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IsoTV/config_example_pdk2.yaml
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##### IsoTV Config File | |
pipeline: "IsoTV" | |
repo: "https://github.molgen.mpg.de/MayerGroup/IsoTV" | |
### Ouput directory | |
outdir: "example" | |
### General pipeline parameters: | |
basecalling: FALSE | |
preprocess: FALSE | |
annotation: TRUE | |
quantification: TRUE | |
###### ONT long read processing config | |
### Basecalling pipeline parameters | |
guppy: "/path/to/Guppy324/bin/guppy_basecaller" | |
flowcell: FLO-MIN106 | |
kit: SQK-DCS109 | |
### Reference Files | |
genome_fasta: "/path/to/GRCh38.p12.primary_assembly.genome.fa" | |
genome_annot: "/path/to/gencode.v32.primary_assembly.annotation.gtf" | |
### Samples | |
# samples with .bottom extension must be placed in the RawData folder | |
# condition_replicate | |
samples: | |
A549_1: "A549_r1_r3" | |
A549_2: "A549_r2_r1" | |
A549_5: "A549_r5_r3" | |
HCT116_1: "HCT116_r1_r4" | |
HCT116_3: "HCT116_r3_r2" | |
HCT116_4: "HCT116_r4_r1" | |
HCT116_5: "HCT116_r5_r1" | |
HEPG2_1: "HEPG2_r1_r1" | |
HEPG2_4: "HEPG2_r4_r2" | |
HEPG2_5: "HEPG2_r5_r3" | |
K562_1: "K562_r1_r2" | |
K562_2: "K562_r2_r1" | |
K562_3: "K562_r3_r1" | |
K562_4: "K562_r4_r2" | |
MCF7_1: "MCF7_r1_r2" | |
MCF7_3: "MCF7_r3_r3" | |
MCF7_4: "MCF7_r4_r2" | |
threads: 16 | |
# Use pychopper results | |
pychopper: TRUE | |
# Use annotation to improve splice junction mapping (minimap2 --junc_bed parameter) | |
minimap2_opts_junction: TRUE | |
# Minimum read quality to keep: | |
min_mean_q: 5 | |
# Stringency of porechop heuristic: | |
porechop_heu_stringency: 0.25 | |
# Options passed to minimap2 during indexing: | |
minimap2_index_opts: "-k14" | |
# Extra options passed to minimap2: | |
minimap2_opts: "-uf" # required for stranded data e.g. when pychopper filtered | |
# Minmum mapping quality: | |
minimum_mapping_quality: 5 | |
# Options passed to spliced_bam2gff: | |
spliced_bam2gff_opts: "-s" # required for stranded data e.g. when pychopper filtered | |
# -c parameter: | |
minimum_cluster_size: 3 | |
# -p parameter: | |
minimum_isoform_percent: 1 | |
# -d parameter: | |
exon_boundary_tolerance: 10 | |
# -e parameter: | |
terminal_exon_boundary_tolerance: 50 | |
# Extra options passed to minimap2 when mapping polished reads: | |
minimap2_opts_polished: "-uf" # required for stranded data e.g. when pychopper filtered | |
# Options passed to spliced_bam2gff when converting alignments of polished reads: | |
spliced_bam2gff_opts_pol: "-s" # required for stranded data e.g. when pychopper filtered | |
# Options passed to collapse_partials when collapsing fragmentation artifacts | |
# Internal exon boundary tolerance: | |
collapse_internal_tol: 5 | |
# Five prime boundary tolerance: | |
collapse_five_tol: 500 | |
# Three prime boundary tolerance: | |
collapse_three_tol: 50 | |
maximum_secondary: 200 | |
secondary_score_ratio: 1 | |
##### Feature Analysis Config | |
### Input genes | |
gene_file: "data/genes.tab" | |
### Output file and folder | |
output_plots: "test.pdf" | |
### Processed file paths - required if not using ONT long read processing workflow | |
nanopore_gtf: "data/PDK2.nanopore.gtf" | |
polished_reads: "data/PDK2.transcriptome.fas" | |
counts_data: "data/PDK2.counts.txt" | |
# Is data continuous | |
continuous: FALSE | |
### External tool paths and functional analysis | |
aa: TRUE | |
iupred2a_path: "/path/to/iupred2a/iupred2a.py" | |
iupred2a: TRUE | |
brewery_path: "/path/to/Brewery/Brewery.py" | |
brewery: TRUE | |
interproScan_path: "/path/to/my_interproscan/interproscan-5.38-76.0/interproscan.sh" | |
pfam: TRUE | |
prositeScan_path: "/path/to/ps_scan/ps_scan.pl" | |
pfScan_path: "/path/to/ps_scan/pfscan" | |
prositeDat_path: "/path/to/prosite.dat" | |
pfScan: TRUE | |
minIsoTPM: 1 | |
maxIsoNum: 8 | |
minIsoPct: 10 | |
### Misc paths | |
java : "/pkg/openjdk-11.0.3.2-0/profile" | |
lock1: "/.../lock.txt" | |
lock2: "/.../lock2.txt" |