samples.tsv
Add samples information to config/samples.tsv. For each sample, you need to specify the sample name under the sample_name column and the corresponding library name under the library_name column.
- Each sample has a
library_name, which can be e.g. a library name, sequencing run or lane. - Each sample has a
sample_name, which associates it with the biological sample it comes from. - For each sample, define the paths for your (columns
fq1,fq2) FASTQ files (these can point to any path in your system). - As an alternative, you can provide an SRA (sequence read archive) accession (starting with e.g. ERR or SRR) by using a column
sra. If ypu provde SRA accession instead of FASTQ file paths, the workflow will automatically download the corresponding paired end reads from SRA. If both local file paths and SRA accession are provided, the local files will be preferred.
| sample_name | library_name | fq1 | fq2 | sra |
|---|---|---|---|---|
| 33-16 | HB1JEADXX_GATCAG | /path/to/your/local/fastq_1/33-16_HB1JEADXX_GATCAG_1.fastq.gz | /path/to/your/local/fastq_2/33-16_HB1JEADXX_GATCAG_2.fastq.gz | |
| 33-16 | HB1LCADXX_GATCAG | /path/to/your/local/fastq_1/33-16_HB1LCADXX_GATCAG_1.fastq.gz | /path/to/your/local/fastq_2/33-16_HB1LCADXX_GATCAG_2.fastq.gz | |
| 33-16 | HLC27CCXX_L7 | /path/to/your/local/fastq_1/33-16/33-16_HLC27CCXX_L7_1.fastq.gz | /path/to/your/local/fastq_2/33-16_HLC27CCXX_L7_2.fastq.gz | |
| 38-11 | HLCY2CCXX_L3 | /path/to/your/local/fastq_1/38-11/38-11_HLCY2CCXX_L3_1.fastq.gz | /path/to/your/local/fastq_2/38-11_HLCY2CCXX_L3_2.fastq.gz | |
| 4226 | H174VBGXX | /path/to/your/local/fastq_1/4226/4226_H174VBGXX_1.fastq.gz | /path/to/your/local/fastq_2/4226_H174VBGXX_2.fastq.gz | |
| 4226 | HLC27CCXX_L3 | /path/to/your/local/fastq_1/4226/4226_HLC27CCXX_L3_1.fastq.gz | /path/to/your/local/fastq_2/4226/4226_HLC27CCXX_L3_2.fastq.gz | |
| 4722 | H3CWKBGXX_GCCAAT | /path/to/your/local/fastq_1/4722_H3CWKBGXX_GCCAAT_1.fastq.gz | /path/to/your/local/fastq_2/4722_H3CWKBGXX_GCCAAT_2.fastq.gz | |
| 4722 | HLCY2CCXX_L3 | /path/to/your/local/fastq_1/4722_HLCY2CCXX_L3_1.fastq.gz | /path/to/your/local/fastq_2/4722_HLCY2CCXX_L3_2.fastq.gz | |
| A188 | HLC27CCXX_L3 | /path/to/your/local/fastq_1/A188_HLC27CCXX_L3_1.fastq.gz | /path/to/your/local/fastq_2/A188_HLC27CCXX_L3_2.fastq.gz | |
| A188 | H174VBGXX | /path/to/your/local/fastq_1/A188_H174VBGXX_1.fastq.gz | /path/to/your/local/fastq_2/A188_H174VBGXX_2.fastq.gz |
| sample_name | library_name | fq1 | fq2 | sra |
|---|---|---|---|---|
| C00022105 | C00022105 | SRR3050845 | ||
| C00022106 | C00022106 | SRR3050846 | ||
| C00022107 | C00022107 | SRR3050847 | ||
| C00022108 | C00022108 | SRR3050848 | ||
| C00022109 | C00022109 | SRR3050849 | ||
| C00022110 | C00022110 | SRR3050850 | ||
| C00022119 | C00022119 | SRR3050851 | ||
| C00022112 | C00022112 | SRR3050852 | ||
| C00022113 | C00022113 | SRR3050853 | ||
| C00022114 | C00022114 | SRR3050854 |
