mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 03:32:10 -05:00
Removed large testing files, will convert to updated testing
This commit is contained in:
sruthipsuresh
parent
4ada27479a
commit
78473edb72
29 changed files with 0 additions and 609 deletions
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chr1 951 1061
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chr1 1300 1420
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chr1 1400 1500
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chr1 1780869
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BEDTOOLS_COMPLEMENT } from '../main.nf' addParams( options: [publish_dir:'test_bed_file'] )
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// Define input channels
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// Run the workflow
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workflow test_bed_file {
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def input = []
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input = [ [ id:'test'],
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[ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
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BEDTOOLS_COMPLEMENT(
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input,
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file("${baseDir}/input/genome.sizes", checkIfExists: true)
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)
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}
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workflow {
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test_bed_file()
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}
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@ -1,20 +0,0 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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}
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profiles {
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conda {
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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@ -1,3 +0,0 @@
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chr1 0 951
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chr1 1061 1300
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chr1 1500 1780869
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Binary file not shown.
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@ -1 +0,0 @@
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chr1 1780869
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@ -1,23 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BEDTOOLS_GENOMECOV } from '../main.nf' addParams( options: [publish_dir:'test_bed_file'] )
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// Define input channels
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// Run the workflow
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workflow test_bed_file {
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def input = []
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input = [ [ id:'test'],
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[ file("${baseDir}/input/JK2067_downsampled_s0.1.bam", checkIfExists: true),] ]
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BEDTOOLS_GENOMECOV (
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input,
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file("${baseDir}/input/genome.sizes", checkIfExists: true) )
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}
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workflow {
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test_bed_file()
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}
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@ -1,20 +0,0 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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}
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profiles {
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conda {
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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|
||||
genome 14 11 3137454505 3.50603e-09
|
||||
genome 15 23 3137454505 7.33078e-09
|
||||
genome 16 30 3137454505 9.56189e-09
|
||||
genome 17 5 3137454505 1.59365e-09
|
||||
genome 18 26 3137454505 8.28697e-09
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
chr1 951 1061
|
||||
chr1 1300 1420
|
||||
chr1 1400 1500
|
||||
|
||||
|
||||
|
|
@ -1 +0,0 @@
|
|||
chr1 999 1010
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
nextflow.enable.dsl = 2
|
||||
include { BEDTOOLS_INTERSECT } from '../main.nf' addParams( options: [publish_dir:'test_bed_file'] )
|
||||
// Run the workflow
|
||||
workflow test_bed_file {
|
||||
def input = []
|
||||
input = [ [ id:'test'],
|
||||
[ file("${baseDir}/input/A.bed", checkIfExists: true),
|
||||
file("${baseDir}/input/B.bed", checkIfExists: true) ] ]
|
||||
|
||||
BEDTOOLS_INTERSECT( input )
|
||||
|
||||
}
|
||||
|
||||
workflow {
|
||||
test_bed_file()
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
|
||||
params {
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
enable_conda = false
|
||||
}
|
||||
|
||||
profiles {
|
||||
conda {
|
||||
params.enable_conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
|
@ -1 +0,0 @@
|
|||
chr1 999 1010
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
chr1 951 1061
|
||||
chr1 1300 1420
|
||||
chr1 1400 1500
|
||||
|
||||
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
nextflow.enable.dsl = 2
|
||||
include { BEDTOOLS_MERGE } from '../main.nf' addParams( options: [publish_dir:'test_bed_file'] )
|
||||
// Define input channels
|
||||
// TODO ensure input file is presorted (could use output of sort module)
|
||||
// Run the workflow
|
||||
workflow test_bed_file {
|
||||
def input = []
|
||||
input = [ [ id:'test'],
|
||||
[ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
|
||||
|
||||
BEDTOOLS_MERGE( input )
|
||||
|
||||
}
|
||||
|
||||
workflow {
|
||||
test_bed_file()
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
|
||||
params {
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
enable_conda = false
|
||||
}
|
||||
|
||||
profiles {
|
||||
conda {
|
||||
params.enable_conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
chr1 951 1061
|
||||
chr1 1300 1500
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
chr1 951 1061
|
||||
chr1 1300 1420
|
||||
chr1 1400 1500
|
||||
|
||||
|
||||
|
|
@ -1 +0,0 @@
|
|||
chr1 1780869
|
||||
|
|
@ -1,44 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BEDTOOLS_SLOP as BEDTOOLS_SLOP_S } from '../main.nf' addParams( options: [ publish_dir:'test_asymmetrical' ], header: true )
|
||||
include { BEDTOOLS_SLOP as BEDTOOLS_SLOP_AS } from '../main.nf' addParams( options: [ publish_dir:'test_symmetrical' ], header: true )
|
||||
|
||||
// To run with header and pct enabled, type --pct true and --header true with nextflow run command.
|
||||
|
||||
// Run the workflow
|
||||
/*
|
||||
Test with l/r method
|
||||
*/
|
||||
workflow test_asymmetrical {
|
||||
def input = []
|
||||
input = [ [ id:'test', symmetry: false ],
|
||||
[ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
|
||||
|
||||
BEDTOOLS_SLOP_AS(
|
||||
input,
|
||||
file("${baseDir}/input/genome.sizes", checkIfExists: true)
|
||||
)
|
||||
|
||||
}
|
||||
/*
|
||||
Test with b method
|
||||
*/
|
||||
workflow test_symmetrical {
|
||||
def input = []
|
||||
input = [ [ id:'test', symmetry: true],
|
||||
[ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
|
||||
|
||||
BEDTOOLS_SLOP_S(
|
||||
input,
|
||||
file("${baseDir}/input/genome.sizes", checkIfExists: true)
|
||||
)
|
||||
|
||||
}
|
||||
|
||||
workflow {
|
||||
test_asymmetrical()
|
||||
test_symmetrical()
|
||||
}
|
||||
|
||||
// output has - b 10 and -l 1 -r 10 as test values. pct and header are both false.
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
|
||||
params {
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
enable_conda = false
|
||||
}
|
||||
|
||||
profiles {
|
||||
conda {
|
||||
params.enable_conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
chr1 851 1161
|
||||
chr1 1200 1520
|
||||
chr1 1300 1600
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
chr1 950 1071
|
||||
chr1 1299 1430
|
||||
chr1 1399 1510
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
chr1 951 1061
|
||||
chr1 1300 1420
|
||||
chr1 1400 1500
|
||||
|
||||
|
||||
|
|
@ -1,21 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
include { BEDTOOLS_SORT } from '../main.nf' addParams( options: [publish_dir:'test_bed_file'] )
|
||||
// Define input channels
|
||||
|
||||
// Run the workflow
|
||||
workflow test_bed_file {
|
||||
def input = []
|
||||
input = [ [ id:'test'],
|
||||
[ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
|
||||
|
||||
BEDTOOLS_SORT( input )
|
||||
|
||||
}
|
||||
|
||||
workflow {
|
||||
test_bed_file()
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
|
||||
params {
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
enable_conda = false
|
||||
}
|
||||
|
||||
profiles {
|
||||
conda {
|
||||
params.enable_conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
chr1 951 1061
|
||||
chr1 1300 1420
|
||||
chr1 1400 1500
|
||||
Loading…
Reference in a new issue