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add intervals to calibratedragstrmodel

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This commit is contained in:
Nicolas Vannieuwkerke 2022-06-02 16:20:12 +02:00
parent 59ce1ec348
commit b4b1f3b81d
4 changed files with 42 additions and 5 deletions
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4
modules/gatk4/calibratedragstrmodel/main.nf
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@ -8,7 +8,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bam_index)
tuple val(meta), path(bam), path(bam_index), path(intervals)
path fasta
path fasta_fai
path dict
@ -24,6 +24,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def intervals_command = intervals ? "--intervals $intervals" : ""
def avail_mem = 3
if (!task.memory) {
@ -37,6 +38,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
--output ${prefix}.txt \\
--reference $fasta \\
--str-table-path $strtablefile \\
$intervals_command \\
--tmp-dir . \\
$args

4
modules/gatk4/calibratedragstrmodel/meta.yml
View file

@ -33,6 +33,10 @@ input:
type: file
description: index of the BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
- intervals:
type: file
description: BED file or interval list containing regions
pattern: "*.{bed,interval_list}"
- fasta:
type: file
description: The reference FASTA file

26
tests/modules/gatk4/calibratedragstrmodel/main.nf
View file

@ -9,7 +9,8 @@ workflow test_gatk4_calibratedragstrmodel_bam {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@ -28,7 +29,28 @@ workflow test_gatk4_calibratedragstrmodel_cram {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
}
workflow test_gatk4_calibratedragstrmodel_beds {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

13
tests/modules/gatk4/calibratedragstrmodel/test.yml
View file

@ -1,8 +1,8 @@
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
tags:
- gatk4
- gatk4/calibratedragstrmodel
- gatk4
files:
- path: output/gatk4/test.txt
md5sum: 0a1a1583b157fa2251dd931ed165da4f
@ -10,8 +10,17 @@
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
tags:
- gatk4
- gatk4/calibratedragstrmodel
- gatk4
files:
- path: output/gatk4/test.txt
md5sum: 1aa7ab38023f724877b3323c5e6b9a4e
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
tags:
- gatk4/calibratedragstrmodel
- gatk4
files:
- path: output/gatk4/test.txt
md5sum: def8baccad7bd59006f08fcb0a6721bf