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Update Genrich module input tuple and argument #3720

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merged 18 commits into from
Oct 18, 2023
Merged

Update Genrich module input tuple and argument #3720

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4316f03
Added treat & control lists inputs and SE modifier
samuelruizperez Aug 8, 2023
32ea406
Added treat & control lists inputs and SE modifier
samuelruizperez Aug 8, 2023
58e0bf7
Genrich: Added multiple reps and SE modifier
samuelruizperez Aug 10, 2023
195f35e
Genrich: Added multiple reps and SE modifier 2
samuelruizperez Aug 10, 2023
5179743
Genrich: simplified layout definition
samuelruizperez Aug 10, 2023
e3256a6
Merge branch 'master' into master
samuelruizperez Aug 10, 2023
7ce8071
Merge branch 'master' into master
samuelruizperez Aug 11, 2023
e7a3b1a
Merge branch 'master' into master
samuelruizperez Aug 14, 2023
6715588
Merge branch 'master' into master
SPPearce Aug 16, 2023
4763305
Merge branch 'master' into master
samuelruizperez Aug 30, 2023
a8c1f0b
Merge branch 'master' into master
samuelruizperez Oct 16, 2023
c56c22b
Removing value channels
samuelruizperez Oct 16, 2023
ef1518e
Line up commas
SPPearce Oct 17, 2023
384f4f9
Align commas
SPPearce Oct 17, 2023
5ac97dc
Increase test -p to avoid empty file
samuelruizperez Oct 17, 2023
d7b5bc3
Merge branch 'master' into master
samuelruizperez Oct 17, 2023
cf1e0c3
Merge branch 'master' into master
FriederikeHanssen Oct 18, 2023
58ce73e
Merge branch 'master' into master
samuelruizperez Oct 18, 2023
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34 changes: 19 additions & 15 deletions modules/nf-core/genrich/main.nf
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Expand Up @@ -8,34 +8,36 @@ process GENRICH {
'biocontainers/genrich:0.6.1--h5bf99c6_1' }"

input:
tuple val(meta), path(treatment_bam)
path control_bam
tuple val(meta), path(treatment_bam), path(control_bam)
path blacklist_bed
val save_pvalues
val save_pileup
val save_bed
val save_duplicates

output:
tuple val(meta), path("*narrowPeak") , emit: peaks
tuple val(meta), path("*.narrowPeak") , emit: peak
tuple val(meta), path("*pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues
tuple val(meta), path("*pileup.bedGraph") , optional:true, emit: bedgraph_pileup
tuple val(meta), path("*intervals.bed") , optional:true, emit: bed_intervals
tuple val(meta), path("*duplicates.txt") , optional:true, emit: duplicates
tuple val(meta), path("*pileup.bedGraph"), optional:true, emit: bedgraph_pileup
tuple val(meta), path("*intervals.bed"), optional:true, emit: bed_intervals
tuple val(meta), path("*duplicates.txt"), optional:true, emit: duplicates
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}"
def control = control_bam ? "-c $control_bam" : ''
def blacklist = blacklist_bed ? "-E $blacklist_bed" : ""
def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
def pileup = save_pileup ? "-k ${prefix}.pileup.bedGraph" : ""
def bed = save_bed ? "-b ${prefix}.intervals.bed" : ""
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def layout = (!args.contains("-y") && meta.single_end) ? "-y" : ""
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What is this doing?

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Yes, would like also to know

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@samuelruizperez samuelruizperez Oct 16, 2023 •
edited
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Single-end data can only be analyzed if unpaired alignments are kept (-y or -w <int>) so it defaults to -y if neither is already in args (jsh58/Genrich#77 (comment)). Should be clearer now.

def treatment = treatment_bam ? "-t ${treatment_bam.sort().join(',')}" : ""
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Why do you sort here?

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Yes, is it trying to maintain the correspondence between control and treatment files?

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Yes, is it trying to maintain the correspondence between control and treatment files?

That was my intention, but I don't think it's necessary (?)

def control = control_bam ? "-c ${control_bam.sort().join(',')}" : ""
def blacklist = blacklist_bed ? "-E $blacklist_bed" : ""
def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
def pileup = save_pileup ? "-k ${prefix}.pileup.bedGraph" : ""
def bed = save_bed ? "-b ${prefix}.intervals.bed" : ""
def duplicates = ""

if (save_duplicates) {
if (args.contains('-r')) {
duplicates = "-R ${prefix}.duplicates.txt"
Expand All @@ -44,11 +46,12 @@ process GENRICH {
duplicates = "-r -R ${prefix}.duplicates.txt"
}
}

"""
Genrich \\
-t $treatment_bam \\
$treatment \\
$args \\
$control \\
$layout \\
$blacklist \\
-o ${prefix}.narrowPeak \\
$pvalues \\
Expand All @@ -62,4 +65,5 @@ process GENRICH {
genrich: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
END_VERSIONS
"""

}
5 changes: 3 additions & 2 deletions modules/nf-core/genrich/meta.yml
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Expand Up @@ -23,11 +23,11 @@ input:
e.g. [ id:'test', single_end:false ]
- treatment_bam:
type: file
description: Coordinate sorted BAM/SAM file from treatment sample
description: Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates
pattern: "*.{bam,sam}"
- control_bam:
type: file
description: Coordinate sorted BAM/SAM file from control sample
description: Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples
pattern: "*.{bam,sam}"
- blacklist_bed:
type: file
Expand Down Expand Up @@ -77,3 +77,4 @@ output:
pattern: "*.{version.txt}"
authors:
- "@JoseEspinosa"
- "@samuelruizperez"
46 changes: 31 additions & 15 deletions tests/modules/nf-core/genrich/main.nf
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Expand Up @@ -6,74 +6,90 @@ include { GENRICH } from '../../../../modules/nf-core/genrich/main.nf'
include { GENRICH as GENRICH_CTRL } from '../../../../modules/nf-core/genrich/main.nf'
include { GENRICH as GENRICH_ALL } from '../../../../modules/nf-core/genrich/main.nf'
include { GENRICH as GENRICH_ATACSEQ } from '../../../../modules/nf-core/genrich/main.nf'
include { GENRICH as GENRICH_LIST } from '../../../../modules/nf-core/genrich/main.nf'

workflow test_genrich {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
[ ]]
blacklist = [ ]

save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false

GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
GENRICH ( input, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}

workflow test_genrich_ctrl {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
[ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
blacklist = [ ]

save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false

GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
GENRICH_CTRL ( input, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}

workflow test_genrich_all_outputs {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
[ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
blacklist = [ ]

save_pvalues = true
save_pileup = true
save_bed = true
save_duplicates = true

GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
GENRICH_ALL ( input, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}

workflow test_genrich_blacklist {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
[ ]]
blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]

save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false

GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
GENRICH ( input, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}

workflow test_genrich_atacseq {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
control = [ ]
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
[ ]]
blacklist = [ ]

save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false

GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
GENRICH_ATACSEQ ( input, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}

workflow test_genrich_list {
input = [ [ id:'test', single_end:false ], // meta map
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)],
[ ]]
blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]

save_pvalues = false
save_pileup = false
save_bed = false
save_duplicates = false

GENRICH_LIST ( input, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
}

3 changes: 3 additions & 0 deletions tests/modules/nf-core/genrich/nextflow.config
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Expand Up @@ -18,4 +18,7 @@ process {
ext.args = '-j -p 0.1'
}

withName: GENRICH_LIST {
ext.args = '-p 0.1'
}
}
14 changes: 14 additions & 0 deletions tests/modules/nf-core/genrich/test.yml
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Expand Up @@ -5,6 +5,7 @@
files:
- path: output/genrich/test.narrowPeak
md5sum: 6afabdd3f691c7c84c66ff8a23984681
- path: output/genrich/versions.yml

- name: genrich test_genrich_ctrl
command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
Expand All @@ -13,6 +14,7 @@
files:
- path: output/genrich/test.narrowPeak
md5sum: 2fcc392360b317f5ebee88cdbc149e05
- path: output/genrich/versions.yml

- name: genrich test_genrich_all_outputs
command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_all_outputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
Expand All @@ -29,6 +31,7 @@
md5sum: 03e53848de695b5794f32f15b2709203
- path: output/genrich/test.pvalues.bedGraph
md5sum: b14feef34b6d2379a173a734ca963cde
- path: output/genrich/versions.yml

- name: genrich test_genrich_blacklist
command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_blacklist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
Expand All @@ -37,6 +40,7 @@
files:
- path: output/genrich/test.narrowPeak
md5sum: 6afabdd3f691c7c84c66ff8a23984681
- path: output/genrich/versions.yml

- name: genrich test_genrich_atacseq
command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_atacseq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
Expand All @@ -45,3 +49,13 @@
files:
- path: output/genrich/test.narrowPeak
md5sum: ddea556b820f8be3695ffdf6c6f70aff
- path: output/genrich/versions.yml

- name: genrich test_genrich_list
command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_list -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
tags:
- genrich
files:
- path: output/genrich/test.narrowPeak
md5sum: f793e0ff59274e6364151a7cd4eeeafd
- path: output/genrich/versions.yml
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