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apply suggestions from review

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thanks @drpatelh
This commit is contained in:
phue 2021-02-20 12:51:01 +01:00
parent a963c67481
commit c67e591caf
4 changed files with 11 additions and 12 deletions
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4
software/bwameth/align/main.nf
View file

@ -31,11 +31,13 @@ process BWAMETH_ALIGN {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : "" def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
""" """
INDEX=`find -L ./ -name "*bwameth.c2t" | sed 's/.bwameth.c2t//'`
bwameth.py \\ bwameth.py \\
$options.args \\ $options.args \\
$read_group \\ $read_group \\
-t $task.cpus \\ -t $task.cpus \\
--reference ${index}/genome.fa \\ --reference \$INDEX \\
$reads \\ $reads \\
| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam - | samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -

3
software/bwameth/align/meta.yml
View file

@ -54,9 +54,6 @@ input:
- index: - index:
type: dir type: dir
description: Directory containing bwameth genome index description: Directory containing bwameth genome index
- fasta:
type: file
description: Input genome fasta file
output: output:
- meta: - meta:
type: map type: map

4
software/bwameth/index/main.nf
View file

@ -19,10 +19,10 @@ process BWAMETH_INDEX {
} }
input: input:
path fasta, stageAs: "index/genome.fa" path fasta, stageAs: "bwameth/*"
output: output:
path "index" , emit: index path "bwameth" , emit: index
path "*.version.txt", emit: version path "*.version.txt", emit: version
script: script:

12
tests/software/bwameth/index/test.yml
View file

@ -4,15 +4,15 @@
- bwameth - bwameth
- bwameth_index - bwameth_index
files: files:
- path: ./output/bwameth/index/genome.fa.bwameth.c2t.pac - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.pac
md5sum: 7586c6a3be45c4dea15376a5c7bb9bf0 md5sum: 7586c6a3be45c4dea15376a5c7bb9bf0
- path: ./output/bwameth/index/genome.fa.bwameth.c2t.amb - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.amb
md5sum: 87e019665cbb66bdee2bacccb26845c9 md5sum: 87e019665cbb66bdee2bacccb26845c9
- path: ./output/bwameth/index/genome.fa.bwameth.c2t.ann - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.ann
md5sum: a4659a63572b6998c67457bd8e95790d md5sum: a4659a63572b6998c67457bd8e95790d
- path: ./output/bwameth/index/genome.fa.bwameth.c2t.bwt - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.bwt
md5sum: 582854008bcbe99d5b51290773a7db5f md5sum: 582854008bcbe99d5b51290773a7db5f
- path: ./output/bwameth/index/genome.fa.bwameth.c2t - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t
md5sum: db670853725f4a31080c991e9df6b330 md5sum: db670853725f4a31080c991e9df6b330
- path: ./output/bwameth/index/genome.fa.bwameth.c2t.sa - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.sa
md5sum: 020db07e7e1544dc961c30c9936f3213 md5sum: 020db07e7e1544dc961c30c9936f3213