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Update input table doc #15

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Feb 10, 2023
Merged

Update input table doc #15

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8 changes: 4 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -60,13 +60,13 @@ Usage:

Input:
* --input_bam: the path to a single BAM (this option is not compatible with --input_files)
* --input_files: the path to a tab-separated values file containing in each row the sample name, sample type (eg: tumor or normal) and path to the BAM file (this option is not compatible with --input_bam)
* --input_files: the path to a tab-separated values file containing in each row the sample name, sample type (eg: tumor or normal) and path to the BAM file. The sample name should be unique for each bam file. (this option is not compatible with --input_bam)
Sample type will be added to the BAM header @SN sample name
The input file does not have header!
Example input file:
name1 tumor tumor.1.bam
name1 normal normal.1.bam
name2 tumor tumor.2.bam
name1_t tumor tumor.1.bam
name1_n normal normal.1.bam
name2_t tumor tumor.2.bam
* --reference: path to the FASTA genome reference (indexes expected *.fai, *.dict)

Optional input:
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8 changes: 4 additions & 4 deletions nextflow.config
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Expand Up @@ -67,13 +67,13 @@ Usage:

Input:
* --input_bam: the path to a single BAM (this option is not compatible with --input_files)
* --input_files: the path to a tab-separated values file containing in each row the sample name, sample type (eg: tumor or normal) and path to the BAM file (this option is not compatible with --input_bam)
* --input_files: the path to a tab-separated values file containing in each row the sample name, sample type (eg: tumor or normal) and path to the BAM file. The sample name should be unique for each bam file. (this option is not compatible with --input_bam)
Sample type will be added to the BAM header @SN sample name
The input file does not have header!
Example input file:
name1 tumor tumor.1.bam
name1 normal normal.1.bam
name2 tumor tumor.2.bam
name1_t tumor tumor.1.bam
name1_n normal normal.1.bam
name2_t tumor tumor.2.bam
* --reference: path to the FASTA genome reference (indexes expected *.fai, *.dict)

Optional input:
Expand Down