feat(pints): Add initial caller module (#1983)

* feat(pints): Add initial caller module

* docs(pints): Add initial documentation

* chore: Add TODOs

* test(pypints): Use docker image for singularity

The image doesn't exist yet for some reason

* test(pints): Remove unidirectional peaks hash

* style(pints): Align emits
This commit is contained in:
Edmund Miller 2022-08-31 09:04:48 -05:00 committed by GitHub
parent 409a308ba4
commit 2f1555bf77
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6 changed files with 152 additions and 0 deletions

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process PINTS_CALLER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' :
'quay.io/biocontainers/pypints:1.1.6--pyh5e36f6f_1' }"
input:
tuple val(meta), path(bams)
output:
tuple val(meta), path("*_divergent_peaks.bed") , emit: divergent_TREs
tuple val(meta), path("*_bidirectional_peaks.bed") , emit: bidirectional_TREs
tuple val(meta), path("*_unidirectional_peaks.bed"), emit: unidirectional_TREs
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
// TODO handle bigwigs
// def input_type = ("${input[0]}".endsWith(".bam")) ? "--bam-file $input" :
// ("$input".contains(".bw")) ? "--bw-pl ${input[0]} --bw-mn ${input[1]}" :
// error "Please use bam or BigWig files"
"""
pints_caller \\
--bam-file $bams \\
--save-to . \\
--file-prefix $prefix \\
--thread $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
pints: \$(pints_caller --version)
END_VERSIONS
"""
}

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name: "pints_caller"
description: Main caller script for peak calling
keywords:
- peak-calling
- CoPRO
- GRO-cap
- PRO-cap
- CAGE
- NETCAGE
- RAMPAGE
- csRNA-seq
- STRIPE-seq
- PRO-seq
- GRO-seq
tools:
- "pints":
description: "Peak Identifier for Nascent Transcripts Starts (PINTS)"
homepage: "https://pints.yulab.org/"
documentation: "https://github.com/hyulab/PINTS/blob/main/README.md"
tool_dev_url: "https://github.com/hyulab/PINTS"
doi: "https://doi.org/10.1038/s41587-022-01211-7"
licence: "['GPL']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bams:
type: file
description: BAM/ file
pattern: "*.{bam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- divergent_TREs:
type: file
description: Divergent TREs
pattern: "*_divergent_peaks.bed"
- bidirectional_TREs:
type: file
description: Divergent TREs and convergent TREs
pattern: "*_bidirectional_peaks.bed"
- unidirectional_TREs:
type: file
description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)
pattern: "*_unidirectional_peaks.bed"
authors:
- "@Emiller88"

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@ -1747,6 +1747,10 @@ picard/sortvcf:
- modules/picard/sortvcf/** - modules/picard/sortvcf/**
- tests/modules/picard/sortvcf/** - tests/modules/picard/sortvcf/**
pints/caller:
- modules/pints/caller/**
- tests/modules/pints/caller/**
pirate: pirate:
- modules/pirate/** - modules/pirate/**
- tests/modules/pirate/** - tests/modules/pirate/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PINTS_CALLER } from '../../../../modules/pints/caller/main.nf'
workflow test_pints_caller {
input = [
[ id:'test', single_end:false ], // meta map
// FIXME Fails if it doesn't find any signals
[file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true),
file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S40mR1.bam", checkIfExists: true)]
]
PINTS_CALLER ( input )
}
// TODO Test single bam input
// TODO Test single bigwig input
// TODO Test multiple bigwig input

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: PINTS_CALLER {
ext.args = "--exp-type GROseq"
ext.singularity_pull_docker_container = true
}
}

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- name: "pints caller"
command: nextflow run ./tests/modules/pints/caller -entry test_pints_caller -c ./tests/config/nextflow.config -c ./tests/modules/pints/caller/nextflow.config
tags:
- "pints"
- "pints/caller"
files:
- path: output/pints/test_1_bidirectional_peaks.bed
md5sum: 8c69305ab896bd772e450e938ddf45f0
- path: output/pints/test_1_divergent_peaks.bed
md5sum: 2078c643951071f5836d365e5dc7ba1c
- path: output/pints/test_1_unidirectional_peaks.bed
- path: output/pints/test_2_bidirectional_peaks.bed
md5sum: c4efa0f297ba4cdb00659c5e6700ebe5
- path: output/pints/test_2_divergent_peaks.bed
md5sum: 213a2ba5d9930768d76bf2a7d8c3f7fb
- path: output/pints/test_2_unidirectional_peaks.bed