nf-core_modules/modules/biscuit/biscuitblaster/main.nf
Nathan Spix 801240a971
Add core Biscuit tools (#1354)
* create files with nf-core command

* update meta.yml files

* starting to work on index main.nf

* prelim test for index

* index test working; not finding all output files

* index passing tests

* index and align passing tests

* prototyping biscuitblaster and pileup

* update containers

* updates to pileup

* pileup passing tests

* template creation for more biscuit tools

* tests passing on blaster,bsconv,pupsom

* epiread passing tests, but need to update SNP bed file path

* vcf2bed working; change test file

* all biscuit commands passing tests

* biscuitblaster rename

* try to fix permissions

* more permission fixes

* trying a couple more permission changes

* hopefully last permission fixes

* really last permission changes

* few more permissions

* add when blocks

* Remove read group meta

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* remove read group meta

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* changes for first round of review

* update meta.yml with more specific links

* Update modules/biscuit/biscuitblaster/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Apply new version reporting

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/biscuit/pileup/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update main.nf

* Update modules/biscuit/pileupsomatic/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* update test file path

* Update modules/biscuit/align/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/biscuit/align/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* tests passing again

* Update modules/biscuit/align/main.nf

* Update modules/biscuit/bsconv/main.nf

* Update modules/biscuit/epiread/main.nf

* Update modules/biscuit/index/main.nf

* Update test.yml

* Update modules/biscuit/pileupsomatic/main.nf

* remove module-specific extension/prefix

* remove module-specific extension/prefix

* add missing args

* switch pileup strategy

* update test.yml

* remove debug

* whitespace cleanup

* add in newline escapes

* requested changes

* Update modules/biscuit/pileup/meta.yml

Co-authored-by: Spix <nathan.spix@submit.cm.cluster>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Spix <nathan.spix@node107.cm.cluster>
Co-authored-by: njspix <nathan.spix@vai.org>
2022-03-14 09:34:22 -04:00

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process BISCUIT_BLASTER {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.bai"), emit: bai
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.95),1)
def samtools_cpus = task.cpus-biscuit_cpus
"""
INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
biscuit align \\
-@ $biscuit_cpus \\
$args \\
\$INDEX \\
$reads | \\
samblaster \\
$args2 | \\
samtools sort \\
-@ $samtools_cpus \\
$args3 \\
--write-index \\
-o ${prefix}.bam##idx##${prefix}.bam.bai
cat <<-END_VERSIONS > versions.yml
"${task.process}":
biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
samblaster: \$( samblaster --version |& sed 's/^.*samblaster: Version //' )
END_VERSIONS
"""
}