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config.yaml
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52 lines (35 loc) · 3.21 KB
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sample_tsv: "sample_fastq_list.txt"
fastqc_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/fastqc/FastQC/fastqc"
trimmomatic_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar"
trimmomatic_adapters: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/trimmomatic/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa_wpoly.fa"
picard_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/picard/picard.jar"
#picard_refflat: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/genomic_references/human/CollectRnaSeqMetrics/Homo_sapiens.GRCh38.97.refFlat.txt"
#picard_rrna_list: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/genomic_references/human/CollectRnaSeqMetrics/Homo_sapiens.GRCh38.97.rRNA.interval_list"
#picard_rrna_list: "sample_ref/hg38_chr567_100k_rRNA.interval.list"
#picard_strand: "SECOND_READ_TRANSCRIPTION_STRAND"
java_path: "/opt/java/jdk1.8.0_66/bin/java"
#java_path: "java"
samtools_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/samtools/samtools-1.11/samtools"
layout: "paired"
#aligner_name: "hisat" #'hisat' or 'star'
#aligner_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/hisat2/hisat2-2.1.0/hisat2"
#aligner_index: "sample_ref/hg38_chr567_100k"
#aligner_index: "/isi/whitfield/shared_lab_space/RNA-seq/2021_data_collection/ref/hisat2/Homo_sapiens.GRCh38.dna.primary_assembly"
#aligner_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/STAR/STAR-2.7.1a/bin/Linux_x86_64/STAR"
#aligner_index: "sample_ref/star_idx"
aligner_name: "bwa"
aligner_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/bwa/bwa-0.7.17/bwa"
aligner_index: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/210428_Schultz_Assembly/ref/U00096_2.fa"
#reference_fasta: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/genomic_references/reference_index_generation/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
reference_fasta: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/210428_Schultz_Assembly/ref/U00096_2.fa"
#annotation_gtf: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/genomic_references/human/ensembl-annotations/Homo_sapiens.GRCh38.97.gtf"
annotation_gff: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/210428_Schultz_Assembly/ref/U00096_2.gff"
freebayes_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/freebayes/freebayes-1.3.4-linux-static-AMD64"
#featurecounts_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/featurecounts/subread-2.0.1-Linux-x86_64/bin/featureCounts"
#featurecounts_strand: "2" #1 for first read transcription strand, 2 for second.
#featurecounts_rscript: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/featurecounts/subread-2.0.1-Linux-x86_64/bin/fc_to_rpkmtpm.R"
#featurecounts_annscript: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/featurecounts/subread-2.0.1-Linux-x86_64/bin/add_gene_to_ensg.py"
spades_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/spades/SPAdes-3.15.2-Linux/bin/spades.py"
minimap2_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/minimap/minimap2-2.18_x64-linux/minimap2"
lumpy_scripts: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/lumpy-sv/scripts/"
lumpyexp_path: "/dartfs-hpc/rc/lab/G/GMBSR_bioinfo/misc/sullivan/tools/lumpy-sv/bin/lumpyexpress"