| group | name | type | description |
|---|---|---|---|
| NA | ch_fastq_input | map | A channel containing fastq files |
| NA | ch_blacklist_index | file | A BWA index created by running BWA/INDEX on a fasta file of blacklisted regions/ |
filter_blacklist
Filter out reads that align to an index
bwa
samtools
fastq
bam
filter
blacklist
nf-core subworkflows \
--git-remote https://github.com/CCBR/nf-modules \
install filter/blacklisthttps://github.com/CCBR/nf-modules/…/subworkflows/CCBR/filter_blacklist/
Input
Output
| group | name | type | description | pattern |
|---|---|---|---|---|
| NA | reads | map | Reads from the fastq files that do not align to the blacklist | NA |
| NA | versions | file | File containing software versions | versions.yml |