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Merge branch 'master' into add-tbi-to-bcftools-concat

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nvnieuwk 2022-05-31 15:20:03 +02:00 committed by GitHub
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4 changed files with 12 additions and 8 deletions
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1
modules/bamtools/convert/meta.yml
View file

@ -42,7 +42,6 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
## TODO nf-core: Delete / customise this example output
- out:
type: file
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)

2
modules/filtlong/main.nf
View file

@ -20,7 +20,7 @@ process FILTLONG {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
"""
filtlong \\
$short_reads \\

2
tests/modules/filtlong/nextflow.config
View file

@ -2,4 +2,6 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = "--min_length 10"
}

9
tests/modules/filtlong/test.yml
View file

@ -4,7 +4,8 @@
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
- name: filtlong test_filtlong_illumina_se
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
@ -12,7 +13,8 @@
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
- name: filtlong test_filtlong_illumina_pe
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
@ -20,4 +22,5 @@
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"