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template-input-FASTQ.yaml
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template-input-FASTQ.yaml
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---
input:
<patient1>: # Replace key with actual patient ID
<sample1>: # Replace key with actual sample ID
state: <state> # normal or tumor
FASTQ:
- read_group_identifier: <rg ID> # Read group identifier for alignment
sequencing_center: <center> # Center where sequencing was performed
library_identifier: <library> # Library used for sample
platform_technology: <platform technology> # Technology used for sequencing
platform_unit: <platform unit> # Name of specific platform unit
bam_header_sm: <sample> # Sample name tag for BAM
lane: <lane> # Lane on platform
read1_fastq: </path/to/r1.fastq.gz> # Absolute path to R1 FASTQ
read2_fastq: </path/to/r2.fastq.gz> # Absolute path to R2 FASTQ
- read_group_identifier: <rg ID> # Read group identifier for alignment
sequencing_center: <center> # Center where sequencing was performed
library_identifier: <library> # Library used for sample
platform_technology: <platform technology> # Technology used for sequencing
platform_unit: <platform unit> # Name of specific platform unit
bam_header_sm: <sample> # Sample name tag for BAM
lane: <lane> # Lane on platform
read1_fastq: </path/to/r1.fastq.gz> # Absolute path to R1 FASTQ
read2_fastq: </path/to/r2.fastq.gz> # Absolute path to R2 FASTQ
<sample2>: # Replace key with actual sample ID
state: <state> # normal or tumor
FASTQ:
- read_group_identifier: <rg ID> # Read group identifier for alignment
sequencing_center: <center> # Center where sequencing was performed
library_identifier: <library> # Library used for sample
platform_technology: <platform technology> # Technology used for sequencing
platform_unit: <platform unit> # Name of specific platform unit
bam_header_sm: <sample> # Sample name tag for BAM
lane: <lane> # Lane on platform
read1_fastq: </path/to/r1.fastq.gz> # Absolute path to R1 FASTQ
read2_fastq: </path/to/r2.fastq.gz> # Absolute path to R2 FASTQ
- read_group_identifier: <rg ID> # Read group identifier for alignment
sequencing_center: <center> # Center where sequencing was performed
library_identifier: <library> # Library used for sample
platform_technology: <platform technology> # Technology used for sequencing
platform_unit: <platform unit> # Name of specific platform unit
bam_header_sm: <sample> # Sample name tag for BAM
lane: <lane> # Lane on platform
read1_fastq: </path/to/r1.fastq.gz> # Absolute path to R1 FASTQ
read2_fastq: </path/to/r2.fastq.gz> # Absolute path to R2 FASTQ
<sample3>: # Replace key with actual sample ID
state: <state> # normal or tumor
FASTQ:
- read_group_identifier: <rg ID> # Read group identifier for alignment
sequencing_center: <center> # Center where sequencing was performed
library_identifier: <library> # Library used for sample
platform_technology: <platform technology> # Technology used for sequencing
platform_unit: <platform unit> # Name of specific platform unit
bam_header_sm: <sample> # Sample name tag for BAM
lane: <lane> # Lane on platform
read1_fastq: </path/to/r1.fastq.gz> # Absolute path to R1 FASTQ
read2_fastq: </path/to/r2.fastq.gz> # Absolute path to R2 FASTQ
- read_group_identifier: <rg ID> # Read group identifier for alignment
sequencing_center: <center> # Center where sequencing was performed
library_identifier: <library> # Library used for sample
platform_technology: <platform technology> # Technology used for sequencing
platform_unit: <platform unit> # Name of specific platform unit
bam_header_sm: <sample> # Sample name tag for BAM
lane: <lane> # Lane on platform
read1_fastq: </path/to/r1.fastq.gz> # Absolute path to R1 FASTQ
read2_fastq: </path/to/r2.fastq.gz> # Absolute path to R2 FASTQ