Workflow Type: Common Workflow Language
Stable

This implementation was done for the ELIXIR EXCELERATE Demonstrator to be run on WES-TES environment.

There is also task related to input file transfer (curl) and the output file transfer to a private FTP server. The needed URLs and FTP credential are given as input parameters.

The input files are assumed to come from a web server. Idea there is to make some configurations more modular and some tools like lftp or curl have easier to write script parameter files instead of command line parameters.

For the output file transfer was installed pureftpd server. It allows to create virtua user account and to execute an upload script (man pure-uploadscript). Thus, it possible to move files automatically to else where that with ftp credential cannot be used to download the files later. Another user account can be used then to access the files.

The .yml files allow to run each cwl files separately with cwltool. There you need to have in the input files in defined in path. Using local files allow faster execution of the pipeline or execution of just a simple task.

Inputs

ID Name Description Type
fastq_files n/a List of paired-end input FASTQ files
  • File[]
reference_genome n/a Compress FASTA files with the reference genome chromosomes
  • File[]
known_indels_file n/a VCF file correlated to reference genome assembly with known indels
  • File
known_sites_file n/a VCF file correlated to reference genome assembly with know sites (for instance dbSNP)
  • File
chromosome n/a Label of the chromosome to be used for the analysis. By default all the chromosomes are used
  • string
readgroup_str n/a Parsing header which should correlate to FASTQ files
  • string
sample_name n/a Sample name
  • string
gqb n/a Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)
  • int[]

Steps

ID Name Description
unzipped_known_sites n/a n/a
unzipped_known_indels n/a n/a
gunzip n/a n/a
picard_dictionary n/a n/a
cutadapt2 n/a n/a
bwa_index n/a n/a
samtools_index n/a n/a
bwa_mem n/a n/a
samtools_sort n/a n/a
picard_markduplicates picard-MD n/a
gatk3-rtc gatk3-rtc n/a
gatk-ir gatk-ir n/a
gatk-base_recalibration gatk-base_recalibration n/a
gatk-base_recalibration_print_reads gatk-base_recalibration_print_reads n/a
gatk_haplotype_caller gatk-haplotype_caller n/a

Outputs

ID Name Description Type
metrics n/a Several metrics about the result
  • File
gvcf n/a unannotated gVCF output file from the mapping and variant calling pipeline
  • File

Version History

Version 4 (latest) Created 11th Jan 2021 at 21:40 by Laura Rodriguez-Navas

new step to unzip known indels file


Open master 8854542

Version 3 Created 3rd Nov 2020 at 11:56 by Laura Rodriguez-Navas

No revision comments

Open master 7e970c0

Version 2 Created 30th Oct 2020 at 10:11 by Laura Rodriguez-Navas

No revision comments

Open master a9d0efc

Version 1 (earliest) Created 2nd Mar 2020 at 10:49 by Laura Rodriguez-Navas

Added/updated 1 files


Open master 816231b
help Creators and Submitter
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Views: 1925   Downloads: 33

Created: 2nd Mar 2020 at 10:49

Last updated: 16th Apr 2021 at 10:38

Last used: 25th Sep 2022 at 17:25

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