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slurm-config.json
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slurm-config.json
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{
"__default__" :
{
"qos": "6hours",
"time": "01:00:00",
"job-name": "{rule}.{wildcards}",
"output": "{params.cluster_log_path}/{rule}.{wildcards}-%j-%N.out"
},
"create_index_star":
{
"qos": "6hours",
"time": "06:00:00"
},
"extract_transcripts_as_bed12":
{
"qos": "30min",
"time": "00:30:00"
},
"extract_transcriptome":
{
"qos": "30min",
"time": "00:30:00"
},
"extract_decoys_salmon":
{
"qos": "30min",
"time": "00:30:00"
},
"concatenate_transcriptome_and_genome":
{
"qos": "30min",
"time": "00:30:00"
},
"create_index_salmon":
{
"qos": "6hours",
"time": "03:00:00"
},
"sort_bed_4_big":
{
"qos": "6hours",
"time": "03:00:00"
},
"create_index_kallisto":
{
"qos": "30min",
"time": "00:30:00"
},
"index_genomic_alignment_samtools":
{
"qos": "30min",
"time": "00:30:00"
},
"star_rpm":
{
"qos": "30min",
"time": "00:30:00"
},
"rename_star_rpm_for_alfa":
{
"qos": "6hours",
"time": "03:00:00"
},
"calculate_TIN_scores":
{
"qos": "6hours",
"time": "06:00:00"
},
"merge_TIN_scores":
{
"qos": "30min",
"time": "00:05:00"
},
"plot_TIN_scores":
{
"qos": "30min",
"time": "00:05:00"
},
"salmon_quantmerge_genes":
{
"qos": "30min",
"time": "00:05:00"
},
"salmon_quantmerge_transcripts":
{
"qos": "30min",
"time": "00:05:00"
},
"generate_alfa_index":
{
"qos": "6hours",
"time": "02:00:00"
},
"alfa_qc":
{
"qos": "30min",
"time": "00:30:00"
},
"alfa_qc_all_samples":
{
"qos": "6hours",
"time": "01:00:00"
},
"pe_fastqc":
{
"qos": "6hours",
"time": "01:00:00"
},
"fastqc":
{
"qos": "6hours",
"time": "01:00:00"
},
"pe_remove_adapters_cutadapt":
{
"qos": "6hours",
"time": "06:00:00"
},
"remove_adapters_cutadapt":
{
"qos": "6hours",
"time": "06:00:00"
},
"pe_remove_polya_cutadapt":
{
"qos": "6hours",
"time": "06:00:00"
},
"remove_polya_cutadapt":
{
"qos": "6hours",
"time": "06:00:00"
},
"pe_map_genome_star":
{
"qos": "6hours",
"time": "06:00:00"
},
"map_genome_star":
{
"qos": "6hours",
"time": "06:00:00"
},
"pe_quantification_salmon":
{
"qos": "6hours",
"time": "03:00:00"
},
"quantification_salmon":
{
"qos": "6hours",
"time": "03:00:00"
},
"pe_genome_quantification_kallisto":
{
"qos": "6hours",
"time": "03:00:00"
},
"genome_quantification_kallisto":
{
"qos": "6hours",
"time": "03:00:00"
},
"sort_genomic_alignment_samtools":
{
"qos": "6hours",
"time": "03:00:00"
}
}