Merge pull request #527 from nf-core/rnavar

Samplesheets for rnavar pipeline

Author: maxulysse

README.md

@@ -1,36 +1,52 @@
-# ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
-Test data to be used for automated testing with the nf-core pipelines
+# test-datasets: `rnavar`
 
-## Introduction
+This branch contains test data to be used for automated testing with the [nf-core/rnavar](https://github.com/nf-core/rnavar) pipeline.
 
-nf-core is a collection of high quality Nextflow pipelines. This repository contains various files for CI and unit testing of nf-core pipelines and infrastructure.
+## Content of this repository
 
-The principle for nf-core test data is as small as possible, as large as necessary. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data.
+`samplesheet/samplesheet.csv`: Experiment design file for minimal test dataset
 
-## Documentation
+`samplesheet/samplesheet_full.csv`: Experiment design file for full test dataset
 
-nf-core/test-datasets comes with documentation in the `docs/` directory:
+## Minimal test dataset origin
 
-01. [Add a new  test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
-02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
+The raw data was retrieved from 'Genome in a Bottle' sample GM12878 (SRA accession [SRX2900878](https://www.ncbi.nlm.nih.gov/sra/?term=SRX2900878), sequenced on NextSeq 500 with 151bpx2 library).
 
-## Downloading test data
+### Sampling procedure
 
-Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use.
+1. The data was downloaded using the SRA Toolkit with:
 
-```bash
-git clone <url> --single-branch --branch <pipeline/modules/branch_name>
-```
+    ```bash
+    prefetch -v <Acc number>
+    sam-dump <Acc number> | samtools view -bS - > <Acc number>.bam
+    ```
 
-To subsequently clone other branches[^1]
+2. Manually verified a region covered by reads in chromsome 22 using IGV genome veiwer.
 
-```bash
-git remote set-branches --add origin [remote-branch]
-git fetch
-```
+    ```bash
+    chr22   16570000        16610000
+    ```
 
-## Support
+3. Extracted all the reads and their pair-mates that overlap the SNP sites in the above region were extracted using [VariantBAM](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920121/) and converted to `fastq.gz` using [qbic-pipelines/bamtofastq](https://github.com/qbic-pipelines/bamtofastq).
 
-For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging).
+## Full test dataset origin
 
-[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856)
+*H. sapiens* paired-end strand-specific RNA-seq dataset was obtained from:
+
+> ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. [Pubmed](https://pubmed.ncbi.nlm.nih.gov/22955616/)
+
+The GM12878 and K562 ENCODE data was also used to benchmark RNA-seq quantification pipelines in the paper below:
+
+> Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, and Rafael A. Irizarry. A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016; 17: 74. Published online 2016 Apr 23. doi: 10.1186/s13059-016-0940-1. [Pubmed](https://pubmed.ncbi.nlm.nih.gov/27107712/)
+
+
+| study_alias | run_accession | experiment_alias | encode_library_id | sample_description | instrument_model | library_layout | read_count | sex | fastq_ftp | fastq_md5 |
+|-------------|---------------|------------------|-------------------|--------------------|------------------|----------------|------------|-----|-----------|-----------|
+  | [GSE78551](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78551) | SRR3192657 | GSM2072350 | ENCLB038ZZZ | Homo sapiens GM12878 immortalized cell line | Illumina HiSeq 2000 | PAIRED | 93555584 | female | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/007/SRR3192657/SRR3192657_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/007/SRR3192657/SRR3192657_2.fastq.gz) | f3a3aee0e1f0f54dc9afd8f7c0442aba;6bff7e7d944736251cfbc36e35c3f431 |
+| [GSE78551](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78551) | SRR3192658 | GSM2072351 | ENCLB037ZZZ | Homo sapiens GM12878 immortalized cell line | Illumina HiSeq 2000 | PAIRED | 97548052 | female | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/008/SRR3192658/SRR3192658_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/008/SRR3192658/SRR3192658_2.fastq.gz) | f6fdb08100033d98bfcba0801a838bf9;b369f63c5d37e515b4e102fa8c8d75e7 |
+| [GSE78557](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78557) | SRR3192408 | GSM2072362 | ENCLB055ZZZ | Homo sapiens K562 immortalized cell line | Illumina HiSeq 2000 | PAIRED | 92172367 | female | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/008/SRR3192408/SRR3192408_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/008/SRR3192408/SRR3192408_2.fastq.gz) | 53815dcaeeb331459ab72bffe0a9432f;e73d0e7b764d96f08cf2caf4a7e880ff |
+| [GSE78557](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78557) | SRR3192409 | GSM2072363 | ENCLB056ZZZ | Homo sapiens K562 immortalized cell line | Illumina HiSeq 2000 | PAIRED | 113327735 | female | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/009/SRR3192409/SRR3192409_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR319/009/SRR3192409/SRR3192409_2.fastq.gz) | 5904c8781f4fd6771a5e9a32696cd49b;b23e23639258c93944ff9a64b08b9f67 |
+| [GSE90237](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90237) | SRR5048099 | GSM2400174 | ENCLB555AQN | Homo sapiens MCF-7 immortalized cell line | Illumina Genome Analyzer IIx | PAIRED | 128178110 | female | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/009/SRR5048099/SRR5048099_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/009/SRR5048099/SRR5048099_2.fastq.gz) | c23adfcad78e9162a83e18fc76e7ebfd;fd0c3baabd67659aecf6c88feef30259 |
+| [GSE90237](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90237) | SRR5048100 | GSM2400175 | ENCLB555AQO | Homo sapiens MCF-7 immortalized cell line | Illumina Genome Analyzer IIx | PAIRED | 131814222 | female | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/000/SRR5048100/SRR5048100_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/000/SRR5048100/SRR5048100_2.fastq.gz) | f7e732c768e4080311a49e6048c4d515;5619f168e72c5ca27b1b805a91de4444 |
+| [GSE90225](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90225) | SRR5048077 | GSM2400152 | ENCLB555AMA | Homo sapiens H1-hESC stem cell male embryo | Illumina Genome Analyzer IIx | PAIRED | 125395196 | male | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_2.fastq.gz) | 6beb20b2cd99542433986b8fe844ef09;4f63ef9e16dc9f0f8be159b02d40f0c6 |
+| [GSE90225](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90225) | SRR5048078 | GSM2400153 | ENCLB555AMB | Homo sapiens H1-hESC stem cell male embryo | Illumina Genome Analyzer IIx | PAIRED | 107101340 | male | [fastq_1](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/008/SRR5048078/SRR5048078_1.fastq.gz) [fastq_2](ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/008/SRR5048078/SRR5048078_2.fastq.gz) | 9c60d407bae58019889b13acb1032116;fc5df7d28daf6df1b212aaac914f1324 |

samplesheet/v1.0/samplesheet.csv

@@ -0,0 +1,2 @@
+sample,fastq_1,fastq_2,strandedness
+GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,reverse

samplesheet/v1.0/samplesheet_full.csv

@@ -0,0 +1,9 @@
+sample,fastq_1,fastq_2,strandedness
+GM12878_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603629_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603629_T1_2.fastq.gz,reverse
+GM12878_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603630_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603630_T1_2.fastq.gz,reverse
+K562_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603392_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603392_T1_2.fastq.gz,reverse
+K562_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603393_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603393_T1_2.fastq.gz,reverse
+MCF7_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370490_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370490_T1_2.fastq.gz,reverse
+MCF7_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370491_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370491_T1_2.fastq.gz,reverse
+H1_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370468_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370468_T1_2.fastq.gz,reverse
+H1_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370469_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX2370469_T1_2.fastq.gz,reverse