control_trimmed_data:
job-name: multiqc_trimmed_data
time: 02:30:00
cpus-per-task: 1
mem-per-cpu: 16000
# Step3b - Decontamination
################################################################################
build_contamination_indices:
job-name: decon_star_index
time: 08:00:00
mem-per-cpu: 16000
cpus-per-task: 20
star_decontaminate_reads:
job-name: star_decontaminate_reads
time: 04:00:00
cpus-per-task: 20
# Step4 - Alignment
################################################################################
star_map_reads:
job-name: star_mapReads
time: 04:00:00
cpus-per-task: 20
# Step5 - TranscriptomeAssembly
################################################################################
transcriptome_assembly_stringtie:
job-name: stringtie
time: 04:00:00
cpus-per-task: 20
merge_samples:
job-name: mergSTRGeSamples
time: 04:00:00
cpus-per-task: 20
# Step6 - Quantification
################################################################################
rsem_calculate_expressions:
job-name: rsem_quant
time: 0-06:00:00
cpus-per-task: 20
featureCounts_quantify:
job-name: fc_quantify
time: 06:00:00
cpus-per-task: 20
nvme: 10
featureCounts_quantify_merged:
job-name: fc_quantify_merged
time: 06:00:00
cpus-per-task: 20
nvme: 10
# Step 7 - Reporting
################################################################################
R_finalReport:
time: 0-04:00:00
job-name: Rreport
mem-per-cpu: 32000