PHIM
RNAja-pipeline

Repository

    git clone git@forge.ird.fr:phim/rnaja-pipeline.git
    cd rnaja-pipeline
    python3 -m pip install .
    # in edition mode (for developpers and debuging)
    #python3 -m pip install -e .
    export PATH=/home/$USER/.local/bin/:$PATH`
   RNAja install_local --help
   RNAja install_local
   RNAja install_cluster --help
   RNAja install_cluster --scheduler slurm --env singularity
rule hisat2_index
rule hisat2_map
rule star_index
rule star_map_count
rule star_to_diffex
rule samtools_stats
rule multiqc
rule stringtie_discovery
rule stringtie_gtf_list_discovery
rule merge_stringtie_gtf_discovery
rule stringtie
rule stringtie_gtf_list
rule merge_stringtie_gtf
rule list_for_prepDE
rule prepDE_stringtie_table
rule htseq_count
rule htseq_to_diffex
rule diff_exp_analysis
_default__:
    cpus-per-task: 4
    mem-per-cpu: 3G
    partition : normal
    output: '{log.output}_cluster'
    error: '{log.error}_cluster'
    job-name: '{rule}.{wildcards}'


rule stringtie_discovery
    nodelist: node4
    cpus-per-task: 8
    mem-per-cpu: 6G
    partition: highmem

   RNAja test_install --help
   RNAja test_install -d TEST
   RNAja run_local --help
   RNAja run_local -t 8 -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"
    RNAja run_local -t 8 -c TEST/data_test_config.yaml --set-threads hisat2_index=4 hisat2_map_paired=2
   RNAja run_cluster --help
   RNAja edit_cluster_config
   RNAja run_cluster --help
   RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"

   # here a example adapted to @IFB HPC
   RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind /shared:/shared"

   #you can also use snakemake parameters as
   RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME" --rerun-incomplete --nolock
RNAja create_config
DATA:
    fastq_dir: "/path/to/FASTQ"
    reference: "/path/to/reference/ref.fna"
    annotation: "/path/to/reference/ref.gtf"
    output_dir: "RNAJA_OUTPUT"
MODE:
    HISAT2_STRINGTIE: true
    HISAT2_HTSEQCOUNT: true
    STARmap_STARcount: true
    STARmap_HTSEQCOUNT: true
    STARmap_STRINGTIE: true
PARAMS:
    HISAT2:
        indexation:
            prefix: "REF"
    STAR:
        indexation:
            params: "--sjdbOverhang 100 --genomeSAindexNbases 10"
        mapping:
            params: "--readFilesCommand zcat" # --outFilterMismatchNoverLmax 0.03
    STRINGTIE:
        discovery_mode : false
    HTSEQCOUNT:
        params: "-r pos -s reverse -m union -t gene "
RNAJA_OUTPUT/
├── COUNT
│   ├── HTSEQCOUNT
│   │   ├── HISAT2
│   │   └── STAR
│   ├── STAR
│   │   ├── Batch-rep1Aligned.out.bam
│   │   ├── Batch-rep1Aligned.toTranscriptome.out.bam
│   │   ├── Batch-rep1Log.final.out
│   │   ├── Batch-rep1Log.out
│   │   ├── Batch-rep1Log.progress.out
│   │   ├── Batch-rep1ReadsPerGene.out.tab
│   │   ├── Batch-rep1SJ.out.tab
...
│   │   ├── CENPK-rep1Aligned.out.bam
│   │   ├── CENPK-rep1Aligned.toTranscriptome.out.bam
│   │   ├── CENPK-rep1Log.final.out
│   │   ├── CENPK-rep1Log.out
│   │   ├── CENPK-rep1Log.progress.out
│   │   ├── CENPK-rep1ReadsPerGene.out.tab
│   │   ├── CENPK-rep1SJ.out.tab
...
│   └── STRINGTIE
│       ├── HISAT2_Batch-rep1.gtf
│       ├── HISAT2_Batch-rep1.tsv
...
│       ├── HISAT2_CENPK-rep3.gtf
│       ├── HISAT2_CENPK-rep3.tsv
│       ├── STAR_Batch-rep1.gtf
│       ├── STAR_Batch-rep1.tsv
...
│       ├── STAR_CENPK-rep3.gtf
│       ├── STAR_CENPK-rep3.tsv
├── LOGS
├── MAPPING
│   ├── HISAT2
│   │   ├── Batch-rep1.bam
│   │   ├── Batch-rep1.bam.csi
│   │   ├── Batch-rep1_HISAT_summary.txt
...
│   │   ├── CENPK-rep3.bam
│   │   ├── CENPK-rep3.bam.csi
│   │   └── CENPK-rep3_HISAT_summary.txt
│   └── STAR
│       ├── Batch-rep1.bam
│       ├── Batch-rep1.bam.csi
...
│       ├── CENPK-rep3.bam
│       └── CENPK-rep3.bam.csi
├── REF
│   ├── HISAT2
│   │   ├── GCF_000146045.2_R64_genomic.fasta -> /scratch/rnaja_test/TEST/DATA_TEST/REF/GCF_000146045.2_R64_genomic.fna
│   └── STAR
│       ├── chrLength.txt
│       ├── chrNameLength.txt
│       ├── chrName.txt
│       ├── chrStart.txt
│       ├── exonGeTrInfo.tab
│       ├── exonInfo.tab
│       ├── GCF_000146045.2_R64_genomic.fasta -> /scratch/rnaja_test/TEST/DATA_TEST/REF/GCF_000146045.2_R64_genomic.fna
│       ├── geneInfo.tab
│       ├── Genome
│       ├── genomeParameters.txt
│       ├── Log.out
│       ├── SA
│       ├── SAindex
│       ├── sjdbInfo.txt
│       ├── sjdbList.fromGTF.out.tab
│       ├── sjdbList.out.tab
│       └── transcriptInfo.tab
└── slurm_logs