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Merge pull request #35 from NBISweden/dev
Bug fixes and updates for GenErode version 0.5.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,287 @@ | ||
| cluster-cancel: "scancel" | ||
| restart-times: "3" | ||
| jobscript: "slurm-jobscript.sh" | ||
| cluster: "slurm-submit.py" | ||
| cluster-status: "slurm-status.py" | ||
| max-jobs-per-second: "10" | ||
| max-status-checks-per-second: "10" | ||
| local-cores: 1 | ||
| latency-wait: "5" | ||
| use-conda: "False" | ||
| use-singularity: "True" | ||
| jobs: "100" | ||
| printshellcmds: "True" | ||
|
|
||
| # Resource configuration for GenErode pipeline jobs, fine-tune if necessary | ||
| default-resources: | ||
| - runtime=120 | ||
| - mem_mb=6400 | ||
| - disk_mb=1000000 | ||
| ## set-threads: map rule names to threads | ||
| set-threads: | ||
| ### repeat identification | ||
| - repeatmodeler=16 | ||
| - repeatclassifier=2 | ||
| - repeatmasker=16 | ||
| ### fastq processing | ||
| - historical_fastq_before_group=2 | ||
| - fastqc_historical_raw=2 | ||
| - fastqc_modern_raw=2 | ||
| - fastp_historical=4 | ||
| - fastp_modern=4 | ||
| - fastqc_historical_merged=2 | ||
| - fastqc_historical_unmerged=2 | ||
| - fastqc_modern_trimmed=2 | ||
| ### map to reference genome | ||
| - map_historical=8 | ||
| - sai2bam=8 | ||
| - map_modern=8 | ||
| - sorted_bam_qualimap=8 | ||
| ### process bam files | ||
| - merge_historical_bams_per_index=2 | ||
| - merge_modern_bams_per_index=2 | ||
| - merged_index_bam_qualimap=8 | ||
| - rmdup_historical_bams=6 | ||
| - rmdup_modern_bams=2 | ||
| - rmdup_bam_qualimap=8 | ||
| - merge_historical_bams_per_sample=2 | ||
| - merge_modern_bams_per_sample=2 | ||
| - merged_sample_bam_qualimap=8 | ||
| - indel_realigner_targets=8 | ||
| - indel_realigner=8 | ||
| - realigned_bam_qualimap=8 | ||
| - realigned_bam_group=2 | ||
| ### rescale bam files | ||
| - rescale_historical=4 | ||
| - rescaled_bam_qualimap=8 | ||
| - rescaled_bam_group=2 | ||
| ### subsample bam files | ||
| - subsample_bams=2 | ||
| - subsampled_bam_qualimap=6 | ||
| ### genotyping | ||
| - variant_calling=3 | ||
| ### identify CpG sites | ||
| - CpG_genotype_bed_formatting_group=4 | ||
| - all_CpG_bed_formatting_group=2 | ||
| - make_noCpG_bed=2 | ||
| - CpG_repeats_bed_formatting_group=2 | ||
| - merge_noCpG_noRepeats_beds=2 | ||
| - make_noCpG_repma_bed=2 | ||
| ### create chromosome bed files | ||
| - intersect_sexchr_repma_beds=2 | ||
| - intersect_autos_repma_beds=2 | ||
| - intersect_sexchr_CpG_repma_beds=2 | ||
| - intersect_autos_CpG_repma_beds=2 | ||
| ### CpG filter VCF files | ||
| - remove_CpG_vcf=6 | ||
| - CpG_vcf2bcf=2 | ||
| ### process VCF files | ||
| - remove_snps_near_indels=2 | ||
| - filter_vcfs_qual_dp=2 | ||
| - filter_vcfs_allelic_balance=2 | ||
| - remove_repeats_vcf=6 | ||
| - filtered_vcf2bcf=2 | ||
| ### merge and process VCF files | ||
| - merge_all_vcfs=6 | ||
| - filter_vcf_biallelic=2 | ||
| - filter_vcf_missing=2 | ||
| ### PCA | ||
| - vcf2plink_pca=2 | ||
| ### runs of homozygosity | ||
| - filter_vcf_hwe=2 | ||
| - vcf2plink_hwe=2 | ||
| ### snpEff | ||
| - repmasked_bcf2vcf_snpEff=2 | ||
| - filter_biallelic_missing_vcf_snpEff=6 | ||
| ### gerp | ||
| - outgroup_fastqc=2 | ||
| - align2target=8 | ||
| - bam2fasta=2 | ||
| - concatenate_fasta_per_contig=2 | ||
| - compute_gerp=4 | ||
| - gerp2coords=2 | ||
| - get_ancestral_state=2 | ||
| - produce_contig_out=2 | ||
| - merge_per_chunk=2 | ||
| - merge_gerp_gz=2 | ||
| - repmasked_bcf2vcf_gerp=2 | ||
| - filter_biallelic_missing_vcf_gerp=6 | ||
| - gerp_derived_alleles=2 | ||
| - merge_gerp_alleles_per_chunk=4 | ||
| - merge_gerp_alleles_gz=4 | ||
| - relative_mutational_load_per_sample=2 | ||
| ## set-resources: map rule names to resources in general | ||
| set-resources: | ||
| ### repeat identification | ||
| - repeatmodeler:runtime=8640 | ||
| - repeatmodeler:mem_mb=102400 | ||
| - repeatclassifier:runtime=1440 | ||
| - repeatclassifier:mem_mb=12800 | ||
| - repeatmasker:runtime=8640 | ||
| - repeatmasker:mem_mb=102400 | ||
| ### fastq processing | ||
| - historical_fastq_before_group:runtime=600 | ||
| - historical_fastq_before_group:mem_mb=12800 | ||
| - fastqc_historical_raw:mem_mb=12800 | ||
| - fastqc_modern_raw:mem_mb=12800 | ||
| - fastp_historical:runtime=600 | ||
| - fastp_historical:mem_mb=25600 | ||
| - fastp_modern:runtime=600 | ||
| - fastp_modern:mem_mb=25600 | ||
| - fastqc_historical_merged:mem_mb=12800 | ||
| - fastqc_historical_unmerged:mem_mb=12800 | ||
| - fastqc_modern_trimmed:mem_mb=12800 | ||
| ### map to mitochondrial genomes | ||
| - map_historical_merged_to_mito:runtime=360 | ||
| - map_historical_unmerged_to_mito:runtime=360 | ||
| - historical_mito_bams_group:runtime=2880 | ||
| - merge_historical_mitogenome_bams_per_sample:runtime=2880 | ||
| - historical_merged_mito_bams_group:runtime=2880 | ||
| ### map to reference genome | ||
| - map_historical:runtime=14400 | ||
| - map_historical:mem_mb=51200 | ||
| - sai2bam:runtime=14400 | ||
| - sai2bam:mem_mb=51200 | ||
| - map_modern:runtime=14400 | ||
| - map_modern:mem_mb=51200 | ||
| - sorted_bam_qualimap:runtime=5760 | ||
| - sorted_bam_qualimap:mem_mb=51200 | ||
| ### process bam files | ||
| - merge_historical_bams_per_index:runtime=2880 | ||
| - merge_historical_bams_per_index:mem_mb=12800 | ||
| - merge_modern_bams_per_index:runtime=2880 | ||
| - merge_modern_bams_per_index:mem_mb=12800 | ||
| - merged_index_bam_qualimap:runtime=5760 | ||
| - merged_index_bam_qualimap:mem_mb=51200 | ||
| - rmdup_historical_bams:runtime=4320 | ||
| - rmdup_historical_bams:mem_mb=38400 | ||
| - rmdup_modern_bams:runtime=4320 | ||
| - rmdup_modern_bams:mem_mb=12800 | ||
| - rmdup_bam_qualimap:runtime=5760 | ||
| - rmdup_bam_qualimap:mem_mb=51200 | ||
| - merge_historical_bams_per_sample:runtime=2880 | ||
| - merge_historical_bams_per_sample:mem_mb=12800 | ||
| - merge_modern_bams_per_sample:runtime=2880 | ||
| - merge_modern_bams_per_sample:mem_mb=12800 | ||
| - merged_sample_bam_qualimap:runtime=5760 | ||
| - merged_sample_bam_qualimap:mem_mb=51200 | ||
| - indel_realigner_targets:runtime=7200 | ||
| - indel_realigner_targets:mem_mb=51200 | ||
| - indel_realigner:runtime=7200 | ||
| - indel_realigner:mem_mb=51200 | ||
| - realigned_bam_qualimap:runtime=5760 | ||
| - realigned_bam_qualimap:mem_mb=51200 | ||
| - realigned_bam_group:runtime=2880 | ||
| - realigned_bam_group:mem_mb=12800 | ||
| ### rescale bam files | ||
| - rescale_historical:runtime=4320 | ||
| - rescale_historical:mem_mb=25600 | ||
| - rescaled_bam_qualimap:runtime=5760 | ||
| - rescaled_bam_qualimap:mem_mb=51200 | ||
| - rescaled_bam_group:runtime=600 | ||
| - rescaled_bam_group:mem_mb=12800 | ||
| ### subsample bam files | ||
| - filter_bam_mapped_mq:runtime=1440 | ||
| - subsample_bams:runtime=5760 | ||
| - subsample_bams:mem_mb=12800 | ||
| - subsampled_bam_qualimap:runtime=5760 | ||
| - subsampled_bam_qualimap:mem_mb=38400 | ||
| - subsampled_bam_group:runtime=2880 | ||
| - subsampled_bam_group:runtime=2880 | ||
| ### genotyping | ||
| - variant_calling:runtime=2880 | ||
| - variant_calling:mem_mb=19200 | ||
| - sort_vcfs:runtime=1440 | ||
| ### identify CpG sites | ||
| - sorted_bcf2vcf:runtime=300 | ||
| - make_CpG_genotype_bed:runtime=1440 | ||
| - CpG_genotype_bed_formatting_group:runtime=1440 | ||
| - CpG_genotype_bed_formatting_group:mem_mb=25600 | ||
| - all_CpG_bed_formatting_group:runtime=1440 | ||
| - all_CpG_bed_formatting_group:mem_mb=12800 | ||
| - make_noCpG_bed:runtime=300 | ||
| - make_noCpG_bed:mem_mb=12800 | ||
| - CpG_repeats_bed_formatting_group:runtime=1440 | ||
| - CpG_repeats_bed_formatting_group:mem_mb=12800 | ||
| - merge_noCpG_noRepeats_beds:runtime=300 | ||
| - merge_noCpG_noRepeats_beds:mem_mb=12800 | ||
| - make_noCpG_repma_bed:runtime=300 | ||
| - make_noCpG_repma_bed:mem_mb=12800 | ||
| ### create chromosome bed files | ||
| - make_autosomes_bed:runtime=300 | ||
| - intersect_sexchr_repma_beds:mem_mb=12800 | ||
| - intersect_autos_repma_beds:mem_mb=12800 | ||
| - intersect_sexchr_CpG_repma_beds:mem_mb=12800 | ||
| - intersect_autos_CpG_repma_beds:mem_mb=12800 | ||
| ### mlRho | ||
| - bam2pro_autos:runtime=1440 | ||
| - bam2pro_sexchr:runtime=1440 | ||
| - bam2pro_all:runtime=1440 | ||
| ### CpG filter VCF files | ||
| - remove_CpG_vcf:mem_mb=38400 | ||
| - CpG_vcf2bcf:mem_mb=12800 | ||
| ### process VCF files | ||
| - remove_snps_near_indels:mem_mb=12800 | ||
| - filter_vcfs_qual_dp:mem_mb=12800 | ||
| - filter_vcfs_allelic_balance:mem_mb=12800 | ||
| - remove_repeats_vcf:mem_mb=38400 | ||
| - filtered_vcf2bcf:mem_mb=12800 | ||
| ### merge and process VCF files | ||
| - merge_all_vcfs:runtime=4320 | ||
| - merge_all_vcfs:mem_mb=38400 | ||
| - filter_vcf_biallelic:runtime=1440 | ||
| - filter_vcf_biallelic:mem_mb=12800 | ||
| - filter_vcf_missing:runtime=1440 | ||
| - filter_vcf_missing:mem_mb=12800 | ||
| - extract_historical_samples:runtime=300 | ||
| - extract_modern_samples:runtime=300 | ||
| ### PCA | ||
| - vcf2plink_pca:runtime=300 | ||
| - vcf2plink_pca:mem_mb=12800 | ||
| ### runs of homozygosity | ||
| - filter_vcf_hwe:runtime=300 | ||
| - filter_vcf_hwe:mem_mb=12800 | ||
| - vcf2plink_hwe:runtime=300 | ||
| - vcf2plink_hwe:mem_mb=12800 | ||
| ### snpEff | ||
| - repmasked_bcf2vcf_snpEff:runtime=300 | ||
| - repmasked_bcf2vcf_snpEff:mem_mb=12800 | ||
| - build_snpEff_db:runtime=300 | ||
| - filter_biallelic_missing_vcf_snpEff:runtime=1440 | ||
| - filter_biallelic_missing_vcf_snpEff:mem_mb=38400 | ||
| - annotate_vcf:runtime=300 | ||
| ### gerp | ||
| - outgroups2fastq:runtime=1440 | ||
| - outgroup_fastqc:mem_mb=12800 | ||
| - align2target:runtime=4320 | ||
| - align2target:mem_mb=51200 | ||
| - bam2fasta:runtime=1440 | ||
| - bam2fasta:mem_mb=12800 | ||
| - split_ref_contigs:runtime=1440 | ||
| - concatenate_fasta_per_contig:runtime=1440 | ||
| - concatenate_fasta_per_contig:mem_mb=12800 | ||
| - compute_gerp:runtime=1440 | ||
| - compute_gerp:mem_mb=25600 | ||
| - gerp2coords:runtime=1440 | ||
| - gerp2coords:mem_mb=12800 | ||
| - get_ancestral_state:runtime=1440 | ||
| - get_ancestral_state:mem_mb=12800 | ||
| - produce_contig_out:runtime=1440 | ||
| - produce_contig_out:mem_mb=12800 | ||
| - merge_per_chunk:runtime=1440 | ||
| - merge_per_chunk:mem_mb=12800 | ||
| - merge_gerp_gz:runtime=1440 | ||
| - merge_gerp_gz:mem_mb=12800 | ||
| - repmasked_bcf2vcf_gerp:runtime=300 | ||
| - repmasked_bcf2vcf_gerp:mem_mb=12800 | ||
| - filter_biallelic_missing_vcf_gerp:runtime=1440 | ||
| - filter_biallelic_missing_vcf_gerp:mem_mb=38400 | ||
| - split_vcf_files:runtime=300 | ||
| - gerp_derived_alleles:runtime=14400 | ||
| - gerp_derived_alleles:mem_mb=12800 | ||
| - merge_gerp_alleles_per_chunk:runtime=1440 | ||
| - merge_gerp_alleles_per_chunk:mem_mb=25600 | ||
| - merge_gerp_alleles_gz:runtime=1440 | ||
| - merge_gerp_alleles_gz:mem_mb=25600 | ||
| - relative_mutational_load_per_sample:runtime=1440 | ||
| - relative_mutational_load_per_sample:mem_mb=12800 |
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