Read Mapping¶
Note: This module only supports illumina data.
Input¶
-entry wReadMapping -params-file example_params/readMapping.yml
Warning
The configuration file shown here is for demonstration and testing purposes only.
Parameters that should be used in production can be viewed in the read mapping section
of one of the yaml files located in the default folder of the Toolkit's Github repository.
tempdir: "tmp"
summary: false
s3SignIn: false
output: "output"
logDir: log
runid: 1
logLevel: 1
scratch: "/vol/scratch"
publishDirMode: "symlink"
steps:
readMapping:
samples:
paired: test_data/readMapping/samples.tsv
single: test_data/readMapping/single.tsv
ont: test_data/readMapping/ont.tsv
mags: test_data/readMapping/mags.tsv
bwa2:
additionalParams:
bwa2_index: ""
bwa2_mem: ""
minimap:
additionalParams:
minimap_index: ""
minimap: ""
coverm: " --min-covered-fraction 0 "
covermONT: " --min-covered-fraction 0 "
resources:
highmemLarge:
cpus: 28
memory: 230
highmemMedium:
cpus: 14
memory: 113
large:
cpus: 28
memory: 58
medium:
cpus: 14
memory: 29
small:
cpus: 7
memory: 14
tiny:
cpus: 1
memory: 1
BINS
https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/bins/bin.1.fa
https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/bins/bin.2.fa
https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/bins/bin.8.fasta
https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/bins/bin.9.fasta
https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/bins/bin.32.fa
SAMPLE READS
test1 https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/small/interleaved.fq.gz
Output¶
The produced output files are the following: count.tsv, mean.tsv, mean_mincov10.tsv, rpkm.tsv, tpm.tsv, trimmed_mean.tsv. The content of the files are produced by coverm. All metrics are explained on the coverm GitHub page: https://github.com/wwood/CoverM .