Recent Releases of meltzerlab_nextflow_pipeline
meltzerlab_nextflow_pipeline - MNP v1.1
- Add Pipeline READme with Overview DAG
- Add Bam2tdf process to create tdf files from bam files.
- Nextflow
Published by vinegang about 2 years ago
meltzerlab_nextflow_pipeline - MNP v1.0
This is a DNA/RNA data processing pipeline.
- Added Preprocessing QC for fastq reads: Fastqc, Fastq-screen, Kraken-krona and Fastp. NGScheckmate is added for human samples.
- Added STAR and BWA to process RNA and DNA samples respectively.
- Added Post alignment processing using Picard-markdup and GATK- Baserecalibration and ApplyBQSR.
- Added common post alignment QC for DNA and RNA samples.
- Samtools - Flagstat. Idxstat
- Picard - Collectmultiplemetrics
- Added RNA specific QC
- NGSderive
- CollectRNAseqmetrics
- RNAseQC
- Added DNA specific QC
- WGSmetrics
- HSmetrics (will run only when capture kit information is provided)
- Added multiqc to generate a combined QC file for all the samples in the sequencing run.
- Nextflow
Published by vinegang about 2 years ago