GDC Samtools mpileup cwl

Original samtools: https://www.htslib.org/

Docker

All the docker images are built from Dockerfiles at https://github.com/NCI-GDC/samtools-mpileup-tool.

CWL

https://www.commonwl.org/

The CWL are tested under multiple cwltools environments. The most tested one is:

• cwltool 1.0.20180306163216

For external users

The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in GDC reference files. For any questions related to GDC data, please contact the GDC Help Desk at [email protected].

There is a production-ready GDC CWL workflow at https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow, which uses this repo as a git submodule.

Please notice that you may want to change the docker image host of dockerPull: for each CWL.

To use CWL directly from this repo, we recommend to run tools/samtools_mpileup.cwl or tools/multi_samtools_mpileup.cwl.

To run multithreading samtools mpileup CWL:

>>>>>>>>>>Multithreading samtools mpileup<<<<<<<<<<
cwltool multi_samtools_mpileup.cwl -h
/home/ubuntu/.virtualenvs/p2/bin/cwltool 1.0.20180306163216
Resolved 'multi_samtools_mpileup.cwl' to 'file:///mnt/SCRATCH/githubs/samtools-mpileup-cwl/tools/multi_samtools_mpileup.cwl'
usage: multi_samtools_mpileup.cwl [-h] [--min_MQ MIN_MQ] --normal_bam
                                  NORMAL_BAM --ref REF --region REGION
                                  --thread_count THREAD_COUNT --tumor_bam
                                  TUMOR_BAM
                                  [job_order]

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --min_MQ MIN_MQ
  --normal_bam NORMAL_BAM
  --ref REF
  --region REGION
  --thread_count THREAD_COUNT
  --tumor_bam TUMOR_BAM

For GDC users

See https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow.