nf__bam2fastq by Manthos Pitoulias

Nextflow workflow starting from bam files, reverse engineering to fastq files. Files can be used for transcript abundance quantification e.g., STAR/RSEM or Kallisto. THIS WORKFLOW IF FOR PAIRED SEQUENCING.

Bam to fastq

Self-explanatory. Bear in mind (again) flow is currently for paired sequencing. Will update it in time to include more cases.

You can edit the config file to include your bam locations or the final results directory.

Fastq split to r1,r2.fastq

Self-explanatory. The input fastq file has a /1 or /2 id next to the reads. This is used to split the fastq to 2 subsequent fastq files that are paired BUT DESYNCED.

Repairing the files

The process of reverse engineering can leave the paired fastq r1,r2 desynced, thus bottlenecking downstream applications ( e.g., using RSEM). That is why we repair the files with BBMAP repair.sh. This script along with its dependencies can be stored in a directory named "bin" inside the main nextflow directory (to avoid absolute paths). E.g.,

.
├── README.md
├── another_flow.nf
├── bin
├── cached
├── main.nf
├── nextflow.config
├── results
├── test_files
└── work

Singleton Reads are not included (Reads without a pair after sync)