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LncPipeTestData

This repo contains a test case for running LncPipe.
Testdata can be download here

Data Information

Only a subset of the whole dataset (trimmed for chrX only) were put on this repo for improving testing efficiency for LncPipe. The file includes

Fastq files with properly named Fastq/*.gz
Genome reference from GENCODE Genome/chrX.fa
Hisat2 index of the genome reference Genome/hisat2Index*.ht2, generated by following command
```
  hisat2-build chrX.fa chrX  
```
GENCODE ANNOTATION file Genome/gencode.v25.annotation.chrX.gtf
LncPipedia ANNOTATION file Genome/lncipedia_4_0.chrX.gtf
Experimental design file design.file
nextflow running config file docker.config (deprecated, now all config file were moved to the conf folder, users could configure the parameter their and run LncPipe with a -profile parameter)

Test command (Assume that docker and nextflow were properly preinstalled )

Step 1. Download the test data

  wget http://download.omicsbio.info/files/DAtools/testdata.tar.gz
  tar -xvzf LncPipeTestData.tar.gz
  cd LncPipeTestData

Step 2. Get the lastest lncPipe

  git clone https://github.com/likelet/LncPipe.git

Step 3. Run the analysis command (about 10 mins)

  #(run the this `cmd` if your are using a centos 7.0 linux system , this cmd can temperally set the selinux into permissive mode )
  sudo setenforce 0 
  
  nextflow run LncPipe/LncRNAanalysisPipe.nf -profile docker,test -with-trace -resume -with-timeline timeline.html

Result content (expected result)

    ```
    ├── hisat_alignment
    │   ├── R1126N.hisat2_summary.txt
    │   ├── R1126N.sort.bam
    │   ├── R1126T.hisat2_summary.txt
    │   ├── R1126T.sort.bam
    │   ├── R1130N.hisat2_summary.txt
    │   ├── R1130N.sort.bam
    │   ├── R1130T.hisat2_summary.txt
    │   ├── R1130T.sort.bam
    │   ├── R1134N.hisat2_summary.txt
    │   ├── R1134N.sort.bam
    │   ├── R1134T.hisat2_summary.txt
    │   ├── R1134T.sort.bam
    │   ├── S483N.hisat2_summary.txt
    │   ├── S483N.sort.bam
    │   ├── S483T.hisat2_summary.txt
    │   ├── S483T.sort.bam
    │   ├── S502N.hisat2_summary.txt
    │   ├── S502N.sort.bam
    │   ├── S502T.hisat2_summary.txt
    │   └── S502T.sort.bam
    ├── Identified_lncRNA
    │   ├── all_lncRNA_for_classifier.gtf
    │   ├── final_all.fa
    │   ├── final_all.gtf
    │   ├── lncRNA_classification.txt
    │   ├── lncRNA.fa
    │   ├── protein_coding.fa
    │   └── protein_coding.final.gtf
    ├── LncPipeReports
    │   ├── figures
    │   ├── libs
    │   ├── reporter_files
    │   ├── reporter.html
    │   └── tables
    ├── Merged_assemblies
    │   └── merged.gtf
    ├── QC
    │   ├── R1126N_fastp.html
    │   ├── R1126T_fastp.html
    │   ├── R1130N_fastp.html
    │   ├── R1130T_fastp.html
    │   ├── R1134N_fastp.html
    │   ├── R1134T_fastp.html
    │   ├── S483N_fastp.html
    │   ├── S483T_fastp.html
    │   ├── S502N_fastp.html
    │   └── S502T_fastp.html
    └── Quantification
        ├── kallisto.count.txt
        └── kallisto.tpm.txt
    ```

Run information

timeline

another test repo for `lncpipe`

https://github.com/nf-core/test-datasets/blob/lncpipe/README.md