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Simplified version of Hello-GATK #376

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merged 12 commits into from
Sep 25, 2024
Merged

Simplified version of Hello-GATK #376

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a84061a
Simplified version of Hello-GATK
vdauwera Sep 25, 2024
292dfd2
Intermediate scripts by section
vdauwera Sep 25, 2024
e8b7591
starter script for hello-gatk
vdauwera Sep 25, 2024
d69c265
Replace bams with Adam's
vdauwera Sep 25, 2024
e543850
Add Adam's smaller reference files
vdauwera Sep 25, 2024
e0ee863
Delete hello-nextflow/data/samplesheet.csv
vdauwera Sep 25, 2024
7a7ccdc
Delete hello-nextflow/data/ref.tar.gz
vdauwera Sep 25, 2024
d096435
Delete hello-nextflow/data/intervals.list
vdauwera Sep 25, 2024
f84afa1
Move ref under data (oops)
vdauwera Sep 25, 2024
3f684fc
convert fromPath().collect() to file()
vdauwera Sep 25, 2024
264c373
Prettier fixes
vdauwera Sep 25, 2024
1fd5c55
addressing review
vdauwera Sep 25, 2024
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430 changes: 191 additions & 239 deletions docs/hello_nextflow/03_hello_gatk.md
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4 changes: 0 additions & 4 deletions hello-nextflow/data/intervals.list
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3 changes: 3 additions & 0 deletions hello-nextflow/data/ref/intervals.bed
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20_10037292_10066351 3276 5495
20_10037292_10066351 7535 9859
20_10037292_10066351 12911 14737
2 changes: 2 additions & 0 deletions hello-nextflow/data/ref/ref.dict
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@HD VN:1.6
@SQ SN:20_10037292_10066351 LN:29059 M5:d9a7bb8816cea7d1e5c55e00d1faeeb4 UR:reads_father_20_10037292_10066351.region.fasta
2 changes: 2 additions & 0 deletions hello-nextflow/data/ref/ref.fasta
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1 change: 1 addition & 0 deletions hello-nextflow/data/ref/ref.fasta.fai
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20_10037292_10066351 29059 22 29059 29060
4 changes: 0 additions & 4 deletions hello-nextflow/data/samplesheet.csv
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6 changes: 4 additions & 2 deletions hello-nextflow/hello-gatk.nf
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Expand Up @@ -2,8 +2,6 @@
* Pipeline parameters
*/

// Execution environment setup

// Primary input

/*
Expand All @@ -13,18 +11,22 @@ process SAMTOOLS_INDEX {

container

publishDir

input:

output:

"""

"""

}

workflow {

// Create input channel

// Create index file for input BAM file

}
17 changes: 8 additions & 9 deletions hello-nextflow/scripts/hello-gatk-1.nf
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Expand Up @@ -2,10 +2,6 @@
* Pipeline parameters
*/

// Execution environment setup
params.projectDir = "/workspace/gitpod/hello-nextflow"
$projectDir = params.projectDir

// Primary input
params.reads_bam = "${projectDir}/data/bam/reads_mother.bam"

Expand All @@ -14,7 +10,9 @@ params.reads_bam = "${projectDir}/data/bam/reads_mother.bam"
*/
process SAMTOOLS_INDEX {

container 'quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1'
container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464'

publishDir 'results', mode: 'copy'

input:
path input_bam
Expand All @@ -24,15 +22,16 @@ process SAMTOOLS_INDEX {

"""
samtools index '$input_bam'

"""
}


workflow {

// Create input channel
reads_ch = Channel.of(params.reads_bam)
// Create input channel (single file via CLI parameter)
reads_ch = Channel.fromPath(params.reads_bam)

// Create index file for input BAM file
SAMTOOLS_INDEX(reads_ch)
}

}
43 changes: 24 additions & 19 deletions hello-nextflow/scripts/hello-gatk-2.nf
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Expand Up @@ -2,25 +2,23 @@
* Pipeline parameters
*/

// Execution environment setup
params.projectDir = "/workspace/gitpod/hello-nextflow"
$projectDir = params.projectDir

// Primary input
params.reads_bam = "${projectDir}/data/bam/reads_mother.bam"

// Accessory files
params.genome_reference = "${projectDir}/data/ref/ref.fasta"
params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
params.calling_intervals = "${projectDir}/data/intervals.list"
params.reference = "${workflow.projectDir}/data/ref/ref.fasta"
params.reference_index = "${workflow.projectDir}/data/ref/ref.fasta.fai"
params.reference_dict = "${workflow.projectDir}/data/ref/ref.dict"
params.intervals = "${workflow.projectDir}/data/ref/intervals.bed"

/*
* Generate BAM index file
*/
process SAMTOOLS_INDEX {

container 'quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1'
container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464'

publishDir 'results', mode: 'copy'

input:
path input_bam
Expand All @@ -30,16 +28,17 @@ process SAMTOOLS_INDEX {

"""
samtools index '$input_bam'

"""
}

/*
* Call variants with GATK HapolotypeCaller in GVCF mode
* Call variants with GATK HaplotypeCaller in GVCF mode
*/
process GATK_HAPLOTYPECALLER {

container "docker.io/broadinstitute/gatk:4.5.0.0"
container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"

publishDir 'results', mode: 'copy'

input:
path input_bam
Expand All @@ -65,8 +64,14 @@ process GATK_HAPLOTYPECALLER {

workflow {

// Create input channel
reads_ch = Channel.of(params.reads_bam)
// Create input channel (single file via CLI parameter)
reads_ch = Channel.fromPath(params.reads_bam)

// Create channels for the accessory files (reference and intervals)
ref_file = file(params.reference)
ref_index_file = file(params.reference_index)
ref_dict_file = file(params.reference_dict)
intervals_file = file(params.intervals)

// Create index file for input BAM file
SAMTOOLS_INDEX(reads_ch)
Expand All @@ -75,9 +80,9 @@ workflow {
GATK_HAPLOTYPECALLER(
reads_ch,
SAMTOOLS_INDEX.out,
params.genome_reference,
params.genome_reference_index,
params.genome_reference_dict,
params.calling_intervals
ref_file,
ref_index_file,
ref_dict_file,
intervals_file
)
}
}
53 changes: 30 additions & 23 deletions hello-nextflow/scripts/hello-gatk-3.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,27 +2,27 @@
* Pipeline parameters
*/

// Execution environment setup
params.projectDir = "/workspace/gitpod/hello-nextflow"
$projectDir = params.projectDir

// Primary input
params.reads_bam = ["${projectDir}/data/bam/reads_mother.bam",
"${projectDir}/data/bam/reads_father.bam",
"${projectDir}/data/bam/reads_son.bam"]
// Primary input (list of three samples)
params.reads_bam = [
"${projectDir}/data/bam/reads_mother.bam",
"${projectDir}/data/bam/reads_father.bam",
"${projectDir}/data/bam/reads_son.bam"
]

// Accessory files
params.genome_reference = "${projectDir}/data/ref/ref.fasta"
params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
params.calling_intervals = "${projectDir}/data/intervals.list"
params.reference = "${projectDir}/data/ref/ref.fasta"
params.reference_index = "${projectDir}/data/ref/ref.fasta.fai"
params.reference_dict = "${projectDir}/data/ref/ref.dict"
params.intervals = "${projectDir}/data/ref/intervals.bed"

/*
* Generate BAM index file
*/
process SAMTOOLS_INDEX {

container 'quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1'
container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464'

publishDir 'results', mode: 'copy'

input:
path input_bam
Expand All @@ -32,16 +32,17 @@ process SAMTOOLS_INDEX {

"""
samtools index '$input_bam'

"""
}

/*
* Call variants with GATK HapolotypeCaller in GVCF mode
* Call variants with GATK HaplotypeCaller in GVCF mode
*/
process GATK_HAPLOTYPECALLER {

container "docker.io/broadinstitute/gatk:4.5.0.0"
container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"

publishDir 'results', mode: 'copy'

input:
tuple path(input_bam), path(input_bam_index)
Expand All @@ -66,18 +67,24 @@ process GATK_HAPLOTYPECALLER {

workflow {

// Create input channel
reads_ch = Channel.of(params.reads_bam)
// Create input channel (single file via CLI parameter)
reads_ch = Channel.fromPath(params.reads_bam)

// Create channels for the accessory files (reference and intervals)
ref_file = file(params.reference)
ref_index_file = file(params.reference_index)
ref_dict_file = file(params.reference_dict)
intervals_file = file(params.intervals)

// Create index file for input BAM file
SAMTOOLS_INDEX(reads_ch)

// Call variants from the indexed BAM file
GATK_HAPLOTYPECALLER(
SAMTOOLS_INDEX.out,
params.genome_reference,
params.genome_reference_index,
params.genome_reference_dict,
params.calling_intervals
ref_file,
ref_index_file,
ref_dict_file,
intervals_file
)
}
}
41 changes: 23 additions & 18 deletions hello-nextflow/scripts/hello-gatk-4.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,25 +2,23 @@
* Pipeline parameters
*/

// Execution environment setup
params.projectDir = "/workspace/gitpod/hello-nextflow"
$projectDir = params.projectDir

// Primary input (list of input files, one per line)
params.reads_bam = "${projectDir}/data/sample_bams.txt"

// Accessory files
params.genome_reference = "${projectDir}/data/ref/ref.fasta"
params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
params.calling_intervals = "${projectDir}/data/intervals.list"
params.reference = "${projectDir}/data/ref/ref.fasta"
params.reference_index = "${projectDir}/data/ref/ref.fasta.fai"
params.reference_dict = "${projectDir}/data/ref/ref.dict"
params.intervals = "${projectDir}/data/ref/intervals.bed"

/*
* Generate BAM index file
*/
process SAMTOOLS_INDEX {

container 'quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1'
container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464'

publishDir 'results', mode: 'copy'

input:
path input_bam
Expand All @@ -30,16 +28,17 @@ process SAMTOOLS_INDEX {

"""
samtools index '$input_bam'

"""
}

/*
* Call variants with GATK HapolotypeCaller in GVCF mode
* Call variants with GATK HaplotypeCaller in GVCF mode
*/
process GATK_HAPLOTYPECALLER {

container "docker.io/broadinstitute/gatk:4.5.0.0"
container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"

publishDir 'results', mode: 'copy'

input:
tuple path(input_bam), path(input_bam_index)
Expand All @@ -64,18 +63,24 @@ process GATK_HAPLOTYPECALLER {

workflow {

// Create input channel from list of input files in plain text
// Create input channel from list of input files in plain text
reads_ch = Channel.fromPath(params.reads_bam).splitText()

// Create channels for the accessory files (reference and intervals)
ref_file = file(params.reference)
ref_index_file = file(params.reference_index)
ref_dict_file = file(params.reference_dict)
intervals_file = file(params.intervals)

// Create index file for input BAM file
SAMTOOLS_INDEX(reads_ch)

// Call variants from the indexed BAM file
GATK_HAPLOTYPECALLER(
SAMTOOLS_INDEX.out,
params.genome_reference,
params.genome_reference_index,
params.genome_reference_dict,
params.calling_intervals
ref_file,
ref_index_file,
ref_dict_file,
intervals_file
)
}
}
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