millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Merge branch 'master' into tool/elprep-merge

Browse source
This commit is contained in:
Matthias De Smet 2022-04-22 13:05:30 +02:00 committed by GitHub
commit d57024ddc0
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
4 changed files with 12 additions and 11 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
modules/elprep/filter/main.nf
View file

@ -23,7 +23,7 @@ process ELPREP_FILTER {
output: output:
tuple val(meta), path("**.{bam,sam}") ,emit: bam tuple val(meta), path("output/**.{bam,sam}") ,emit: bam
tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics
tuple val(meta), path("*.recall") ,optional: true, emit: recall tuple val(meta), path("*.recall") ,optional: true, emit: recall
tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf
@ -65,7 +65,7 @@ process ELPREP_FILTER {
def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": "" def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
""" """
elprep filter ${bam} ${prefix}.${suffix} \\ elprep filter ${bam} output/${prefix}.${suffix} \\
${reference_sequences_cmd} \\ ${reference_sequences_cmd} \\
${filter_regions_cmd} \\ ${filter_regions_cmd} \\
${markdup_cmd} \\ ${markdup_cmd} \\

11
modules/elprep/split/main.nf
View file

@ -11,16 +11,16 @@ process ELPREP_SPLIT {
tuple val(meta), path(bam) tuple val(meta), path(bam)
output: output:
tuple val(meta), path("**.{bam,sam}"), emit: bam tuple val(meta), path("output/**.{bam,sam}"), emit: bam
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
meta.single_end ? args += " --single-end": "" def single_end = meta.single_end ? " --single-end": ""
""" """
# create directory and move all input so elprep can find and merge them before splitting # create directory and move all input so elprep can find and merge them before splitting
@ -31,8 +31,9 @@ process ELPREP_SPLIT {
elprep split \\ elprep split \\
input \\ input \\
. \\ output/ \\
$args \\ $args \\
$single_end \\
--nr-of-threads $task.cpus \\ --nr-of-threads $task.cpus \\
--output-prefix $prefix --output-prefix $prefix

2
tests/modules/elprep/filter/test.yml
View file

@ -6,7 +6,7 @@
files: files:
- path: output/elprep/test.activity_profile.igv - path: output/elprep/test.activity_profile.igv
- path: output/elprep/test.assembly_regions.igv - path: output/elprep/test.assembly_regions.igv
- path: output/elprep/test.bam - path: output/elprep/output/test.bam
- path: output/elprep/test.g.vcf.gz - path: output/elprep/test.g.vcf.gz
- path: output/elprep/test.metrics.txt - path: output/elprep/test.metrics.txt
- path: output/elprep/test.recall - path: output/elprep/test.recall

6
tests/modules/elprep/split/test.yml
View file

@ -4,7 +4,7 @@
- elprep - elprep
- elprep/split - elprep/split
files: files:
- path: output/elprep/splits/test-group00001.bam - path: output/elprep/output/splits/test-group00001.bam
- path: output/elprep/splits/test-unmapped.bam - path: output/elprep/output/splits/test-unmapped.bam
- path: output/elprep/test-spread.bam - path: output/elprep/output/test-spread.bam
- path: output/elprep/versions.yml - path: output/elprep/versions.yml